Owl Posting

Sterling Hooten, founder and CEO building PCB-based microfluidic bioreactors to make high-throughput media optimization cheap and sensor-rich. He explains using PCBs for mass-manufacturable chip reactors, embedded sensors, and vastly lower per-lane costs. Conversations cover media as a high-dimensional control, on-chip sensor strategies, scale-up validation, and a vision for chip-first lab automation.

Elise Jenkins, neuroengineer and Coherence Neuro co‑founder, explains cancer–nerve crosstalk, electrophysiological biomarkers, and stimulation regimes. Ben Woodington, device engineer and co‑founder, describes SOMA implant design, MRI compatibility, surgical workflow, and commercialization plans. They discuss intracranial stimulation advantages, targeting recurrence margins, preclinical reductions, and pathways from animal models to first‑in‑human studies.

Matthew Osman and Fabio Boniolo, co-founders of Polyphron, delve into the revolutionary concept of growing functional human tissue outside the body. They discuss the potential of recapitulating embryogenesis, aiming to repair organ damage by creating modular tissue instead of relying on full organ transplants. Topics include the challenges of current tissue engineering, the significance of 3D architecture, and the hurdles like vascularization that must be overcome for success. Their ambitious vision redefines the future of regenerative medicine.

Yunha Hwang, an assistant professor at MIT and co-founder of Tatta Bio, tackles the enigmatic world of microbial genome function annotation. She discusses the vast unknowns in microbial genes and how her lab is pioneering the application of genomic language models to address this challenge. Yunha highlights innovations like OMG, a machine-learning-ready metagenome, and GLM2, a multimodal genomic model. She shares insights on how these tools could revolutionize our understanding of genome functions and reshape evolutionary perspectives.

In a fascinating discussion, Hunter Davis, the Chief Scientific Officer and co-founder of Until Labs, dives into the pioneering world of organ-scale cryopreservation. He shares the challenges of scaling from embryos to human organs, the complexities of cryoprotectants, and innovative methods like using magnetic nanoparticles for rapid warming. With insights on organ viability and ongoing recruitment for a multidisciplinary team, Hunter reveals how this cutting-edge research could revolutionize organ transplants and save countless lives.

Ellen Zhong, a computer science professor at Princeton University, is revolutionizing molecular imaging through deep learning applications in cryo-EM. She discusses how her lab addresses challenges in reconstructing 3D structures from 2D images. Ellen also explores the use of machine learning to uncover previously hidden structures and the ongoing issues of heterogeneity in protein analysis. She emphasizes the importance of improving algorithms alongside experimental data collection for effective results, and reflects on the future of cryo-EM in biomedical applications.

Alan Tomusiak, the founder and CEO of Permanence Bio and a PhD holder in aging biology, dives deep into innovative approaches to genome protection. He discusses the importance of stabilizing DNA to prevent age-related damage, offering a contrarian view to conventional cellular reprogramming. The conversation also highlights the role of genome stability in cancer prevention and the potential of epigenetic clocks in evaluating health. With groundbreaking insights into hematopoietic stem cells, Tomusiak presents a bold vision for enhancing longevity through DNA protection.

X: https://x.com/owl_postingSergey's X: https://x.com/sokryptonYoutube: https://youtu.be/6_RFXNxy62cSpotify: https://open.spotify.com/episode/0wPs3rmp0zrfauqToozrcv?si=DCtRf-xQTPiVYwslo-b2rQApple Podcasts: https://podcasts.apple.com/us/podcast/what-could-alphafold-4-look-like-sergey-ovchinnikov-3/id1758545538?i=1000704927828Transcript: https://www.owlposting.com/p/what-could-alphafold-4-look-like?open=false#%C2%A7transcriptTo those in the protein design space, Dr. Sergey Ovchinnikov is a very, very well-recognized name.A recent MIT professor (circa early 2024), he has played a part in a staggering number of recent innovations in the field: ColabFold, RFDiffusion, Bindcraft, automated design of soluble proxies of membrane proteins, elucidating what protein language models are learning, conformational sampling via Alphafold2, and many more. Of course, all these papers were group efforts, but Sergey's name comes up astonishingly frequently! And even beyond the research that have come from his lab in the last few years, the co-evolution work he did during his PhD/fellowship also laid some of the groundwork for the original Alphafold paper, being cited twice in it.As a result, Sergey’s work has gained a reputation for being something that is worth reading. But nobody has ever interviewed him before! Which was shocking for someone who was so pivotally important for the field.So, obviously, I wanted to be the first one to do it. After an initial call, I took a train down to Boston, booked a studio, and chatted with him for a few hours, asking every question I could think of. We talk about his own journey into biology research, some issues he has with Alphafold3, what Alphafold4-and-beyond models may look like, what research he’d want to spend a hundred million dollars on, and lots more. Take a look at the timestamps to get an overview!Final note: I’m extremely grateful to Asimov Press for helping fund the travel + studio time required for this episode! They are a non-profit publisher dedicated to thoughtful writing on biology and metascience, such as articles over synthetic blood and interviews with plant geneticists. I myself have published within them twice! I highly recommend checking out their essays at asimov.press, or reaching out to editors@asimov.com if you’re interested in contributing.Timestamps:[00:00:00] Highlight clips[00:01:10] Introduction + Sergey's background and how he got into the field[00:18:14] Is conservation all you need?[00:23:26] Ambiguous vs non-ambiguous regions in proteins[00:24:59] What will AlphaFold 4/5/6 look like?[00:36:19] Diffusion vs. inversion for protein design[00:44:52] A problem with Alphafold3[00:53:41] MSA vs. single sequence models[01:06:52] How Sergey picks research problems[01:21:06] What are DNA models like Evo learning?[01:29:11] The problem with train/test splits in biology[01:49:07] What Sergey would do with $100 million Get full access to Owl Posting at www.owlposting.com/subscribe

Soham Sankaran, founder and CEO of PopVax and former computer scientist-turned-vaccine entrepreneur. He explains why India can deliver radical, low-cost vaccine R&D, how PopVax pairs ML with massive empirical testing to design smarter immunogens, and why end-to-end, India-based labs speed iteration and cut costs dramatically.

In this engaging discussion, Corin Wagen, co-founder of Rowan, a breakthrough molecular simulation company, shares insights alongside his brother Ari. They delve into neural network potentials and their potential to revolutionize drug design and materials science. The conversation tackles the dichotomy between classical and quantum simulations, along with the importance of improved accuracy in computational chemistry. Corin and Ari also explore the challenges of benchmarking simulations and the role of AI in enhancing molecular dynamics, making a complex field more accessible.