Space cowboy riding a massive rock across the galaxy, wrangling genomes and herding data. PhD in Biochemistry @TAMUBCBP. Working @LanzaTech.

Chicago, Illinois
Joined October 2020
The names that built American manufacturing are iconic. Slater, who brought the mill. Lowell, who integrated it. Carnegie, who scaled steel. Ford, who set the line in motion. Deming, who taught the world quality. The forces of production that once built America are rebuilding America again. This is one of the most important economic and national security imperatives of our time. General Catalyst has backed @ReBuildMFG since 2024, and today we are co-leading their $2.1B round alongside JPMorganChaseโ€™s Security and Resiliency Initiative.
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Dan Browne retweeted
Today we're coming out of stealth, introducing Neywa Labs ๐Ÿš€ We built the infrastructure to build and deploy AI that runs on the devices people already own. Private, offline, unlimited. One mission: make AI available to everyone in the world. neywalabs.ai/
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Dan Browne retweeted
Many of you don't understand how serious this is, so let me break it down. In computer science there is a famous kind of puzzle called 3-SAT. You are given a long list of yes-or-no switches and a set of rules about how they must be arranged, and you have to find a combination that satisfies every rule. The obvious way to solve it is to try every combination, but each new switch doubles the number of possibilities, so a puzzle with a few hundred switches would take longer than the age of the universe to brute force. For decades, the smartest people in the field found clever tricks that made this a little faster, but every trick still hit the same wall: the time required kept exploding as the puzzle grew. About 25 years ago, two computer scientists, Russell Impagliazzo and Ramamohan Paturi, working with Francis Zane, turned that wall into a formal idea. They proposed the Exponential Time Hypothesis, which says this explosion is not a failure of human cleverness but a law of nature. No algorithm, however brilliant, will ever solve 3-SAT without the time blowing up exponentially. Nobody could prove it, but almost everyone believed it, and it became one of the foundations of modern computer science. Researchers used it as a measuring stick. If you could show that solving some other problem quickly would also crack 3-SAT quickly, you had shown that problem was hopelessly hard too. Hundreds of papers, across scheduling, graphs, logic and much more, rest on this one assumption. Now an internal AI model at OpenAI claims to have broken it. It says it found an algorithm that solves these puzzles meaningfully faster than the hypothesis allows, and it has checked the proof in a computer verification system called Lean. And here is the remarkable part: the very people who proposed the hypothesis, Impagliazzo and Paturi, along with MIT's Ryan Williams, are now leading the public review of whether a machine has disproved their own idea. So what happens next? If the disproof holds, a large part of theoretical computer science has to be revisited. Every result that said "this problem cannot be solved faster, assuming ETH" loses its foundation, and researchers will have to work out which of those walls were real and which were simply where we stopped looking. It does not mean everything becomes easy. The new algorithm is still slow in absolute terms and this is not the famous P versus NP problem being solved. But it means our map of what is possible was wrong in a place we were very confident about, and it was an AI that redrew it. If the disproof fails, the hypothesis survives and the field breathes out, but we will still have watched an AI produce serious, checkable work on one of the deepest questions in the discipline, closely enough that the founders of the idea had to take it seriously. Either way, something has shifted.
An internal model at OpenAI has produced a claimed refutation of ETH! Russell Impagliazzo, Mohan Paturi, and I have been asked to help organize an open and independent examination of this claim. 1/4
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This is going to be a big week, in terms of releases. First up: Cherimoya CATv1 is now in proto-tools (github.com/evo-design/proto-โ€ฆ), making our ~7.5k DNase+ATAC models available for design using this extremely cool tool. Thanks @benviggiano!
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PCBs made in America. Twice as fast as Shenzhen. Today @CircuitHub is unveiling The Grid, our factory-scale robot in Massachusetts that builds circuit boards on demand. No changeovers, no per-design setup. Prototypes and production batches, fully automated.
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I've been meaning to share these thoughts for a while and touched on them briefly in a recent conference talk. They are relevant to a lot of the discussions today.
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Look at this 33B monster LLM! ๐Ÿ‘€
๐Ÿš€Excited to announce Nanbeige4.3-33B! To push the performance ceiling of small agents, our strategy in Nanbeige4.3 starts with building a powerful teacher first. Nanbeige4.3-33B delivers SOTA agentic performance among open models at ~30B parameters: * Strong results on agentic coding and cowork benchmarks. * When integrated into mainstream agent harnesses, it tackles real-world tasks with cost-efficient inference. * It will serve as a teacher for upcoming smaller Nanbeige models, starting with Nanbeige4.3-3B. huggingface.co/Nanbeige/Nanbโ€ฆ huggingface.co/Nanbeige/Nanbโ€ฆ #LLM #Agent
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Everyone who works in โ€œAI or Techbioโ€ should be forced to shadow in a lab for at least 1-4 weeks to see what the next steps after you have a structure on your computer. And thatโ€™s just boring brute force research, not exploratory research with new hypothesis.
there will be within the next few years stunning advances in biology. there will whole new ways to think about what biological study even means. i would be only mildly surprised if there were near term solutions to problems like cancer, neurodegenerative disease, etc
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Dan Browne retweeted
Thereโ€™s a really pronounced divide between people who are on the AI side of things and people who are on the biology side of things. Even among people working in AI, the divide persists based on where theyโ€™re focused. The AI side, adherents of scaling laws and the bitter lesson, believe that AI getting better means AI being more capable of novel discoveries in medicine (that go beyond discovering new drugs in well understood targets or speeding up dry lab work etc). The biology people think the idea of a bitter lesson in biology is kind of ridiculous and that regardless of AIโ€™s capabilities itโ€™s going to be at least 5-10 years until you could hope to reliably simulate human toxicology in silico (right now AI/ML canโ€™t even reliably simulate in vivo studies like binding affinities or functional assays). Even the most AI pilled of them, who will list all the areas that AI can reduce the time spent on various areas, donโ€™t think the concept of AI discovering novel targets or generating new understanding of causal biology is realistic in the near term. Most, in fact, will readily characterize the assumption that even an โ€œASIโ€ level model could find cures hidden in our current understanding (without expanding that understanding with significantly more biological data) as patently false. This was a big part of why we wanted to experience it ourselves by using AI for a (very) small portion of what it can do in biology. It was both mind blowing and revealed some poignant insights into how different the problem of making AI better at something like coding is to the problems of biology. Even if it unlocked the ability to generate new molecules at a stunning pace, its simulation (in silico) of binding only had 49% accuracy. And if we wanted to improve that, weโ€™d need to feed it back the data from the lab - data that took about 30x as long to get as it took to generate the molecules. And these were tests in a test tube (turn of phrase), imagine how long it would take if we wanted to improve the model with data that required recruiting humans and monitoring their reactions. Human biology is very complex, and adding a drug - especially a novel drug and doubly so for a novel drug acting on a novel mechanism - means mapping interactions that have nth-order-effects that we donโ€™t have the data to predict. Virtual cells have made advancements enabled by AI, but the perturbations equate to a small fraction of the possible. This is before you even get into curing disease, especially uniquely human diseases. Brain function involves cellular identities that are unique to humans, meaning animal studies are of little use. How long does it take to understand what the side effects of chronic administration of a drug in humans are? AI can speed up analyzing the data, or designing the trial or even getting it approvedโ€ฆbut it canโ€™t make a 6 month trial complete in 3 months. I think its important to point out that significant advancements can be made in AI that contribute to biology, while also being realistic about how much it speeds up something as complex as curing a specific cancer or diseases of the brain.
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Ever wonder if eventually cells could be trained out of disease states? We're on the path; first steps: New #preprint - @WesleyPClawson "Goal directed closed-loop training of network bursts in cortical cultures produces improved performance and error correction over days" biorxiv.org/content/10.64898โ€ฆ
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Dan Browne retweeted
๐Ÿงฌ We have been using ๐—”๐—œ-๐—ฎ๐—ฐ๐—ฐ๐—ฒ๐—น๐—ฒ๐—ฟ๐—ฎ๐˜๐—ฒ๐—ฑ ๐—ฎ๐—น๐—ด๐—ผ๐—ฟ๐—ถ๐˜๐—ต๐—บ ๐—ฑ๐—ฒ๐˜€๐—ถ๐—ด๐—ป to rethink foundational methods in molecular evolution from first principles. ๐Ÿš€ Our new preprint introduces ๐—ฅ๐—ต๐—ถ๐˜‡๐—”๐—ฒ๐—ผ๐—ปโ€”a new paradigm for recombination analysis that replaces discrete tree searches and combinatorial triplet tests with ๐—ฐ๐—ผ๐—ป๐˜๐—ถ๐—ป๐˜‚๐—ผ๐˜‚๐˜€ ๐˜๐—ฟ๐—ฎ๐—ท๐—ฒ๐—ฐ๐˜๐—ผ๐—ฟ๐˜† ๐—บ๐—ฒ๐—ฐ๐—ต๐—ฎ๐—ป๐—ถ๐—ฐ๐˜€ in linear O(NKL) time. ๐Ÿ“„ Preprint: biorxiv.org/content/10.64898โ€ฆ ๐Ÿ“– Blog & 60-sec slides: spond.github.io/CV.js/blog/2โ€ฆ ๐ŸŒ Browser app: veg.github.io/rhizaeon-code/ ๐Ÿ’ป Code: github.com/veg/rhizaeon-code โš™๏ธ ๐—›๐—ผ๐˜„ ๐˜๐—ต๐—ฒ ๐˜€๐˜๐—ฎ๐—ฐ๐—ธ ๐˜„๐—ผ๐—ฟ๐—ธ๐˜€: ๐Ÿงญ ๐— ๐—ฒ๐˜๐—ฟ๐—ถ๐—ฐ ๐— ๐—ฎ๐—ฝ & ๐—ฅ๐—ผ๐—ผ๐˜ ๐—ฆ๐—ถ๐—ป๐—ธ: K reference genomes form a fixed metric map with an unpolarized root sink at the origin. Branch-specific rate bursts flow into the sink, holding false positives at 0.58%โ€“1.01% across 333,334 clonal genomes in a 1,000,000-alignment sweep. ๐ŸŽฏ ๐—”๐˜๐˜๐—ฒ๐—ป๐˜๐—ถ๐—ผ๐—ป ๐— ๐—ฎ๐—ฝ๐˜€ & ๐—š๐—ต๐—ผ๐˜€๐˜ ๐—”๐˜…๐—ถ๐˜€: Each sequence is tracked along the chromosome via soft attention weights over the landmarks, plus an orthogonal projection that captures unsampled ("ghost") donor lineages. โšก ๐—™๐—ผ๐—ฟ๐—ฐ๐—ฒ ๐——๐—ถ๐—ฝ๐—ผ๐—น๐—ฒ๐˜€: Crossovers shift attention from one donor to another, creating an equal-and-opposite force dipole across the breakpoint that we test against a Brownian-bridge null. ๐ŸŒŠ ๐——๐˜†๐—ฎ๐—ฑ๐—ถ๐—ฐ ๐—ช๐—ฎ๐˜ƒ๐—ฒ๐—น๐—ฒ๐˜ ๐—ฃ๐—ผ๐—น๐—ถ๐˜€๐—ต๐—ถ๐—ป๐—ด: Multi-scale wavelet filters, 5-state Viterbi decoding, likelihood polishing, and iterative tract scrubbing resolve nested transfers from 80 bp gene conversions to 30 kb cassettes while merging shared clade transfers into a single ancestral event (98.8% exact). ๐Ÿฆ€ Written in Rust and Python and compiled to WebAssembly for zero-install browser runs, RhizAeon maps: ๐Ÿฆ  83 whole sarbecovirus genomes (31 kb) in 2.6 seconds ๐Ÿงซ 240 S. pneumoniae chromosomes (2.22 Mb) in 36.1 seconds ๐Ÿ›ก๏ธ 379 primate HLA Class I alleles in 1.1 seconds ๐Ÿค With Danielle Callan, @stvnwvr Hannah Verdonk, @JD_zehr @SpyrosLytras, @nekrut, @tpaisie, and @DarrenM98230782 .
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A systems-level atlas of carbon-response transcriptional states in Escherichia coli doi.org/10.1073/pnas.2531884โ€ฆ
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Dan Browne retweeted
We connected X-Scientist to our lab robots and watched the lab come alive. ๐Ÿฆพ๐Ÿงช AI coordinating workflows. Robots moving samples. Experiments running into the night. Itโ€™s incredibly rewarding to watch the future of biotech unfold right in front of us.
Meet X-Scientist: our step toward a self-improving virtual drug hunter! Today, weโ€™re introducing Xairaโ€™s agentic AI platform for drug discovery: ๐Ÿง  Beats Codex using the same Astra model by 7.4 percentage points on DrugDiscoveryBench. ๐Ÿงฌ Nominates targets ~10ร— faster than human curation, with a comparable wet-lab hit rate. ๐Ÿ” Conducts autonomous research, outperforming AutoResearch and AutoScientists in the PerturbQA benchmark. Hereโ€™s what we built, what we tested, and where weโ€™re going. ๐Ÿงต
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Dan Browne retweeted
Delighted to share a landmark preprint from our lab, using genome language models and AI agents for biological discovery and genome mining! The stretches of DNA between protein-coding genes are often called the genomeโ€™s โ€œdark matter,โ€ but they are far from empty. They encode RNA molecules that sense metabolites, regulate genes, and control some of molecular biology's most important tools (such as programmable genome editors e.g. CRISPR/bridge) Much of this biology is unexplored. One reason is that RNAs can retain similar structures and functions even as their DNA sequences change dramatically, making their relationships difficult to recognize with conventional computational tools
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Last month, we demonstrated high-rate alchemy: turning mercury into real, stable gold, beating CERNโ€™s record by a factor of 10. Last week, we enriched isotopes in the worldโ€™s most powerful plasma centrifuge, beating the Soviet record that stood for 40 years. Now, weโ€™re building a fusion reactor in San Francisco to achieve record power density.
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Dan Browne retweeted
Thrilled to share my freshly "baked" Baker lab paper. We took a bottom-up approach to designing transcriptional regulators. Instead of relying on natural activation domains, we designed compact proteins that recruit specific cofactors. Activators for now, repressors to come!
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Today in @NatureBiotech we introduce the "recordanelle", a synthetic organelle that enables transcriptome-wide single-cell RNA recording in human cells. Big thanks to team: @ReinkemeierCD, Marcos Manero-Carranza, et al. ๐Ÿงต๐Ÿ‘‡ @ETH_en @ETH_BSSE @BRC_CH rdcu.be/5Pus7dyu63ta
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