Devon Stork
258 posts
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
408 Takip Edilen688 Takipçiler
Devon Stork retweetledi
America is exceptional. But I noticed few people write about WHY America is so exceptional, especially San Francisco. And even fewer write for the high-skilled talent around the world.
So here's a few raw obvious observations on America, from a European fresh off the boat.
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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
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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@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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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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@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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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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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
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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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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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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Devon Stork retweetledi
New Blog Post: How to Not Make a Scientific Journal by Accident
pracheeac.substack.com/p/how-to-not-m…
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@ATinyGreenCell Answered over in other post! As far as we can tell, nothing weird, just contamination somewhere in multiple days of antibiotic-free passaging. x.com/StorkDevon/sta…
Devon Stork@StorkDevon
@ATinyGreenCell 7. Stock stuff that looks good. 16S/WGS it. The plates above are from step 5, so they'd gone through 3 cultures, 144 hours of growth without antibiotics, and the contamination happened somewhere in there, and maybe earlier.
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@StorkDevon Wow, what was the ID on the contam? Maybe sporulation in the incubator? Its so uniform thay it seems to have come from the innoculum. Very invested now in this detective work
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You don't realize how much you're leaning on antibiotics and fast growth times to prevent contamination until you need to do experiments without them.
These excisions need almost the same level of sterile technique as human stem cell culture.
PioneerLabs@Pioneer__Labs
⛔result 10: For genomic integration in C. necator, we do repeated rounds of integration & excision🧬🔁That means days of growth without selection, and C. necator is so slow-growing it usually gets contaminated 😭 Other strains outgrow hitchhikers, but not this little guy🐌🧫
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@ATinyGreenCell 7. Stock stuff that looks good. 16S/WGS it.
The plates above are from step 5, so they'd gone through 3 cultures, 144 hours of growth without antibiotics, and the contamination happened somewhere in there, and maybe earlier.
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@ATinyGreenCell 4. Cure out the excision plasmid with sucrose/novobiocin. 48 hours.
5. Drop dilutions on antibiotics to estimate excision/curing success. Plate to isolate colonies. 48 hours.
6. Pick colonies, grow up in +/- antibiotics to look for things that don't have any resistances. 48 hours
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Very invested in the mystery contam source here. The art and craft of biological research is a lifelong pursuit and we can always learn from each others stumbles and everests. This sort of transparent reporting of negative results is deeply refreshing.
Devon Stork@StorkDevon
@ATinyGreenCell That's the thing - this was done in a downdraft hood, and it still got contaminated. Those sleeves you wear to cover your wrists help, but we think some of it came from other stuff in the incubator too.
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@ATinyGreenCell That's the thing - this was done in a downdraft hood, and it still got contaminated. Those sleeves you wear to cover your wrists help, but we think some of it came from other stuff in the incubator too.
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@StorkDevon I always found it odd that microbio peeps who have access to hoods dont just work in hood always. I do all my work in my downdraft sterile air cabinet and my background contam is literally 0%. I only get contam from silly mistakes or overloaded autoclave run.
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@ATinyGreenCell @Pioneer__Labs Yeah, we saw it get all snotty at higher salt too. Was this MG1655-derived? I'm curious as to the selection regimen. Our strains can tolerate only ~4% at the start.
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@StorkDevon @Pioneer__Labs I was stress testing the bug after pushing for 100 cycles at 80. Im trying to find where it shat the bed but iirc it was ~125. It went full sticky fillament and crashed
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⛔ result 5: Because of our LB drama, we switched to measuring salt tolerance in M9, a defined minimal medium🧫➡️📏 And then…😅Strains that looked great in high-salt LB showed no improved salt tolerance in M9. Turns out “salt-tolerant” depends a lot on the exact media🧂🤷♂️
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@ATinyGreenCell @Pioneer__Labs You jumped straight from 8% to 12%? Wow, amazed that worked. Have you tried to push it higher than 12?
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