Ayan @ayanobacter

PhD in Synbio, Entrepreneur, Open Science, Researching and Writing About Futures and Frontiers editlife.substack.com Joined February 2022

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Ayan @ayanobacter

10 hours ago

@jackdent @chaidiscovery @pfizer Congrats!! 🙌🏽

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Ayan @ayanobacter

6 days ago

so lovely to learn more about @NonfictionBio It's also really cool to see a team page where the co-founder/CSO and 7 out of 9 Scientists are all women

The Magnetobiology Episode: A company in San Francisco, called @NonfictionBio, is building proteins (like antibodies and enzymes) that can be controlled using small magnets. In this episode, co-founder Maria Ingaramo and scientific advisor Andrew York explain how they

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Alex Rives @alexrives

a week ago

Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.

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Ayan @ayanobacter

a week ago

i love that claude opus 4.8 is refusing to engage with some pretty basic bio questions by essentially saying it's too powerful, and things could get dangerous...?? lol

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Ayan @ayanobacter

a week ago

I’ve reached the stage of the Paris heatwave where I’ve transcended the human form I am not hot I am the heat We are all Energy

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Ayan @ayanobacter

2 weeks ago

space is the ultimate shifter of limiting perspectives

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Cyrus @cyrusclarke

2 weeks ago

After two years in the US I'm sorry to say i've finally fallen in love with A/C. Also I'm running a Physical AI event next week at Media Lab next week for #BosTechWeek with demos from all the viral AI projects you've seen on your feed. Get on the list before it gets full: partiful.com/e/4wahZxSOBB3I…

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Ayan @ayanobacter

2 weeks ago

Thanks for reading and sharing! I think finding this balance between adapting to existing measurement frameworks/tools vs. the more messy, less tangible dimensions of life itself will actually be a big test for modern bio. I hope you’ll also enjoy the next piece, which will explore some of the less obvious edges of this question.

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Ayan @ayanobacter

2 weeks ago

@mkoeris Glad this reached you, would love to know your thoughts on this especially from your position. I wrote it thinking a lot about the post Sputnik mobilization in the US around education reform where it was being treated as a national security problem- intuition being a core pillar.

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Yang Fan 范阳 @Yang_Supertramp

3 weeks ago

Do you believe in scientific intuition — and if so, how would you define it? A great read today: “Scientific Intuition in the Agentic Age On taste, tacit knowledge, and the critical parts of scientific cognition that you can't just scale past. ” By Ayan Abukar.

Fyodor Urnov @UrnovFyodor

3 weeks ago

I prompted the “deep literature” mode of Edison Scientific to write a comprehensive review on the biology of a gene that I know well. Twenty five min later it sent a 17 page PDF. It was, as best as I can tell, flawless. Folks, we are not in Kansas anymore. Don’t at me - try it.

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Ayan @ayanobacter

2 weeks ago

Post Sputnik, the US responded by treating education as a national security problem. In 1959 they gathered the leading scientific minds, backed by major national bodies, and held a conference in Woods Hole, MA to identify where science education was going wrong and how to reform it at scale. 4 core themes emerged, one being: “the nature of intuition” They understood the significance of intuition. (though they ultimately struggled to define and operationalize it) Today we spend enormous resources advancing tools and more easily measurable methods. Yet we see comparatively negligible investment in trying to understand scientific intuition itself and the important role it appears to play in Nobel worthy breakthrough ideas/generally extraordinary scientific outcomes.

Ayan @ayanobacter

4 weeks ago

In my new piece I'm confronting the critical parts of scientific cognition that you can't just scale past. I’ve been thinking a lot about which human intelligences we’re actually aiming to replicate and optimize artificially, and which ones we seemingly reveal in the process.

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Ayan @ayanobacter

2 weeks ago

in light of recent outbreaks, I must ask who's working on xenonite PPE

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Ayan @ayanobacter

3 weeks ago

more of this >>>

Tristan Farmer @001TMF

3 weeks ago

Planning to make antibodies for Ebola. Anyone interested in collaborating.

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Ayan @ayanobacter

3 weeks ago

@dwddao This is v true, lots of academic research is still trapped in the reputation and reward systems of trad publishing

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Ayan @ayanobacter

3 weeks ago

It’s time for a pre-pre-print platform

Thomas G. Dietterich @tdietterich

3 weeks ago

The penalty is a 1-year ban from arXiv followed by the requirement that subsequent arXiv submissions must first be accepted at a reputable peer-reviewed venue. 4/

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Ayan @ayanobacter

3 weeks ago

the biosecurity urge to tell the world in detail what the super dangerous thing we should never do is

Noema Magazine @NoemaMag

3 weeks ago

Scientists working on synthetic "mirror life" have come to realize that, if created, it could pose an existential threat to life on Earth. Can the genie be put back in the bottle? Joe Zadeh explores. noemamag.com/the-doomsday-o…

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Ayan @ayanobacter

3 weeks ago

I'm seeing a lot of criticism of these guys, which on one side I get, but on the other, the whole point of being young is that you do wake up and think you can build a company that's first goal is to cure all cancers there's something really cool about that, even if bio folks are initially left with lots of technical question marks

Y Combinator @ycombinator

3 weeks ago

FinalDose is building the first programmable drug platform - a single smart drug molecule that finds diseased cells by their DNA and destroys them. They're starting with all cancers. Congrats on the launch, @Jeffliu6068Liu, @sklin_lite, and @LiYaoHuang2! ycombinator.com/launches/QKj-f…