Discovery Engines – with Nabil Laoudji

Gabriele Corso, CEO and co-founder of Boltz, believes the most powerful AI models for drug discovery should be accessible to all, starting with the open models his team has put in the hands of over 100,000 scientists. In this episode, I sit down with Gabriele to explore the leap from predicting protein structures to designing new molecules with Boltz-1, Boltz-2, and BoltzGen, why he champions open access, their multi-year partnership with Pfizer, and the vision of "zero-shot" drug design.

Hosted by Nabil Laoudji. See below for episode links, chapters, and our socials. 🙏🙌

Episode Links:

• Boltz
• Boltz Repository
• Gabriele's LinkedIn
• Worldwide Protein Data Bank
• Ginkgo Lab Tour
• Pfizer Partnership Announcement

Chapters:

• (00:00) - Preview
• (00:56) - Intro
• (02:15) - Why Proteins Matter and Rational Drug Design
• (05:51) - Target Identification, the Toughest Problem in Drug Discovery
• (07:55) - Small Molecules and Biologics
• (12:57) - Does a Disease Have One Target or Many?
• (15:36) - The Billion Dollar Molecule and How Boltz's Models Work
• (22:05) - The Protein Data Bank (PDB) and the Role of Sequencing Data
• (25:55) - What New Data Could Improve AI Bio Models?
• (29:02) - Where Boltz's Training Data Comes From
• (31:46) - Unlocking Private Bio Data
• (35:34) - Boltz's Open Approach vs. DeepMind's Isomorphic Labs
• (39:18) - What Boltz's 100,000 Users Get Access To
• (41:32) - Inside the Pfizer Partnership
• (43:55) - Why Biotech Business Models Are So Hard (Microsoft, Apple, Red Hat)
• (49:17) - How Boltz Differs from Schrödinger, Recursion and Others
• (52:31) - Regulation, the FDA, and Trust in Computational Data
• (56:42) - Autonomous Labs and the Data Feedback Loop
• (1:00:25) - Faster Trials, Virtual Cells, and Other Speedups
• (1:03:34) - When Will a Boltz-Designed Drug Reach a Patient?
• (1:04:55) - How Listeners Can Help (Hiring, Partnerships, Investing)
• (1:06:27) - Closing Reflections on Access

Connect With Us:

• Our Newsletter
• Twitter
• LinkedIn
• Bluesky
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Jason Kelly, CEO of Ginkgo Bioworks, believes the future of life science R&D is autonomous, starting with the 52-cart lab he and his team have built in Boston. In this episode, I sit down with Jason to explore Ginkgo's autonomous biology lab, its collaboration with OpenAI, the POTUS-backed Genesis Mission, and where autonomous physical systems could take science next.

Hosted by Nabil Laoudji. See below for episode links, chapters, and our socials. 🙏🙌

Episode Links:

• Ginkgo Bioworks
• Jason Kelly's LinkedIn
• OpenAI x Ginkgo Cell-Free Protein Synthesis Collaboration
• Genesis Mission to Accelerate AI for Scientific Discovery
• PNNL's Anaerobic Microbial Phenotyping Platform (AMP2)
• Society for Lab Automation and Screening
• GlobalData Report: Large Pharma Drug Licensing from China

Chapters:

• (00:00) - Preview
• (01:54) - Jurassic Park and the Value of Storytelling in Science
• (04:50) - What Is the Department of Energy's AMP2 at PNNL?
• (07:17) - How Autonomous Labs Can Be Used to Run Experiments
• (11:49) - Principles of the Autonomous Lab (Waymo Analogy)
• (17:12) - Project Genesis, Competing with China in Scientific Discovery
• (23:42) - Reindustrializing America via Automation
• (37:03) - OpenAI Designing and Running Bio Experiments
• (47:17) - Advice to Frontier Labs Designing AI Intelligence for Science
• (49:24) - Ginkgo Autonomous Lab Tour
• (1:00:38) - OpenAI's Interface With Ginkgo
• (1:02:51) - Lab Scheduler Platform
• (1:16:19) - Advice for Deep Tech Startups
• (1:22:22) - Advice for Scientists and Founders Thinking About Where to Focus in Biotech
• (1:25:18) - How Research Labs Could Better Collaborate and Communicate Results
• (1:29:23) - Advantages and Challenges of Going Public
• (1:32:14) - Public Perception of Ginkgo
• (1:33:57) - How Ginkgo's Business Model Has Changed

Connect With Us:

• Our Newsletter
• Twitter
• LinkedIn
• Bluesky
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Riya and Gatlen are board members of MIT AI Alignment, an organization focused on reducing risks from advanced artificial intelligence. Join us as we map the AI safety landscape, define key risks, examine generational perspectives, and explore how we can work together to build a safer future for humanity.

Hosted by Nabil Laoudji. See below for episode links, chapters, and our socials. 🙏🙌

Episode Links:

• MIT AI Alignment
• Cambridge Boston Alignment Initiative (CBAI)
• Riya's LinkedIn
• Gatlen's LinkedIn
• Gatlen's Projects
• Slaughterbots x Future of Life Institute
• Track II Diplomacy
• Tegmark AI Safety Group
• "Nexus" by Yuval Noah Harari
• RAND Institute
• BlueDot Impact
• "If Anyone Builds It, Everyone Dies" by Eliezer Yudkowsky and Nate Soares

Chapters:

• (00:00) - Preview & Intro
• (01:48) - What Is MAIA?
• (02:47) - Why AI Safety?
• (09:26) - Trends in AI Safety Interest
• (12:46) - AI Safety Techniques: MechInterp & Beyond
• (17:15) - Model Situational Awareness
• (20:58) - Hybrid, Mixture of Experts Models
• (24:40) - Decomposing a Model & Parallels with Human Brains
• (29:00) - Private Capital for Safety Research
• (32:23) - Frontier Lab Mentorship Programs
• (34:14) - Policy Perspectives & China Competition
• (36:53) - Ways In Which AI Might Threaten Us
• (39:31) - Track 2 Diplomacy & International Collaboration Examples
• (43:13) - Slaughterbots & Dangerous Capability Demos
• (46:54) - AI-Driven Unemployment
• (52:06) - Generational Attitudes Towards AI
• (57:44) - How to Get Involved - Non Technical
• (01:01:00) - Learning Resources: BlueDot Impact, etc
• (01:01:46) - Importance of Communicators & Artists
• (01:03:50) - How to Support MAIA

Connect With Us:

• Our Newsletter
• Twitter
• LinkedIn
• Bluesky
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Jesse Thaler is Director of the National Science Foundation's AI for Physics "Institute for Artificial Intelligence and Fundamental Interactions" (IAIFI), and Professor of Physics at MIT's Center for Theoretical Physics. In this episode we explore how AI is reshaping physics, how physics is reshaping AI, and mind-bending implications of theoretical physics. Join us!"

See below for episode links, chapters, and our socials. Hosted by Nabil Laoudji.

Support the podcast! Subscribe to our newsletter: www.discoveryengines.co. Thanks for watching 🙏🤙

Episode Links:

• Jesse's Website
• National Science Foundation's IAIFI
• MIT Department of Physics
• Jesse's MIT Page
• Quantum Field Theory
• CERN Large Hadron Collider

Chapters:

• (00:00) - Preview & Introduction
• (04:00) - Jesse's Journey Into Physics
• (05:49) - Curiosity For Understanding The Nature Of Reality
• (07:27) - What Is A Theoretical Particle Physicist?
• (09:34) - Quantum Field Theory
• (11:05) - Particle-Wave Duality
• (12:53) - What is the Large Hadron Collider?
• (15:04) - Data Generated From Particle Collisions
• (17:52) - How LHC Experiments Are Scheduled
• (19:24) - The Future of the LHC and Particle Colliders
• (26:29) - National Science Foundation's Institute for AI and Fundamental Interactions (IAIFI)
• (30:52) - How AI Is Accelerating Physics Discovery
• (40:42) - How Physics is Accelerating AI Discovery (Diffusion models and beyond)
• (48:27) - Physics Popcorn! – Einstein on Time
• (49:32) - Donald Hoffman's Interface Theory of Perception
• (50:48) - Many-Worlds Theory of Quantum Mechanics
• (53:12) - DeepMind's Demis Hassabis on Superintelligence for Science
• (54:03) - Human-Style Intelligence Alone Is Not Enough
• (55:17) - Advocate For Curiosity-Driven Research, Hire IAIFI Talent, Engage With AI

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Featured Images:

• "Standard Model of Elementary Particles", Cush, Public Domain
• "First proton-lead ion collisions at the LHC", Pcharito, CC BY-SA 3.0
• Book cover: "The Case Against Reality: Why Evolution Hid the Truth from Our Eyes", by Donald Hoffman
• X Screenshot, Demis Hassabis, @demishassabis

Rick Wierenga is creator of PyLabRobot, an open-source, hardware-agnostic Python SDK that's lowering the barriers to lab automation for scientists, startups and hackers.

See below for episode links, chapters, and our socials. Hosted by Nabil Laoudji.

Support the podcast! Subscribe to our newsletter: www.discoveryengines.co. Thanks for watching 🙏🤙

Episode Links:

• Rick's Twitter
• Rick's LinkedIn
• PyLabRobot GitHub
• PyLabRobot Forum
• PyLabRobot Twitter
• Dana Gretton, PyHamilton
• PyTorch
• Flow Cytometry

Chapters:

• (00:00) - Preview & Introduction
• (03:33) - Rick's Serendipitous Foray Into Lab Automation
• (07:00) - Why AWS for Biology
• (09:17) - Understanding Liquid Handling Robots
• (10:49) - Generic Robotics Stack
• (13:20) - Robot Automation With PyLabRobot
• (15:07) - The Community Building PyLabRobot
• (16:54) - Why A Big Pharma Would Support PyLabRobot
• (18:36) - PyTorch: An Open Source Inspiration
• (20:32) - Sharing Technology In A Competitive Industry
• (23:11) - Supported Device Ecosystem
• (25:49) - Surprises in Device Integration
• (27:54) - Reverse Engineering 101
• (31:26) - How Useful Are Github CoPilot, Codex, LLMS for Reverse Engineering
• (34:34) - How Device Manufacturers, Automation Experts, Are Reacting to PyLabRobot
• (39:17) - Open Source Efforts and Device Safety
• (41:11) - How PyLabRobot Enables Sharing Protocols, Reproducibility
• (45:03) - Creating a 3D Scanner From a Liquid Handler
• (48:49) - Supporting Self-Driving Labs
• (54:49) - How PyLabRobot Will Evolve
• (55:40) - Automating Flow Cytometry
• (58:17) - How To Contribute and Connect

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Alishba Imran is a deep learning researcher at UC Berkeley's BAIR AI Lab, a Research Fellow at the Arc Institute, a former Research Intern at the Chan Zuckerberg Biohub, co-founder of battery tech startup Voltx, and co-author of "AI for Robotics: Toward Embodied and General Intelligence in the Physical World"

See below for episode links, chapters, and our socials. Hosted by Nabil Laoudji.

Support the podcast! Subscribe to our newsletter: www.discoveryengines.co. Thanks for watching 🙏🤙

Episode Links:

• Alishba's LinkedIn
• Alishba's Twitter
• "AI for Robotics" book
• Arc Institute
• UC Berkeley BAIR AI Lab
• Chan Zuckerberg Biohub
• DynaCLR Paper
• Biopunk Lab

Chapters:

• (00:00) - Preview & Introduction
• (05:02) - Why AI for Science?
• (10:34) - Bootstrapping Your Own Learning
• (16:02) - Why Battery Testing Matters: Launching Voltx
• (20:19) - Batteries, Raw Earth Minerals: Incremental vs Transformative Chemistries
• (23:54) - The Business Side of Deep Tech Entrepreneurship
• (29:14) - The State of Battery Tech Today
• (30:50) - Working with Chan Zuckerberg Biohub
• (33:37) - DynaCLR For Contrastive Learning of Cell State Dynamics
• (36:21) - Why Self-Supervised + Contrastive Learning
• (41:06) - Generalizing to Different Cells Contexts With Embeddings
• (42:06) - Microscopy or ML Advancements for Unlocking Progress
• (43:54) - Managing Terabytes of Data
• (46:51) - Arc Institute: Collecting Largest Single Cell Dataset
• (48:40) - Role of Tech-Founder Funded Institute To Advance Foundational Work
• (50:41) - Book Launch! Merging Classical Robotics Methods With Cutting-Edge Deep Learning
• (53:42) - Robotics Progress: Hype vs Reality
• (57:09) - Robotics for Science
• (58:54) - Future Trends: Automation, Foundational Single Cell Models, Protein and Genome Language Models, Transcriptomics
• (01:00:41) - Pivoting into AI for Science Early, Mid, or Late Career
• (01:02:49) - Exchanging Ideas; DynaCLR Paper; AI for Robotics Book

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Nicholas Larus-Stone is the Founder & CEO of Sphinx Bio, a startup helping life science labs unlock the full potential of their data to accelerate discovery. He’s also the Founder of Bits in Bio, a global community advancing science through software.

See below for episode links, chapters, and our socials. Hosted by Nabil Laoudji.

Support the podcast! Subscribe to our newsletter: www.discoveryengines.co. Thanks for watching 🙏🤙

Episode Links:

• Nicholas' LinkedIn
• Sphinx Bio
• Bits in Bio
• Folding Playground
• Google Co-Scientist Paper
• Recursion
• Defining TechBio

Chapters:

• (00:00) - Preview & Introduction
• (04:34) - Why Biotech & Life Science
• (07:33) - About Small Molecule Discovery Companies Octant & Benevolent AI
• (11:47) - Why Is Software Second in Biotech?
• (14:35) - What Engineers Bring to Biotech
• (16:00) - Is Science Data-Starved or Data Rich?
• (19:23) - How Scientists Work With Data
• (28:10) - Observations That Led to Founding Sphinx Bio
• (31:48) - AI Co-Scientists
• (37:57) - How Platforms like Sphinx Are Powered
• (40:31) - Foundation Model Companies' Interest in Science
• (43:58) - How Sphinx Leverages AI Models
• (45:59) - Managing Hallucinations
• (47:52) - Scientists: Give AI Another Try
• (49:02) - The Business and Cycles of TechBio
• (53:32) - Google's Co-Scientist, Notebook LM, and Other Science Ventures
• (57:43) - Protein Folding Playground
• (00:58:58) - "Wrapper" Companies In Era of Foundation Model Commoditization
• (01:01:56) - Bits in Bio Community & Growth
• (01:04:25) - Try Sphinx's Platform; Work for Sphinx; Support Your Local Scientist

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

David Milsted is a postdoctoral researcher at the “A-Lab” for autonomous materials discovery, located at the Department of Energy’s Lawrence Berkeley National Laboratory. Please note: The views expressed in this video by David are his own and not those of his colleagues.

See below for episode links, chapters, and our socials. Hosted by Nabil Laoudji.

Support the podcast! Subscribe to our newsletter: www.discoveryengines.co. Thanks for watching 🙏🤙

Episode Links:

• David's LinkedIn
• Lawrence Berkeley National Lab
• A-Lab
• Ceder Group
• UC Berkeley
• Mississippi State University
• Wood Science

Chapters:

• (00:00) - Preview & Introduction
• (04:37) - LBNL Fun Facts
• (05:40) - David’s Journey Into Lab Automation (Wood Science, Automation Engineering)
• (10:26) - Why Wood Science
• (14:54) - Journey From Brazil To LBNL
• (25:50) - Material Discovery Process Steps
• (29:37) - Predicting Materials Properties
• (35:07) - Synthesizing Materials With Automation
• (43:21) - Testing Novel Materials
• (44:58) - Orchestrating Automated Labs (A-Lab OS)
• (49:14) - Shifting From Independent to Team-Based Projects
• (53:28) - University-Government Lab Structure
• (57:41) - What Inspired A Lab’s Vision
• (01:02:40) - Growth in Autonomous Lab Investment
• (01:05:34) - Future of Characterization Via Microscopy
• (01:10:22) - A Lab Tour (Core Components)
• (01:15:44) - Vendor Support: Mitsubishi, Labman, MTI, etc
• (01:18:58) - Managing Input Inventory For Runs
• (01:20:12) - Furnace Deep Dive
• (01:24:06) - Parallel Processing
• (01:25:43) - Vendor Automation Out of the Box; Importance of Societal Awareness

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Transon Nguyen is the CEO and Co-Founder of Eigen Therapeutics, a biotech startup leveraging AI and lab automation to develop priming therapies that make cancer easier to find and eliminate.

Hosted by Nabil Laoudji. My guest co-host is Jimmy Sastra! This episode is sponsored by Monomer Bio. See below for episode links, chapters, and how to connect with us.

Thanks for watching 🙏🤙

Episode Links:

• Eigen Therapeutics
• Transon Nguyen's LinkedIn
• Monomer Bio
• Jimmy Sastra's LinkedIn
• Radioligand Therapy
• Antibody–Drug Conjugates (ADCs)
• Laboratory Information Management System (LIMS)

Chapters:

• (00:00) - Teaser
• (00:36) - Introducing My Guest Co-Host: Jimmy Sastra of Monomer Bio
• (11:24) - Introducing Transon Nguyen, CEO of Eigen Therapeutics
• (12:54) - Transon's Path Into Biomedical Engineering
• (15:45) - Science In Industry vs Academia: Importance of Culture
• (18:27) - Co-Founding Eigen Tx: A Confluence of Factors
• (24:27) - How to Find New Ideas
• (25:15) - Cost of ADCs and Radioligand Therapies
• (27:00) - Testing The Effectiveness of Priming Therapies
• (31:23) - How Patients Take Priming Therapies
• (33:19) - Importance of Empathy In Multidisciplinary Teams
• (37:54) - Lab Tour: Intro, Flexible Design
• (39:33) - Different "Homes" / Areas of The Lab
• (43:32) - Custom Built LIMS
• (48:54) - Robot Test Suite Demo
• (51:41) - A Look At Custom-Built LIMS
• (55:56) - Favorite Instruments
• (57:44) - Business of BioTech: Making The Numbers Work
• (59:09) - Don't Over-Automate
• (01:01:13) - Keeping The Lab Clean
• (01:03:01) - Moving Beyond Just Solving Problems
• (01:05:05) - Reframing Personal Identity and Seeing the Whole System
• (01:08:31) - Relevance of AI Foundation Models, Virtual Cells to Eigen's Mission
• (01:12:50) - Contact Transon to Learn More About Priming Therapies

Connect With Us:

• Our Newsletter
• Twitter
• Bluesky
• LinkedIn
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts

Sudha Gollapudi & Madeline Wolf (ex Genentech, Ginkgo Bioworks, Calico/Alphabet) are lab automation experts and co-founders of The Automated Lab: an open resource and contract engineering service for building automated labs. See below for episode links and chapters.

Support the podcast! Subscribe to our newsletter.

Thanks for watching 🙏🤙

Episode Links:

• The Automated Lab
• Open Source Resource Page
• Vivo Hamilton Liquid Handler Chatbot
• Automated Lab Patreon
• Sudha's LinkedIn
• Madeline's LinkedIn
• ELISA Biochemistry Assay
• Society for Laboratory Automation and Screening (SLAS)

Chapters:

• (00:00) - Teaser
• (00:54) - Episode Introduction & Preview
• (05:38) - Sudha and Madeline’s Academic + Professional Experience
• (06:53) - Madeline’s Path Into Biotech Lab Automation
• (09:40) - Sudha’s Path Into Biotech Lab Automation
• (10:55) - Career Pathways Into Lab Automation
• (15:38) - What Encompasses Lab Automation?
• (17:29) - Lab Automation Example: Workcell for ELISA Immunological Assay
• (22:19) - Environmental Impact of Lab Automation
• (27:31) - SLAS Conference Hot Takes; Move to Smaller Footprint Products
• (36:28) - Modular-First Design In Lab Automation
• (41:51) - LIMs, ELNs, And Making Data More Accessible
• (46:10) - Solving the Human-Robot Interface With NLP, Flexible Data Infrastructure
• (52:23) - Automation For R&D vs Manufacturing
• (57:07) - Adapting The Culture of Science To Increased Automation
• (01:00:29) - Standardizing Scientific Language
• (01:08:02) - How To Partner With The Automated Lab

Connect With Us:

• Twitter
• Bluesky
• LinkedIn
• Instagram
• Newsletter
• Feedback or questions

Platforms:

• YouTube
• Apple Podcasts
• Spotify Podcasts