iiinova — where your digital self keeps evolving

Simon Kozlov @sim0nsays.bsky.social · 04/05/2026

Bro resurrected NASA simulator in a weekend with Claude Code and used data from the real space launches to find the parameters to run it, and turns out it still works really damn well.

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Simon Kozlov @sim0nsays.bsky.social · 01/05/2026

Yours truly is a proper scientist now! TL;DR: we used AI to redesign parts of essential cell machinery with only 19 canonical amino acids instead of 20. Why? Great thread by @harriswang.bsky.social provides more context and details. Let me talk a bit about the AI design part of this. 1/

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Reposted by Simon Kozlov

Gaurav Bhardwaj @gauravbhardwaj.bsky.social · 23/05/2025

Great to have our manuscript with @sokrypton.org 's lab describing AfCyDesign finally out in @natcomms.bsky.social . Structure prediction, sequence redesign, de novo hallucination of cyclic peptides, and some binder design examples in this version. rdcu.be/em0vA

rdcu.be

Cyclic peptide structure prediction and design using AlphaFold2

Nature Communications - AfCycDesign: Cyclic offset to the relative positional encoding in AlphaFold2 enables accurate structure prediction, sequence redesign, and de novo hallucination of cyclic...

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Reposted by Simon Kozlov

Eric Columbus @ericcolumbus.bsky.social · 16/04/2025

Oh wow great @haleaziz.bsky.social piece on a 2018 case in which Trump’s ICE screwed up and erroneously deported a guy. AND THEY BROUGHT HIM BACK because why wouldn’t they? We’re in a much darker place now. Free link: www.nytimes.com/2025/04/15/u...

In one court document from Aug. 23, 2018, the government owned up to its mistake, saying Mr. Subaihani had been removed to Iraq despite the court's order.
Locating Mr. Subaihani was complicated because nobody knew where he had gone, or even if he had made it to Iraq. By September 2018, several weeks after Mr. Subaihani had been deported, a federal judge demanded ICE go to great lengths to find him.

ICE officials complied, explaining to the court that they were in touch with State Department staff in Iraq and in other countries he had transited through. They even called airline officials — Mr.
Subaihani had been deported on a commercial flight — for more on his whereabouts.
n late September, ICE officials notified the court that they had und evidence Mr. Subaihani had made it to Iraq. By October, Mr.
Subaihani's attorneys had tracked him down with the help of an investigator, and set about working with ICE to get him back to the United States.

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Yehlin Cho @yehlincho.bsky.social · 08/04/2025

Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with @martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org 🧬 Code will be released in a couple weeks

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Reposted by Simon Kozlov

Axel Visel @axelvisel.bsky.social · 04/12/2024

BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse) To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜 Paper: www.cell.com/developmenta...

Figure from the paper, showing BOOSTER-overexpressing poplar plants that are about twice as tall as the negative controls. Googly eyes (not from original paper) look at the taller plants.

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Reposted by Simon Kozlov

Harris Wang @harriswang.bsky.social · 30/11/2024

💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)

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Simon Kozlov @sim0nsays.bsky.social · 29/11/2024

Fully accepting nothing may work out is a surprisingly effective way to work something out. Here’s the catch: knowing this fights against acceptance.

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Simon Kozlov @sim0nsays.bsky.social · 25/11/2024

I would love for a social network to exist where questions like this get a meaningful discussion. I don’t think Twitter had it even if it’s best days, with a few exceptions when tweet randomly goes viral. Can we make it work here? That would take the whole community to a next level.

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Reposted by Simon Kozlov

Jason Kelly @jasonrkelly.bsky.social · 20/11/2024

Made a biotech founders starter pack, DM me to be added! go.bsky.app/LWm8uPE

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Simon Kozlov @sim0nsays.bsky.social · 20/11/2024

Noticed that whenever I see a tweet I like, the first thing I do is check if author is on BlueSky. Glad to be here!

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