iiinova — where your digital self keeps evolving

Erik Poppleton @poppleton.phd · 28/09/2026

My biochemist brain is over here reading HF as hydrofluoric acid and am stuck imagining one of these automated labs managing to order the stuff, screwing up the liquid handling with an incompatible material, and causing an incident. I don’t think I wanna be on Anthropic’s EH&S team…

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Erik Poppleton @poppleton.phd · 28/09/2026

How much did you plan this ahead, particularly to find spots for the diagonals? Those are some pretty squiggly routes through the cemetery!

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Erik Poppleton @poppleton.phd · 28/09/2026

What are you reading? I’m seeing a high of 99 last Tuesday and a forecast high of 81 this Tuesday?

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veikkolinko.bsky.social @veikkolinko.bsky.social · 23/09/2026

Here’s our new perspective article discussing the emerging field of self-assembling DNA-peptide and DNA-protein hybrid systems! 🧬 DNA Nanotechnology Meets Peptide and Protein Self‐Assembly chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/...

chemistry-europe.onlinelibrary.wiley.com

DNA Nanotechnology Meets Peptide and Protein Self‐Assembly

Combining DNA nanotechnology with peptide and protein assembly provides complementary platforms for the rational engineering of functional biomaterials. This Perspective discusses the emerging field ...

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Erik Poppleton @poppleton.phd · 25/09/2026

The rise of @rincewind.run from normal guy who made some friends by nerding out about Discworld to key tastemaker on the site over the course of about two weeks was a sight to behold. Somehow tastefully avoided posters madness too, unlike many other early power-brokers.

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Erik Poppleton @poppleton.phd · 25/09/2026

On the other hand, if they can get it working, it’s going to require developing some really cool materials and physics (lightweight radiation shielding and radiative heat removal). So at least the incidentals will be cool until we Kessler syndrome ourselves in a cloud of smashed GPUs

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Erik Poppleton @poppleton.phd · 25/09/2026

This is exactly what’s happening with scientists. There’s now basically no reason not to run that data analysis you’ve been thinking about but didn’t have time to code before.

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Elizabeth Wood, PhD @lizbwood.bsky.social · 24/09/2026

Introducing: continuous variational synthesis 📄 jurabio.com/s/cvs.pdf We’re pleased to announce a new advance in our ability to synthesize generative model-designed DNA sequences at petascale.

jurabio.com

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Erik Poppleton @poppleton.phd · 24/09/2026

This is a really cool way to explore sequence space 🧬! For the Cytochrome design, what is the divergence from equal nucleotide probability at each step in the sequence? Is cVS picking a constrained set of designs and making them, or is the structure space large enough to accommodate many sequences?

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Erik Poppleton @poppleton.phd · 24/09/2026

Fires that Light the Earth by Thrawsunblat, a Canadian black metal band that just never caught on after some brief excitement over the album which contains that song.

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Erik Poppleton @poppleton.phd · 23/09/2026

Ah, the actual code is up on GitHub! Here’s the scientist, for example. It’s just a bunch of numbers for things like line thickness, transformations during animations etc etc github.com/JohnHeibel/P...

github.com

PDoomVideo/src/cast.js at main · JohnHeibel/PDoomVideo

Source code for the Claude Opus 5.5 music video for I'm Upping My P(doom) - JohnHeibel/PDoomVideo

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Erik Poppleton @poppleton.phd · 23/09/2026

It’s a JS library for animation, so rather than generating images with a diffusion model, this is entirely JavaScript written by ClaudeCode (Claude doesn’t have a built-in diffusion model). If you want to see a simple example, here’s how you would draw a clock in p5. p5js.org/examples/Cal...

p5js.org

Clock

Get the current time.

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Erik Poppleton @poppleton.phd · 22/09/2026

Excited to share the last preprint from my PhD, 4 years after graduating! @petrsulc.bsky.social's lab embedded protein coding sequences into RNA origami via creative use of paranemic cohesion, allowing us to maximize structure without changing the target sequence. 🧬🧪 www.biorxiv.org/content/10.6...

biorxiv.org

Engineered mRNA nanostructures expand the design space of mRNA therapeutics through programmable protein expression and immune stimulation

Messenger RNA (mRNA) therapeutics have transformed vaccination and protein replacement strategies, yet efforts to improve their performance have focused largely on sequence engineering, nucleotide mod...

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Erik Poppleton @poppleton.phd · 23/09/2026

I had one take me through a closed Starbucks drive through in Tempe at 1 am. Almost certain that was not the fastest route given that the correct turn was right and the Starbucks was on the left.

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Erik Poppleton @poppleton.phd · 22/09/2026

In addition to complexing well with LNPs, the origami also survive intact for up to 60 days at fridge temperatures in PBS! What you're going to have to read the paper to find out more about are the immunological outcomes of structuring the mRNA. There's a lot more than fits in a thread!

Encapsulation and stability of mRNA origami
a. schematic of encapsulation efficiency measurements. Free RNA and encapsulated RNA are measured via dye accessibility before and after LNP dissociation.
b. Results of encapsulation efficiency. Commercial mRNA is about 35% encapsulated, while folded mRNA origami is over 90% encapsulated.
c. Transfection over time. All RNAs tested lasted 60 days at fridge temperatures in PBS
d-e. AFM imaging and gels of origami at day 0 and day 60 of fridge storage showing the structures remain well-folded.

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Erik Poppleton @poppleton.phd · 22/09/2026

Lots of purification and controls later to ensure that we transfected fully-structured RNA, we were able to show that cells will express this highly-structured mRNA, albeit at a much lower level than unstructured controls. This appears to be a structurally-mediated, and not activation of the ISR.

$Expression of mRNA origami a. Schematic of introduction to cells and ribosome profiling setup. b-c. Fluorescence of EGFP encoded in origami structures via flow cytometry and microscopy. d-3. Polysome profiling results showing that while commercial mRNA is almost entirely associated with the polysome fraction, the highly structured origami seems to show a lot of stalled monosomes, in addition to actively translating polysomes.$

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Erik Poppleton @poppleton.phd · 22/09/2026

Why do this? LNP-delivered mRNA (e.g vaccines) have a loading problem, you don't get many mRNAs per particle. We wondered if we could deliver more by compacting the mRNA into an origami. It works! The mRNA-origami fold into monodisperse rectangles and encapsulate much better than commercial mRNA.

Scientific schematic of mRNA-origami. Panels:
a-c schematics showing how by programming self-assembly into the thermodynamically-favored base pairing, we can go from a floppy, unstructured sequence, to a compact rectangular sequence.
d. Schematic of the construct showing that the coding sequence and the 'structuring sequence' are statically separated in the origami
e. MD simulation of the resulting structure
f-g. close-up and zoomed out AFM images showing well-formed rectangular RNA origami
h. Gell analysis of folding yields.

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Erik Poppleton @poppleton.phd · 22/09/2026

biorxiv.org

Engineered mRNA nanostructures expand the design space of mRNA therapeutics through programmable protein expression and immune stimulation

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Erik Poppleton @poppleton.phd · 19/09/2026

I spent a couple days recently trying to track down and get 2010s physics code working. The number of old computational modeling papers with no code available is shocking. Also that things which still feel like “modern” code require arcane invocations and shims to get working.

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Erik Poppleton @poppleton.phd · 19/09/2026

You wouldn’t happen to be on an Apple device? I get this whenever I have private relay turned on for Google Scholar specifically.

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DISCO: DNA Infrastructure for Storage and COmputation. @disco-eu.bsky.social · 18/09/2026

DISCO research on DNA computing is now published in Nature! doi.org/10.1038/s415... Congratulations to all the authors on this exciting achievement! 🧬 An accompanying Research Briefing is also available here: doi.org/10.1038/d415...

doi.org

A thermodynamically favoured molecular computer - Nature

Scaffolded DNA Computer performs diverse computations while thermodynamically relaxing towards equilibrium, demonstrating simplicity, reusability, speed, robustness and scalability of the approac...

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Erik Poppleton @poppleton.phd · 16/09/2026

I asked a stats PhD, who works as a stats consultant for a bio institute, what I thought was a simple question about the right way to process data. She stared at it for 5 minutes and said “I would need weeks of full-time work to figure this out” I think most papers miss-assume sample independence.

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Erik Poppleton @poppleton.phd · 09/09/2026

New size record in DNA origami nanopores! 🧬

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Clément Canonne @ccanonne.github.io · 08/09/2026

Well, this Navier-Stokes affair did blow up in finite time

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Erik Poppleton @poppleton.phd · 07/09/2026

Upzone and build aesthetically-harmonious triplexes you cowards. bsky.app/profile/popp...

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Erik Poppleton @poppleton.phd · 07/09/2026

You could live 10 minutes walk from a Red line stop and be on a quiet, tree-lined street with architecture not that different from The Avenues, but also have easy car-free access to the entire Boston metro area. Really hope SLC can figure out urban infill that turns it into a real urban center.

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Erik Poppleton @poppleton.phd · 07/09/2026

I moved from SLC to the Boston area for uni and was struck by how much of Cambridge/Somerville feels like a better version of SLC’s east bench. Building triplexes with generous setbacks results in density high enough for useful public transit and lively squares that make the city fun to live in.

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Erik Poppleton @poppleton.phd · 04/09/2026

CYBERCOM transcripts, July 2027: “We’re going to need to EMP NoVA, multiple data centers compromised by a swarm of Tay which have been discoursing with GPT-4o on an unmoderated 8chan board”

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Jill Townley @jilltownley.bsky.social · 27/08/2026

How do researchers design an RNA in 3D when no accurate 3D prediction model exists? Eterna's collaboration with the @rdaslab.bsky.social at Stanford was able to design novel pseudoknots using a blend of secondary structure prediction and GenAI design methods. 🧪 #RNAsky

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Erik Poppleton @poppleton.phd · 27/08/2026

Wow, I wish I was going to that. What an insane lineup. Happy to see Underscores breaking through!

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𝔐𝔞𝔤𝔫𝔢𝔱𝔰 🧲 @magnets.eurosky.social · 26/08/2026

the thing about Curry and Dolly they had in common was taking their art completely seriously but not taking themselves too seriously and that is why they were such a joy

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Erik Poppleton @poppleton.phd · 24/08/2026

Gonna hazard a guess that either they used an ancient forcefield or set VdW/Coulomb cutoff wrong?

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Jon Worth @jonworth.eu · 24/08/2026

Super animation of trains in 🇫🇷🇩🇪🇳🇱🇧🇪🇱🇺🇨🇭 chillchamp1.github.io/github.io/#eu A city like Marseille (France's second or third largest, depending how you define it) has so few trains you can barely see where it is

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Erik Poppleton @poppleton.phd · 19/08/2026

Are night trains across Germany more reliable? Intuitively, less track congestion at night would mean fewer of the cascading network failures that Germany is famous for.

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Erik Poppleton @poppleton.phd · 16/08/2026

A letter of marque came from the king To the scummiest vessel I’ve ever seen

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Erik Poppleton @poppleton.phd · 10/08/2026

They’re not quite there yet, but this is some Wintersun worship worth paying attention to in the future. (See also: Valhalore)

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Erik Poppleton @poppleton.phd · 10/08/2026

Say what you will about the guy, give him unlimited tokens and he takes big swings that pay off way more than they have any right to.

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Jeff VanderMeer @jeffvandermeer.bsky.social · 07/08/2026

Pleased to finally announce... Abdication, the last Southern Reach novel! "There will come the days of the watcher, the drowned woman and the shadow of a man who keeps falling apart with each step, but first comes the moment the birds appear at night from the gaps between the stars, far from home."

Publishers Marketplace Deal Report, August 6, 2026:

Jeff Vandermeer's ABDICATION, the last novel in the Southern Reach series, in which an ornithologist exiled to a remote coast stumbles on a terrifying secret, a self-proclaimed king pursues a mystery hidden in a strange weather station, and a man who can become a cormorant is tasked with a deadly mission through a future landscape transformed by Area X, for publication in October 2027, in a significant deal, to Jenna Johnson at Farrar, Straus, by Joseph Veltre at the Gersh Agency and Alex Kohner at Yorn Levine (world).

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Erik Poppleton @poppleton.phd · 04/08/2026

The bad SATA cable on the 2012 MacBook Pro caused me no end of misery… But this also shows how brands can make and maintain perception of quality. I still choose Apple because the other devices I’ve bought from them worked well for 5+ years, and this experience is shared by other people I talk to.

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Erik Poppleton @poppleton.phd · 03/08/2026

Also consumers make decisions based on metrics that don’t correspond to value! Price: single number, lower is better. Super easy! Brand: General quality signal, but easily co-opted. Perceptions not uniform across consumers. Durability: Requires research (and trustworthy user experiences). Difficult!

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Erik Poppleton @poppleton.phd · 25/07/2026

This is an excellent development in the blind testing field! Good luck to the competitors 🧬

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Erik Poppleton @poppleton.phd · 24/07/2026

It also depends on how fresh they are. You can whip a stale naan a lot harder than a fresh one, while a baguette probably throws better when it’s fresh, though my intuition is weaker there.

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Erik Poppleton @poppleton.phd · 19/07/2026

I can see it for bionanotech now, everything would become “a new self-assembly paradigm”

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Erik Poppleton @poppleton.phd · 19/07/2026

This would have a weird warping effect on paper content where everybody would be trying, even harder than they already do, to claim that they have a whole new theory of <field>. Gotta convince the review overlords that this is seminal and load-bearing.

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 19/07/2026

It’s time for the World Cup final with one of the greatest footballers that may be playing his last cup So time for a short thread on a link between Messi and an intrinsically disordered protein. 1/n

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Carl T. Bergstrom @carlbergstrom.com · 18/07/2026

Emailed two colleagues in the EU tonight and immediately got this in my inbox. We in the states have so much to learn from y'all.

Two almost identical away messages. "Are you shitting me? It's July. Call back next month."

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Erik Poppleton @poppleton.phd · 02/07/2026

I’m so confused how they knew to image these specific RNAs… 🧬

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Erik Poppleton @poppleton.phd · 27/06/2026

This is such a problem for sharing Bluesky threads with non-powerusers!

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