Howard Salis

3.6K posts

Howard Salis

Howard Salis

@hsalis

Professor of synthetic biology & chemical engineering. De Novo DNA founder. Engineering microbes with predictive models & algorithms.

UC Riverside, CA Katılım Nisan 2009
267 Takip Edilen4.1K Takipçiler
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Howard Salis
Howard Salis@hsalis·
NEW PAPER led by @grace_vezeau! We rationally engineered synthetic riboswitches to carry out sense & respond for human biomarker proteins [mCRP and IL32-gamma] that indicate disease or infection. 16-fold activation without trial-and-error! nature.com/articles/s4146…
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Howard Salis
Howard Salis@hsalis·
@0x1F9ED LC/MS^3 is an example of a “sufficiently advanced technology indistinguishable from magic” … more people should use it!
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AJ@0x1F9ED·
Remember all the interest in "metabolomics" from the 2010s? Yeah neither do I. Turns out lizard peptide endocrinology is all it took to shut that field down.
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Howard Salis
Howard Salis@hsalis·
@curcuas @srikosuri After moving to SoCal, we switched to Kaiser and it’s just fine. The joke is that Kaiser is great if you’re healthy, which is probably close to the truth. Appts are immediately available & service is faaast. But we haven’t stress tested our coverage.
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Jacob Oppenheim
Jacob Oppenheim@curcuas·
@srikosuri Yeah, absolutely. The number of haters is just high compared to the number of people who think they want single payer.
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Sri Kosuri
Sri Kosuri@srikosuri·
~25% of the US population has access to Kaiser Permanente. Do people really think a Medicare4All is going to better than Kaiser (a nonprofit that combines insurance and provider)? Why not Kaiser4All?
Tweets from Zach Weinberg@zachweinberg

Medicare *option* for all would be a nice compromise. Let employers buy their population into Medicare with pre-tax dollars. Employers can then offer supplemental benefits on top. If you prefer private insurance the whole way? Go for it. Up to you. Choice & competition.

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Edward 8675309
Edward 8675309@Eduardo335876·
@anshulkundaje Yes! Also QED is probably just a skills.md file using Claude or something anyway
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Howard Salis
Howard Salis@hsalis·
@BrianHie @anshulkundaje Important Q: when Proto calls one of the 120+ models & tools, does the user know which one is being called and who created it? Agentic AI is a great “glue language” across models, but it’s very important to attribute authorship. Otherwise, the incentive structure is broken.
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Brian Hie
Brian Hie@BrianHie·
It was really important for us to make Proto an easy-to-use visual programming language, and to try out the underlying tools. Take a look at our website to run some example programs and tools!
Daniel Guo@dan_guo_

Check out our website proto.evodesign.org, which visualizes our designs and provides open access to 120+ biological AI models and tools! To learn how to navigate the UI and start designing with our Proto agent, check out youtu.be/8UnOrC_0jmo?si… We've received amazing feedback over the past day and we're excited to see what the community builds! proto.evodesign.org

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Howard Salis
Howard Salis@hsalis·
@BrianHie after reading your methods section: eGFP expression is end-point measured after 8 hours after “normalizing to OD of 1”. Any OD over 0.5 is early stationary phase. Cells slow down growth. eGFP expression saturates (repressed or not). Lower fold-change in expression.
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Howard Salis
Howard Salis@hsalis·
@BrianHie Overall, your designed TFs may be able to bind & repress (which is cool), but the circuit design isn’t clearly showing it. I recommend varying TF expression & measuring output (at steady-state) to provide clear evidence. A good benchmark is: nature.com/articles/nchem…
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Brian Hie
Brian Hie@BrianHie·
In new work, we lay out a vision for a high-level programming language for generative biology, called Proto. Proto composes generative and predictive models spanning DNA, RNA, proteins, ligands, and their interactions, which we use to design complex biological functions. 1/n
Brian Hie tweet media
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Howard Salis
Howard Salis@hsalis·
@hankgreen Let me introduce you to Seven of Nine and T’pol … the ST writers had a type …
GIF
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Hank Green
Hank Green@hankgreen·
Star Trek writers creating a kind, wise, 389 year old alien who is also a succession of smoking hot young women is a very Star Trek-writers thing to do.
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Howard Salis
Howard Salis@hsalis·
@hhlee And all phage tests are done on lab E. coli that don’t methylate or cut DNA, and don’t have working CRISPR. No immune system. So not a good test of nefarious applications either.
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Howard Salis
Howard Salis@hsalis·
@hhlee Btw making a viable phage is the easiest genome design & DNA assembly test. They tolerate *many* mutations, DNA synthesis gives you free mutations to explore fitness, and all it takes is one semi-fit particle to create a plaque (“success!”)
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Howard Salis
Howard Salis@hsalis·
@frederikschu Same thing happened with the EvoScale’s “500 million years of evolution” GFP paper. Let’s say it altogether now: ML models, great for interpolation, but they can’t extrapolate!
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Frederik Schulz
Frederik Schulz@frederikschu·
Evo 2 efficiently generated experimentally viable bacteriophage genomes, but the viable outputs stayed phylogenetically close to natural genomes rather than occupying highly novel sequence space. doi.org/10.64898/2026.…
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Howard Salis
Howard Salis@hsalis·
@thedillona @dbasch @slatestarcodex @wolftivy No, SNPs are not a great way to diagnose disease. 23&me shut down because they couldn’t upsell or repeat customers on what is effectively a one-and-done test. No one gets their SNPs sequenced twice.
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Wolf Tivy
Wolf Tivy@wolftivy·
Emergency reading for all Students with the release of Midjourney’s new medical scanner: Ivan Illich’s “tools for conviviality”. MJ has potential to commoditize medical scans as a public affordance. For this reason alone, the medical cartel will try to stop it.
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Howard Salis
Howard Salis@hsalis·
@ATinyGreenCell Just prompt to move all functions related to high-level task XX to a new file YY and rewire accordingly. Then refactor file YY to generalize functions & remove redundancy/repetition. 131000 LOC in a single file is … hmmm … not good.
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Sebastian S. Cocioba🪄🌷
Sebastian S. Cocioba🪄🌷@ATinyGreenCell·
Asking the Ai for some copium as I do a really risky and heavy lift to detangle and modularize SpliceCraft. From a 131,000 lines of code monolith into very robust modules that fit into open source LLM context windows. Specifically designed to work if I ever lose Claude access.
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Howard Salis
Howard Salis@hsalis·
@ProfTomEllis @ATinyGreenCell The head / project leader for Gardasil manufacturing is a Penn State alumni and … he did iGEM as an undergrad! He graciously donated to the recent PSU iGEM teams. Great guy!
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Tom Ellis
Tom Ellis@ProfTomEllis·
The HPV vaccine - Gardasil 9 - is made by secreting 9 different virus capsid proteins from 9 different engineered yeast strains and having the proteins self-assemble into injectable VLPs. Nice tech!
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Tom Ellis
Tom Ellis@ProfTomEllis·
S.cerevisiae yeast does all the best things - beer, bread, champagne, chocolate, vaccines that cure cancer.... BBC: Young women now have 'close to zero' risk of cervical cancer death after HPV jab bbc.com/news/articles/…
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Anshul Kundaje
Anshul Kundaje@anshulkundaje·
The new Omnii model previewed here looks interesting & promising for the following reasons. But before I say anything, it is hard to really tell what is going on without details about the model or access to it (I have applied for early access today) 1/
Eric Nguyen@exnx

Together with my co-founders Michael @MichaelPoli6, Stefano @Massastrello and Armin @athmsx, I am excited to announce @RadicalNumerics is emerging from stealth with a $50M seed round to build general biological intelligence. We’re also sharing an early preview of our new model Omnii, the most powerful genome language model to date. Omnii preview link: radicalnumerics.ai/blog/radical-n… At Radical Numerics, our mission is to master the code of life, and to drive the frontier of biological AI for both design and defense. This is our dual mandate, which comes from something our own team helped make possible. Our founding team trained Evo and Evo 2, the largest biological AI models (40B params) trained on DNA sequences. Trillions of tokens across all of life, from microbes to mammals. It’s fully open source, and created the field now known as generative genomics. Last year, scientists used Evo to generate the world’s first complete genome from scratch using AI. Turns out it was a bacteriophage—a type of virus. It functioned in the real world, and in this case it was harmless. But for us, it was a clear turning point. It showed that AI is no longer just analyzing biology. It is on the cusp of generating functional lifeforms. Eventually, AI will have the power to design and control life itself. That should make all of us incredibly excited, and incredibly uneasy. (Anyone can design DNA with a new function, and have it synthesized and delivered, like something from Amazon Prime). The same technology that will help us cure cancer is the very technology that might create the next global pandemic, or worse, allow the creation of bioweapons that can wipe out populations. We believe these forces are inseparable. If you work on the frontier of biology, you have to build technology to safeguard it from its misuse. Existing biosecurity tools are sorely losing the arms race, relying on outdated “have I seen this exact thing before?” style algorithms. We founded Radical Numerics to turn the tide. And we can’t do that by training on textbooks and natural language. We must understand the language of biology from the raw physical data itself, to reason across every molecule and modality, from DNA to proteins. The next frontier for AI goes far beyond chatbots or video generators to models that can understand and engineer life. Today, we’re previewing Omnii, which is already far surpassing Evo 2, and will continue improving as we scale and add new modalities (training now). 1. For human health, Omnii can read and write whole genomes (more on writing later). It’s state of the art (SOTA) on detecting causal variants for disease, and can rank Alzheimer's mutations zero-shot. We’re partnering with a diagnostics company to use Omnii for early cancer detection (pancreatic and multi-cancer). 2. For defense, Omnii is SOTA at detecting AI-generated pathogens. We benchmarked existing detection tools, and they simply can’t detect the AI-generated ones (“deepfake viruses”). We’re partnering with a US national lab to pilot Omnii for detecting the next pandemic, both natural and AI-generated. We have a data center full of Blackwells in construction now to build the most powerful biological AI models ever. This mission takes a new kind of AI lab that can actually scale on physical, biological data: new alignment research (mid/post training), scaling long context, building out mech interp teams to dissect what these models learn, new architectures and systems designs, all from the ground up. Our team is made up of AI researchers and scientists from top labs and institutions (e.g. Stanford, MIT, Google DeepMind), but more importantly, we all share the belief that this is the most important challenge of our lifetime. If you feel similarly, we are hiring. We aim to bring the brightest minds in AI and science together to save lives. Thanks to our partners on this journey, led by Emergence Capital @emergencecap, with Obvious Ventures @obviousvc, Triatomic @TriatomicCap , and Patrick Collison @patrickc. Our advisors include Eric Horvitz @erichorvitz, CSO of Microsoft, Chris Re @HazyResearch of Stanford, George Church @geochurch of Harvard, and Andrew Weber @AndyWeberNCB, former Assistant Secretary of Defense for Nuclear, Chemical and Biological Defense Programs. Fortune article: fortune.com/2026/06/15/exc… Jobs: radicalnumerics.ai/join-us

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Olivier Borkowski
Olivier Borkowski@O_Borkowski·
A Low-Cost, High-Throughput Design-Build-Test Pipeline for Engineering Genetic Systems: Stress Testing with Complex Structural Proteins doi.org/10.64898/2026.…
Olivier Borkowski tweet media
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Howard Salis
Howard Salis@hsalis·
@dwidmaier @elonmusk I love Starship, but Musk should stay out of government as his DOGE days are now directly responsible for many negatives, including the largest Ebola epidemic, losing the lead in U.S. fundamental research, and a general further enshitiffication of the federal work force.
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Howard Salis
Howard Salis@hsalis·
@0x1F9ED We built this city We built this city … We built this city With Rock and Roll … ohhhh ohh!
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AJ@0x1F9ED·
Does SF have a song about itself that everyone can sing off by heart?
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