Biology for Programmers
Curated by Claude · 12 videos · 5 hr 39 min
HN commenters keep finding biology through computing: Sussman's talk on how we don't know how to compute, Levin's NeurIPS talk, a DEF CON talk on hacking the genome. This playlist starts with that framing, shows you the molecular machinery in animation, moves to Levin's idea that tissues compute shape, then to security, static analysis and DIY gene therapy, and ends with the Lisp hacker designing molecules.
Play all on YouTube- 11:04:19
"We Really Don't Know How to Compute!" - Gerald Sussman (2011)
96K views • 5 years agoStrange Loop ConferenceGerald Sussman's 2011 Strange Loop keynote argues we still do not know how to compute, comparing biological systems with how we program machines. It touches on propagators, constraint programming and robustness.The framing: Sussman sets biology's robustness against how brittle our programs are, and one commenter says it made them question what programming is.
- 29:09
Animations of unseeable biology | Drew Berry | TED
2.7M views • 14 years agoTEDDrew Berry shows scientifically accurate animations of molecular processes inside cells, such as DNA replication, at TEDxSydney.Now look at the hardware: Drew Berry's accurate animations of DNA replication, which left one commenter in awe of the trillions of protein machines inside us.
- 37:20
DNA animation (2002-2014) by Drew Berry and Etsuko Uno wehi.tv #ScienceArt
7.3M views • 8 years agoWEHImoviesA compilation of molecular animations of DNA replication and gene transcription by Drew Berry and Etsuko Uno at WEHI, made with no narration. It shows molecular machinery at work inside cells.Seven minutes of the same molecular machinery with no narration, jostling and mechanical, and the clip HN posts most often to show it.
- 43:04
mRNA Translation (Advanced)
1.5M views • 16 years agoDNA Learning CenterA short animation from the DNA Learning Center showing how mRNA carries a gene's message to the ribosome, where tRNA and codons are used to assemble amino acids into a protein.Three minutes on the ribosome reading codons and assembling a protein, the clip HN posted widely in the mRNA-vaccine threads.
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7:45Electron transport chain
3.7M views • 9 years agoHarvard OnlineA short Harvard Online animated lesson on how the mitochondrial electron transport chain works. It shows proton pumping and the machinery that drives ATP synthesis.The power supply: proton pumps and ATP synthase as an actual rotary motor, which commenters share as the clearest example of nanomachines in cells.
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1:55The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)
3M views • 10 years agoHarvard Medical SchoolA two-minute time-lapse from the Kishony Lab showing bacteria spreading across a giant petri dish with increasing antibiotic doses, evolving resistance as they go.Evolution as a search algorithm you can watch, as bacteria work their way across rising antibiotic doses in days.
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19:41Michael Levin: The electrical blueprints that orchestrate life | TED
575K views • 5 years agoTEDBiologist Michael Levin explains the bioelectric layer that coordinates cells to build organs and bodies, showing footage of two-headed worms and introducing xenobots. He discusses implications for medicine and the nature of life.Up from molecules to tissues: Levin's 20-minute introduction to the bioelectric layer, with two-headed worms and xenobots.
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52:07What Bodies Think About: Bioelectric Computation Outside the Nervous System - NeurIPS 2018
103K views • 7 years agoThe Artificial Intelligence ChannelMichael Levin's NeurIPS 2018 talk on bioelectric computation outside the nervous system, showing how cell electrical networks shape development and regeneration. It covers morphological information processing in living tissue.The full version given to an ML audience, and the talk that introduced many HN readers to Levin's view of cell collectives as computers that store pattern memories.
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49:47DEF CON 25 - John Sotos - Genetic Diseases to Guide Digital Hacks of the Human Genome
14K views • 9 years agoDEFCONConferenceJohn Sotos, a physician and former Intel chief medical officer, argues at DEF CON 25 that genetic diseases are exploitable vulnerabilities in the genome. He warns that CRISPR and related tools will make malicious genome hacks and targeted bioweapons feasible.The security engineer's view: genetic diseases as known exploits, a talk that convinced several commenters to keep their DNA out of databases.
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48:36Matt Might - Winning the War on Error Solving the Halting Problem and Curing Cancer
9K views • 9 years agoCurry On!Matt Might's Curry On talk on ending errors in code, both software and the human genome. He covers conservative approximation of the halting problem via static analysis and a computational approach to precision medicine.Static analysis and precision medicine in one talk, built on Might's search for his son's diagnosis, which commenters call a must-see.
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18:33I Genetically Engineered *MYSELF* to Fix Lactose Intolerance
640K views • 8 years agoThe Thought EmporiumThe Thought Emporium's host describes making and taking a DIY gene therapy to treat his own lactose intolerance. It uses an AAV virus to deliver DNA coding for the lactose-digesting enzyme, made with biohacker Gabriel Licina's help.Biology as a garage hack: a home-made AAV gene therapy tested on the host himself, the example HN keeps citing in biohacking threads.
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57:38Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming
52K views • 11 years agoGoogle TechTalksChristian Schafmeister's Google Tech Talk on designing spiroligomer molecules and building Clasp, a Common Lisp on LLVM that interoperates with C++, to program molecular design. It covers the chemistry, automatic differentiation for force fields, and how the compiler is built.The closer: a chemist writes his own Lisp compiler to design molecules, and commenters dare anyone to watch it and not be impressed.