Devon Stork

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Devon Stork

Devon Stork

@StorkDevon

Co-founder at Pioneer Labs, SAB at Tenza, Molecular Biology. I edit microbial genomes and take lots of notes. All views my own, He/Him.

San Francisco, CA Katılım Haziran 2019
409 Takip Edilen692 Takipçiler
Devon Stork retweetledi
Erika Alden DeBenedictis
Erika Alden DeBenedictis@erika_alden_d·
I think the first successful virtual cells are going to model prokaryotes, not eukaryotes. It’s technologies like BioBloom that are going to be the difference between being able to collect enough data and NOT. Thoughts? @ChanZuckerberg @DBBurkhardt @arcinstitute @joncalles
PioneerLabs@Pioneer__Labs

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: biorxiv.org/content/10.648… Retweet if you want more data, and read on if you want to use the library! 🧵

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Devon Stork
Devon Stork@StorkDevon·
@hhlee @ProfTomEllis We'll do it in other organisms if people are interested enough. What do you think should be next? P. putida?
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Henry Lee
Henry Lee@hhlee·
@ProfTomEllis Totally right gotta start somewhere. It’s the new … in mice modifier.
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Tom Ellis
Tom Ellis@ProfTomEllis·
New preprint from Pioneer Labs - BioBloom: a retron-based method for barcoded saturation mutagenesis of the entire E.coli bacterial genome. biorxiv.org/content/10.648…
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Devon Stork
Devon Stork@StorkDevon·
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! 🧪👇
PioneerLabs@Pioneer__Labs

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: biorxiv.org/content/10.648… Retweet if you want more data, and read on if you want to use the library! 🧵

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Devon Stork
Devon Stork@StorkDevon·
@owl_posting Oh, I talked to a Real Journalist at one point, and they told me what the process is like. Checking my notes, it's basically "email the editor," and they sent me this video youtube.com/watch?v=vA6qb3…
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owl
owl@owl_posting·
how do people submit things to the Serious Literary Magazines i have an essay about a (failed) cancer drug that i think is fun and readable to a more general audience. but the Atlantic's submission page has a picture of a creepypasta'd Tom from Tom And Jerry and nothing else
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Devon Stork
Devon Stork@StorkDevon·
@owl_posting The success of the best PIs I knew was more about the lab culture they fostered than their own personal knowledge. That being said, the figures that stand out to me are Adam Marblestone & Rob Carlson.
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owl
owl@owl_posting·
i wish there was a jensen-esque figure in biology that i could interview but nobody actually knows whats going on in this field. if you do, please dm me
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Devon Stork retweetledi
PioneerLabs
PioneerLabs@Pioneer__Labs·
We spent months thinking about atmosphere models and climate calculations for a habitable Mars. We did not, until now, consider the maximum acceptable arthropod dimensions. 🦟
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Vega Shah
Vega Shah@dr_alphalyrae·
@srikosuri yeah that’s the only logical conclusion here, a futuristic, space appropriate, self balancing centrifuge
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Vega Shah
Vega Shah@dr_alphalyrae·
project hail mary was fantastic but did anyone else catch the scene where the centrifuge is not properly balanced? its bothering me so much
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Devon Stork
Devon Stork@StorkDevon·
@baym I've always gotten better reviews from asking a friend than journals. The best solution is to make friends with other people in your field!
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Michael Baym
Michael Baym@baym·
Remember that you, by definition, cannot distinguish between a good idea and a failure of your own knowledge, judgement, or taste. This is why external (ideally expert) feedback is crucial
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Devon Stork
Devon Stork@StorkDevon·
@boycereads Short stories my dude. Go pick up some Alastair Reynolds, Ted Chaing, or Stanislaw Lem.
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Shane Boyce
Shane Boyce@boycereads·
What’s the best sci-fi you’ve ever read not named Dune, Red Rising or Sun Eater?
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lada
lada@ladanuzhna·
Biology woke up and chose violence
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Devon Stork
Devon Stork@StorkDevon·
Cory taught me a lot back in grad school, and it was great to catch up and discuss what we're doing at Pioneer!
Cory J Smith 🧬@GalaxyBalanceHQ

What if the key to becoming a multi-planetary species isn’t rockets, but microbes? In the latest episode of Galaxy Balance, I sat down with Devon Stork, founder of the nonprofit Pioneer Labs, to explore a bold and necessary frontier: engineering microbes to support human life beyond Earth. Devon’s work focuses ono microbial evolution as infrastructure, developing robust biological systems that can survive extreme environments and transform Martian regolith into usable soil. Rather than shipping everything from Earth, Pioneer labs is asking a deeper question: How do we let biology do the heavy lifting? We discuss: · Why microbes may be the first true settlers on Mars · Designing evolutionary “chassis” for extreme environments · Converting regolith into fertile soil using biology · The role of open science in accelerating planetary-scale challenges · What is really means to think about life support as a living system. This conversation is about aligning evolution, engineering, and long-term human survival. If you are interested in synthetic biology, space exploration, or how life adapts at planetary scales, this episode is for you. #SyntheticBiology #SpaceBiology #Mars #MicrobialEvolution #OpenScience #LongTermFutures

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Devon Stork retweetledi
The Align Foundation
The Align Foundation@Align_Bio·
In partnership with @Pioneer__Labs, 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: zenodo.org/records/179902…
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Devon Stork
Devon Stork@StorkDevon·
@DanielleFong I still find it ridiculous that steam is the only mainstream way to do heat to electricity. Too many moving parts.
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Danielle Fong 🔆
Danielle Fong 🔆@DanielleFong·
sadly there is no supply for the desired helium turbomachinery to generate power for space nuclear microreactors. if only someone were working on a solid state nuclear power generator 🤔💭🔆
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Devon Stork
Devon Stork@StorkDevon·
@ramez As a scientist and author (under pen name) I think it's one part creative anxiety, one part torment nexus and one part clique mentality/solidarity. There's a couple people bullish on it - @alexanderwales has the best opinions here.
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Ramez Naam
Ramez Naam@ramez·
Science fiction authors seem, on average, remarkably hostile to LLMs. I find it shocking. I understand their angst about creators being disruped. But it turns into this deep skepticism that AI is useful or societally beneficial at all. Real cognitive dissonance.
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Devon Stork
Devon Stork@StorkDevon·
We learned something from each of these, and I hope that by sharing, we can help someone else learn the same lessons without the failure part. Posting negative results publicly should be more normal!
PioneerLabs@Pioneer__Labs

We just wrapped our 12-day Negative Results Advent Calendar 🎄⛔🧪 Now it’s all in one place, with extra context + a few runner-up failures we didn’t post the first time 📉🤦 Take a look for a behind-the-scenes look at how science happens. 🔬❤️#aHR0cHM6Ly9vcGVuLnN1YnN0YWNrLmNvbS9wdWIvcGlvbmVlcmxhYnMvcC8xMi1kYXlzLW9mLW5lZ2F0aXZlLXJlc3VsdHM=" target="_blank" rel="nofollow noopener">rynomad.github.io/stubsack/#aHR0…

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Devon Stork retweetledi
PioneerLabs
PioneerLabs@Pioneer__Labs·
That’s the end of our Negative Results Advent Calendar🎁🚫😜12 days of mistakes and weird data, and what we learned along the way🔬😅We'll post the collation of them all and a few honorable mentions tomorrow❤️
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Devon Stork
Devon Stork@StorkDevon·
Not all libraries are created equal, and we're still figuring out which summary statistics and cutoffs to use when evaluating them. I'd love to hear any tips on Gini coefficients or Simpson indices, and how to apply them to large DNA libraries.
PioneerLabs@Pioneer__Labs

⛔ result 12: Some of our libraries are already pretty skewed before we start selection 😅📊 Not always bad enough to trash, but it means we need much bigger bottlenecks to avoid chopping off all the low-abundance members 🧬🔍🧵

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Devon Stork
Devon Stork@StorkDevon·
Good QC metrics are essential to good science, and I especially like this one. It'e asking if our variance is explainable by sampling noise (var/mean = 1) for every barcode in the library. From there you can track down the problem. In this case, insufficient DNA input into PCR.
PioneerLabs@Pioneer__Labs

⛔ result 11: We barcode the genome and use Illumina reads to track fitness of 5E6 strains at once 🧬📊 But at that scale, you need to add µg’s of gDNA to avoid bottlenecks. We didn’t, so our variance ended up far above Poisson noise 🤦‍♀️📉🎲

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Keşfet

@ChanZuckerberg @DBBurkhardt @arcinstitute @joncalles @hhlee @ProfTomEllis @owl_posting @pylabrobot