I engineer life for Mars. Most frequently asked Q: "But can't you just evolve organisms by slowly making it more and more Mars-like?" The answer is MAYBE. Step 1: figure out how to simulate Mars properly. Here's how we do it ➡️ t.co/TwNHzkmyXK

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

How do we simulate Mars here on Earth? We scrutinized Mars rover data so you don’t have to. 😛 Here’s what it tells us about how to simulate Mars on Earth, and which organisms could grow on Mars! 📄 Report: www.biorxiv.org/content/10.6...

Happy to announce a new preprint from my former academic lab, where we use PACE to evolve halogenase enzymes! Congrats to Andre Pulschen and Justin Booth who led the study!

bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 10mo ago

Continuous evolution of a halogenase enzyme with improved solubility and activity for sustainable bioproduction https://www.biorxiv.org/content/10.1101/2025.10.08.681035v1

🧫 Meet the keynote speakers for the 2025 scverse conference! Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs @erika-alden.bsky.social ‪ @alignbio.bsky.social @pioneerlabs.bsky.social #scverse #scverse2025 #StructuralBiology #Biotech #Stanford

📣 Evolutionary Scale is supporting the 2025 Protein Engineering Tournament! Teams get sponsored ESM inference through @evolutionaryscale.bsky.social's API (Forge), bringing frontier protein AI models into the competition. Level playing field, real experiments, open results. Register now 👇

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! 👇

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. 🧬 + 🔢 = 📈 -> 🤖?

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...

This proposal is really interesting. Can you measure enzyme kinetics by adjusting substrate concentration *inside* the cell? On one hand, cells are noisy. On the other, enzymes behave differently in vitro & in vivo. Best to measure in the conditions you care about!

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

Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇

Very excited by all the execution that's happening at Align! 💪 You know me, I just want to be drowning in data 😛

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

Q1 at Align = ✅ Team doubled ✅ 65k GROQ-seq datapoints ✅ Genotype-by-Phenotype platform ✅ Global conf. circuit ✅ Tournament prep underway Get the full download → hubs.la/Q03hT_V60 #ProteinEngineering #AIxBiology #SynBio #OpenScience

Time for a LOT of microbe data! 📊 🦠 🤖 @alignbio.bsky.social is aiming to gather a core dataset composed of phenotypes for 1000 diverse microbes cultivated in 1000 diverse conditions. This labeled data has the potential to take our ability to predict how microbes will behave to the next level!

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

🚀 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

Government funding mechanisms for science need to evolve in the age of AI. 🤖 💰 How? Check out our Day One memo on how to repurpose 'Center' grants to fund large dataset acquisition.

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

🚀 Collaborative, AI-Ready datasets would revolutionize life sciences and catalyze progress. Government funding plays a critical role in making this a reality. 📖 Read our policy memo here:

🎄 @alignbio.bsky.social is hiring! Join The Align Foundation as the Chief of Staff or Open Science Admin and help make life science reproducible, scalable, shareable. 📍 Remote-friendly roles 🗓 Apply now, aiming to hire by Feb 2025 📧 Email cover letter + resume to contact@alignbio.org

•Switched gears to @erika-alden.bsky.social and Align to Innovate!! •she also switched gears from mathematical sims in astrophysics to biology and later on proteins ;) •mission: “interface of biology, automation, and machine learning to rapidly convert the life sciences to a data-first discipline”

Had a lot of fun with this interview with @agapakis.com. If you don’t know Christina, she is the one who resurrected an extinct flower scent during her time at Ginkgo. 🌸 Who better to talk about the big questions - like WHY we do science!

Christina Agapakis@agapakis.com · 2y ago

Was so fun to talk with @asterainstitute.bsky.social resident and @pioneerlabs.bsky.social founder @erika-alden.bsky.social! Read our convo if you want to be inspired about the future of life, bioengineering, and engineered life on Mars asterainstitute.substack.com/p/lets-go-do...

The first astronauts on Mars will use bacteria to make food, therapeutics & building materials. What do you feed the 🦠? Here's the recipe: - 40g of Mars dirt - 1 liter of water - Mix and strain In our substack post, Pioneer Labs defines how to mimic this recipe on Earth. 🚀🌼

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

E11 Bio making *headway* on brain mapping... 🧠😜

Andrew Payne@andrewcpayne.bsky.social · 2y ago

🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains. Read more: e11.bio/news/roadmap

Started as Head of Data at Align to Innovate today! I am thrilled to join this team and be part of their mission! www.alignbio.org

In our most recent post we describe fragmenting a halophilic genome 🔪, building functional libraries 🪡 and selecting them 🤼 to find genes that measurably 📏 improved salt tolerance🛠🧂! Lab notebook links once more included if you want to dive into the details! open.substack.com/pub/pioneerl...

The first turn of our engineering crank 🛠🧂

Beyond deletions: additive strain engineering and adaptation

open.substack.com

The next few years will see a huge transformation in how science works, on par with the enlightenment. FutureHouse is building AIs that can automate science and put the resulting knowledge into the open. Conversation with Freethink, now online here: www.freethink.com/artificial-i...

Can we automate science? Sam Rodriques is already doing it.

People need to anticipate the revolution that’s coming in how humans and AI will collaborate to create discoveries, argues Sam Rodrigues.

freethink.com