13 years ago, I read a paper that changed how I think about science. No new experiments, just decades of scattered findings reasoned into one answer to "why are bacteria different from eukaryotes?" My breakdown of Julie Theriot's masterclass: www.devonstork.com/p/a-demonstr...

A demonstration of Scientific Mastery

Reasoning through why prokaryotes are different from eukaryotes

devonstork.com

When you evolve bacteria, you get a random smattering of mutations. Now, you can measure fitness for every possible SNP mutation in the genome with a single experiment! BioBloom Libraries available on Addgene now! 🧪👇

Pioneer Labs@pioneerlabs.bsky.social · 4mo ago

This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded. 🧪Growth + barcode sequencing = data on millions of mutations. 📄 Report: www.biorxiv.org/content/10.6... Retweet if you want more data, and read on if you want to use the library! 🧵

This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded. 🧪Growth + barcode sequencing = data on millions of mutations. 📄 Report: www.biorxiv.org/content/10.6... Retweet if you want more data, and read on if you want to use the library! 🧵

In partnership with @pioneerlabs.bsky.social, we’re proposing Tesseract: a large-scale, open microbial phenomics dataset to functionally annotate microbial genomes at scale. 🧬🤖 ✅5M diverse genes x 50 host strains × 100 conditions 🔗 Read the proposal:https://zenodo.org/records/17990299

By this time next year, either: 🏆 we'll have engineered PETase enzymes actually work industrially & recycle plastic ... or we'll know that AI-for-proteins is still a bit underbaked 😜 Excited to see what happens!!!! 😬 Spread the word ⬇️

The Align Foundation@alignbio.bsky.social · last yr.

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

Heads up: terraforming Mars isn’t just sci-fi, it’s a real possibility that’s possible with today’s technology. Mars could be green in MY lifetime. 🚀 🌼 What’s stopping us? We need a lot more real research into how to do it right. Don’t nuke Mars! 👇

Can we do BETTER than evolution with the help of AI? It starts with data. 🧬 🔢 Check out @pioneerlabs.bsky.social's breakdown of how we get large-scale, high-fidelity data out of every engineering and evolution experiment!

Pioneer Labs@pioneerlabs.bsky.social · last yr.

pioneerlabs.substack.com/p/laying-the...

I went to the 2025 Symposium on Biomaterials, Fuels and Chemicals with an invitation from @nils-averesch.bsky.social to speak about our work at @pioneerlabs.bsky.social engineering organisms for sustainable biomanufacturing on Mars! I took 80 pages of notes. docs.google.com/document/d/1...

Devon SBFC 2025 Notes

These are Devon’s conference notes for the 2025 Society for Industrial Microbiology and Biotechnology (SIMB) 47th Symposium on Biomaterials, Fuels, and Chemicals (SBFC). This version is intended for p...

docs.google.com

Pioneer Labs@pioneerlabs.bsky.social · last yr.

With bioinformatics, we’re now measuring the fitnesses of millions of DNA fragments! This gets us data on whole genomes and is the first step toward big data for modeling genotype -> phenotype with AI/ML for microbial evolution. Link in comments. 🧬 + 🔢 = 📈 -> 🤖?

🚀 New proposal from Align! The experimental platform aims to standardize #microbial #phenotyping & support predictive modeling. 🦠 Capturing data across 1k strains & 1k conditions; using BacterAI; generating high-quality datasets for ML @jensen_lab

Ever wonder how we’ll unlock Mars as a living world? 🌏 In our substack post we break down the 'red planet recipe'—the chemistry of mars soil — for growing life on another world. Dive into the science to find out more!

Pioneer Labs@pioneerlabs.bsky.social · 2y ago

Check out 🏆A Biologist’s Guide to Mars Dirt, where we present a receipt for soluble Mars Regolith Media (sMRM) that best simulates what you’d get if you added water to Mars dirt. Will anything grow in this media? Stay tuned! 💧+ 🪨 → 🌱 ? open.substack.com/pub/pioneerl...

The next Alphafold2 will be a predictive model of protein expression. I think it's possible, and @alignbio.bsky.social is going for it! 🧬 Every single protein engineering project I have ever worked on at one point or another ran into expression issues. 😠 It can't come soon enough! 🙏

The Align Foundation@alignbio.bsky.social · 2y ago

🚀 News from Align! Today, we're sharing our proposal for building a predictive model of protein expression. Check it out here! ➡️ https://buff.ly/3OqtPZf ⬅️ 🌍✨#ProteinExpression #Bioengineering #Collaboration #MachineLearning #DataScience #AlignToInnovate

💡💥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)

I just read the Evo paper www.science.org/doi/10.1126/... from the @arcinstitute.org and have some thoughts. Tl;dr: I can see this being a fundamental part of the future of biology, but this paper is light on experimental data and I don’t think many of their demos are very interesting. 🧵

Sequence modeling and design from molecular to genome scale with Evo

The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism’s function. We present Evo, a long-context genomic foundation model with a frontier architecture trained o...

science.org

Want to follow along as we engineer microbes for circular biomanufacturing in space? We're launching open science updates through our substack! ⬇️