Daniel Siegle
@danielsiegle.bsky.social
Teaching Biology at NCSSM
Reposted by Daniel Siegle
I semi-vibe coded a frontend for all the protein folding tools I've been running. It runs on modal and has 5 different open-source algorithms: Chai1, Boltz2, AF2, Protenix(-mini).
Not 100% polished but hopefully of use to some use to people in the field!
github.com/hgbrian/fold...
Not 100% polished but hopefully of use to some use to people in the field!
github.com/hgbrian/fold...
GitHub - hgbrian/foldism: protein folding app running on modal
protein folding app running on modal. Contribute to hgbrian/foldism development by creating an account on GitHub.
github.com
December 26, 2025 at 4:33 PM
I semi-vibe coded a frontend for all the protein folding tools I've been running. It runs on modal and has 5 different open-source algorithms: Chai1, Boltz2, AF2, Protenix(-mini).
Not 100% polished but hopefully of use to some use to people in the field!
github.com/hgbrian/fold...
Not 100% polished but hopefully of use to some use to people in the field!
github.com/hgbrian/fold...
Reposted by Daniel Siegle
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
December 9, 2025 at 1:58 PM
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
Reposted by Daniel Siegle
Have you heard of the Sanger Prize? It is a three-month undergrad placement at the Institute, and applications are open.
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
November 20, 2025 at 10:55 AM
Have you heard of the Sanger Prize? It is a three-month undergrad placement at the Institute, and applications are open.
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Reposted by Daniel Siegle
Goes immediately to the top of the "To Read" list ⬇️
It has been so so fun to think with some of my favorite scientists about what it means to understand!
What does it mean to understand language? We argue that the brain’s core language system is limited, and that *deeply* understanding language requires EXPORTING info to other brain regions.
w/ @neuranna.bsky.social @evfedorenko.bsky.social @nancykanwisher.bsky.social
arxiv.org/abs/2511.19757
1/n🧵👇
w/ @neuranna.bsky.social @evfedorenko.bsky.social @nancykanwisher.bsky.social
arxiv.org/abs/2511.19757
1/n🧵👇
November 26, 2025 at 5:12 PM
Goes immediately to the top of the "To Read" list ⬇️
Reposted by Daniel Siegle
“Our findings challenge the conventional focus on low-dimensional coding subspaces as a sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.”
Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification
Most behaviors involve neural dynamics in high-dimensional activity spaces. A common approach is to extract dimensions that capture task-related variability, such as those separating stimuli or choice...
www.biorxiv.org
November 23, 2025 at 1:38 PM
“Our findings challenge the conventional focus on low-dimensional coding subspaces as a sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.”
Reposted by Daniel Siegle
on #3, this paper uses a method where they can directly attribute specific documents from the pretraining dataset
they used it to show that LLMs do in fact learn procedures, not just autocomplete. But you could take this so much further with Olmo3
arxiv.org/abs/2411.12580
they used it to show that LLMs do in fact learn procedures, not just autocomplete. But you could take this so much further with Olmo3
arxiv.org/abs/2411.12580
November 23, 2025 at 3:20 PM
on #3, this paper uses a method where they can directly attribute specific documents from the pretraining dataset
they used it to show that LLMs do in fact learn procedures, not just autocomplete. But you could take this so much further with Olmo3
arxiv.org/abs/2411.12580
they used it to show that LLMs do in fact learn procedures, not just autocomplete. But you could take this so much further with Olmo3
arxiv.org/abs/2411.12580
Reposted by Daniel Siegle
Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.
November 18, 2025 at 2:19 AM
Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.
Reposted by Daniel Siegle
I curated some readings for class on "data tensions" and the list felt worth sharing. Come on a tour of datasets, books, the web, and AI with me...
We'll start with this piece on the Google Books project: the hopes, dreams, disasters, and aftermath of building a public library on the internet.
1/n
We'll start with this piece on the Google Books project: the hopes, dreams, disasters, and aftermath of building a public library on the internet.
1/n
Torching the Modern-Day Library of Alexandria
“Somewhere at Google there is a database containing 25 million books and nobody is allowed to read them.”
www.theatlantic.com
November 14, 2025 at 4:39 PM
I curated some readings for class on "data tensions" and the list felt worth sharing. Come on a tour of datasets, books, the web, and AI with me...
We'll start with this piece on the Google Books project: the hopes, dreams, disasters, and aftermath of building a public library on the internet.
1/n
We'll start with this piece on the Google Books project: the hopes, dreams, disasters, and aftermath of building a public library on the internet.
1/n
Reposted by Daniel Siegle
Solar’s price drop is astonishing: panels are now 98% cheaper than when I first analyzed them in 2004.
Today, building a fence with solar can be cheaper than using wood.
Today, building a fence with solar can be cheaper than using wood.
November 10, 2025 at 8:10 AM
Solar’s price drop is astonishing: panels are now 98% cheaper than when I first analyzed them in 2004.
Today, building a fence with solar can be cheaper than using wood.
Today, building a fence with solar can be cheaper than using wood.
Reposted by Daniel Siegle
A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩🔬👩🎓 in just a few weeks!
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
October 26, 2025 at 1:48 PM
A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩🔬👩🎓 in just a few weeks!
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
Reposted by Daniel Siegle
It’s not the thought that counts: Allostasis at the core of brain function
www.cell.com/neuron/fullt...
#neuroscience
www.cell.com/neuron/fullt...
#neuroscience
It’s not the thought that counts: Allostasis at the core of brain function
The authors review evidence that the primary function of the brain, supported by distributed
neural systems, is the predictive regulation of physiology (i.e., allostasis). An
example from Alzheimer’s ...
www.cell.com
October 18, 2025 at 1:54 PM
It’s not the thought that counts: Allostasis at the core of brain function
www.cell.com/neuron/fullt...
#neuroscience
www.cell.com/neuron/fullt...
#neuroscience
Reposted by Daniel Siegle
I decided to experiment with my own (small) protein design competition!
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
October 16, 2025 at 4:54 PM
I decided to experiment with my own (small) protein design competition!
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
Reposted by Daniel Siegle
If only we had some way of know what things were really true. Some system of testing over time, where we could build up our knowledge about the best way to do things...
September 22, 2025 at 9:16 PM
If only we had some way of know what things were really true. Some system of testing over time, where we could build up our knowledge about the best way to do things...
Reposted by Daniel Siegle
Hello! I'm Behnoush, structural biology scientist from the Broad Institute. I also like to combine proteins structures and other scientific topics with art. Here are some journal cover arts I've created recently. Hope to find old and new friends here.
#Blender #b3d #MolecularNodes #GeometryNodes
#Blender #b3d #MolecularNodes #GeometryNodes
September 19, 2025 at 7:28 PM
Hello! I'm Behnoush, structural biology scientist from the Broad Institute. I also like to combine proteins structures and other scientific topics with art. Here are some journal cover arts I've created recently. Hope to find old and new friends here.
#Blender #b3d #MolecularNodes #GeometryNodes
#Blender #b3d #MolecularNodes #GeometryNodes
Reposted by Daniel Siegle
This is the shit they’re defunding. Scientists can make your teeth see so you can get back to balling and they want to take that away from you forever
TIL that for some people with irreparably damaged corneas, you can pull one of their teeth, drill a hole in it, install an artificial lens, sew it into their cheek (so tissue attaches), then pull it out and stick it in their damaged eye, and ... it works fine!?! www.nbcboston.com/news/health/...
Man, 34, is no longer blind after tooth is implanted in eye in 'crazy' surgery
Tooth-in-eye surgery sounds like science fiction, but it can help people with severely damaged corneas see again. A patient and his doctors describe what it's like.
www.nbcboston.com
September 12, 2025 at 3:04 PM
This is the shit they’re defunding. Scientists can make your teeth see so you can get back to balling and they want to take that away from you forever
Reposted by Daniel Siegle
Q. Who aligns the aligners?
A. alignmentalignment.ai
Today I’m humbled to announce an epoch-defining event: the launch of the 𝗖𝗲𝗻𝘁𝗲𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗼𝗳 𝗔𝗜 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗖𝗲𝗻𝘁𝗲𝗿𝘀.
A. alignmentalignment.ai
Today I’m humbled to announce an epoch-defining event: the launch of the 𝗖𝗲𝗻𝘁𝗲𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗼𝗳 𝗔𝗜 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗖𝗲𝗻𝘁𝗲𝗿𝘀.
Center for the Alignment of AI Alignment Centers
We align the aligners
alignmentalignment.ai
September 11, 2025 at 1:17 PM
Q. Who aligns the aligners?
A. alignmentalignment.ai
Today I’m humbled to announce an epoch-defining event: the launch of the 𝗖𝗲𝗻𝘁𝗲𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗼𝗳 𝗔𝗜 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗖𝗲𝗻𝘁𝗲𝗿𝘀.
A. alignmentalignment.ai
Today I’m humbled to announce an epoch-defining event: the launch of the 𝗖𝗲𝗻𝘁𝗲𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗼𝗳 𝗔𝗜 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗖𝗲𝗻𝘁𝗲𝗿𝘀.
Reposted by Daniel Siegle
What are your pros/cons of using AI in science?
Feel free to respond wrt use or harm in the design of experiments, coding experiments, coding analysis, brain storming analysis, summarizing literature, synthesis of ideas, modeling, novel model development, mathematical proofs, writing, editing.
Feel free to respond wrt use or harm in the design of experiments, coding experiments, coding analysis, brain storming analysis, summarizing literature, synthesis of ideas, modeling, novel model development, mathematical proofs, writing, editing.
September 3, 2025 at 9:09 PM
What are your pros/cons of using AI in science?
Feel free to respond wrt use or harm in the design of experiments, coding experiments, coding analysis, brain storming analysis, summarizing literature, synthesis of ideas, modeling, novel model development, mathematical proofs, writing, editing.
Feel free to respond wrt use or harm in the design of experiments, coding experiments, coding analysis, brain storming analysis, summarizing literature, synthesis of ideas, modeling, novel model development, mathematical proofs, writing, editing.
Reposted by Daniel Siegle
It says a lot about society that the reaction to AlphaFold was a couple of excited news articles and a tiny amount of funding.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
August 20, 2025 at 10:42 AM
It says a lot about society that the reaction to AlphaFold was a couple of excited news articles and a tiny amount of funding.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
Reposted by Daniel Siegle
Why PETase for our tournament? In 2024, the world made about 30 million tonnes of PET plastic, most from fossil fuels.
PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.
Register by Oct 17 alignbio.org/protein-engi...
PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.
Register by Oct 17 alignbio.org/protein-engi...
August 13, 2025 at 5:38 PM
Why PETase for our tournament? In 2024, the world made about 30 million tonnes of PET plastic, most from fossil fuels.
PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.
Register by Oct 17 alignbio.org/protein-engi...
PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.
Register by Oct 17 alignbio.org/protein-engi...
Reposted by Daniel Siegle
A thread of protein-themed card, board, and video games 🧵
Play the PDB board game that explores the process of structure discovery and deposition. Then, move on to the next project...but keep an eye on the competition and try not to get scooped! #GenCon
pdb101.rcsb.org/lear...
pdb101.rcsb.org/lear...
PDB101: Learn: Other Resources: PDB50 the Game
A PDB “worker placement” board game that explores the process of structure discovery
pdb101.rcsb.org
August 4, 2025 at 8:07 PM
A thread of protein-themed card, board, and video games 🧵
Reposted by Daniel Siegle
A new one to me: a protein structure board game.
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
Play the PDB board game that explores the process of structure discovery and deposition. Then, move on to the next project...but keep an eye on the competition and try not to get scooped! #GenCon
pdb101.rcsb.org/lear...
pdb101.rcsb.org/lear...
PDB101: Learn: Other Resources: PDB50 the Game
A PDB “worker placement” board game that explores the process of structure discovery
pdb101.rcsb.org
August 2, 2025 at 6:16 PM
A new one to me: a protein structure board game.
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
Reposted by Daniel Siegle
We turned medicinal chemistry into a card game, which takes 3-10 years to play.
PDF: jabde.com/wp-content/u...
PDF: jabde.com/wp-content/u...
July 25, 2025 at 8:45 AM
We turned medicinal chemistry into a card game, which takes 3-10 years to play.
PDF: jabde.com/wp-content/u...
PDF: jabde.com/wp-content/u...
Reposted by Daniel Siegle
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Which Kind of Science Reform
What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.
elevanth.org
July 9, 2025 at 1:40 PM
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Reposted by Daniel Siegle
🤖 Apropos of , reminder that AI-generated videos can--and ought to--minimally have visible watermarks disclosing that they are synthetic. You can do it trivially using @hf.co tools. Before sharing something synthetic, please run it through this.
huggingface.co/spaces/meg/w...
huggingface.co/spaces/meg/w...
Watermark Demo - a Hugging Face Space by meg
Add a watermark to any video file by uploading both the video and the watermark image. The result is a watermarked video.
huggingface.co
July 11, 2025 at 4:20 PM
🤖 Apropos of , reminder that AI-generated videos can--and ought to--minimally have visible watermarks disclosing that they are synthetic. You can do it trivially using @hf.co tools. Before sharing something synthetic, please run it through this.
huggingface.co/spaces/meg/w...
huggingface.co/spaces/meg/w...