Episode
#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
2:18:10
Published: Mon Jan 11 2021
Description
Dmitry Korkin is a professor of bioinformatics and computational biology at WPI. Please support this podcast by checking out our sponsors: - Brave: https://brave.com/lex - NetSuite: http://netsuite.com/lex to get free product tour - Magic Spoon: https://magicspoon.com/lex and use code LEX to get $5 off - Eight Sleep: https://www.eightsleep.com/lex and use code LEX to get special savings EPISODE LINKS: Dmitry's Website: http://korkinlab.org/ Dmitry's Twitter: https://twitter.com/dmkorkin PODCAST INFO: Podcast website: https://lexfridman.com/podcast Apple Podcasts: https://apple.co/2lwqZIr Spotify: https://spoti.fi/2nEwCF8 RSS: https://lexfridman.com/feed/podcast/ YouTube Full Episodes: https://youtube.com/lexfridman YouTube Clips: https://youtube.com/lexclips SUPPORT & CONNECT: - Check out the sponsors above, it's the best way to support this podcast - Support on Patreon: https://www.patreon.com/lexfridman - Twitter: https://twitter.com/lexfridman - Instagram: https://www.instagram.com/lexfridman - LinkedIn: https://www.linkedin.com/in/lexfridman - Facebook: https://www.facebook.com/LexFridmanPage - Medium: https://medium.com/@lexfridman OUTLINE: Here's the timestamps for the episode. On some podcast players you should be able to click the timestamp to jump to that time. (00:00) - Introduction (07:21) - Proteins and the building blocks of life (14:23) - Spike protein (21:11) - Coronavirus biological structure explained (26:09) - Virus mutations (32:39) - Evolution of proteins (42:25) - Self-replicating computer programs (50:02) - Origin of life (57:34) - Extraterrestrial life in our solar system (59:31) - Joshua Lederberg (1:05:30) - Dendral (1:08:24) - Why did expert systems fail? (1:10:35) - AlphaFold 2 (1:32:13) - Will AI revolutionize art and music? (1:39:12) - Multi-protein folding (1:43:39) - Will AlphaFold 2 result in a Nobel Prize? (1:46:10) - Will AI be used to engineer deadly viruses? (2:01:17) - Book recommendations (2:11:00) - Family (2:13:38) - A poem in Russian
Chapters
This transcript contains advertisements for Brave, a privacy-preserving browser, and 8Sleep's PodPro mattress cover with heating and cooling capabilities.
00:00 - 06:57 (06:57)
Summary
This transcript contains advertisements for Brave, a privacy-preserving browser, and 8Sleep's PodPro mattress cover with heating and cooling capabilities. It also mentions NetSuite's free product tour to benefit businesses.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
Proteins are not just simple globular molecules, but rather complex structures made up of protein domains.
06:57 - 13:14 (06:16)
Summary
Proteins are not just simple globular molecules, but rather complex structures made up of protein domains. Research has shown that studying proteins across different species reveals a vast level of complexity in their structures and functions.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
Researchers are using their research to understand the structural basis of COVID-19 by decoding every single protein in its proteome, in particular the spike protein, which is being studied as a possible target for antibodies and treatments.
13:14 - 26:38 (13:24)
Summary
Researchers are using their research to understand the structural basis of COVID-19 by decoding every single protein in its proteome, in particular the spike protein, which is being studied as a possible target for antibodies and treatments.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
Understanding the evolution of viruses is critical to understanding the mechanisms that enable them to jump from one species to another.
26:38 - 36:07 (09:28)
Summary
Understanding the evolution of viruses is critical to understanding the mechanisms that enable them to jump from one species to another. Mutations can diversify the function of protein domains, but splitting a domain into fragments can cancel out or reduce its function.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
Proteins evolve differently compared to genes as they do not need to preserve certain structure.
36:07 - 42:18 (06:10)
Summary
Proteins evolve differently compared to genes as they do not need to preserve certain structure. Short linkers between two protein domains allow for effective interaction with other proteins.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
In this episode, the host interviews a computational biologist about the limits of machine learning and the origin of life.
42:18 - 52:29 (10:11)
Summary
In this episode, the host interviews a computational biologist about the limits of machine learning and the origin of life. They touch on the concept of Quine, a computer program that copies itself, and how it relates to evolution.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The speaker ponders the idea that life may be more common in the universe than we realize, given that the existence of proteins and basic living organisms may require an Earth-like planet.
52:29 - 1:00:23 (07:53)
Summary
The speaker ponders the idea that life may be more common in the universe than we realize, given that the existence of proteins and basic living organisms may require an Earth-like planet.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The combination of chemistry, computer science, and expert systems has led to a powerful tool for identifying molecules using mass spec data.
1:00:23 - 1:10:13 (09:49)
Summary
The combination of chemistry, computer science, and expert systems has led to a powerful tool for identifying molecules using mass spec data. This interdisciplinary approach was pioneered by Leatherberg and highlights the importance of AI in modern research.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The speaker discusses how when a protein is being translated, there is already some structural fragmentation happening, and how state-of-the-art machine learning systems can be used for structure prediction.
1:10:13 - 1:20:08 (09:54)
Summary
The speaker discusses how when a protein is being translated, there is already some structural fragmentation happening, and how state-of-the-art machine learning systems can be used for structure prediction. This includes a combination of biophysics and bioinformatics in order to obtain protein structures of proteins without any known structure.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The Alpha Fold can solve a majority of the more compact proteins at a near experimental level.
1:20:08 - 1:27:16 (07:08)
Summary
The Alpha Fold can solve a majority of the more compact proteins at a near experimental level. By aligning the same protein from different organisms, we can determine what is conserved and structurally stable in the protein and what is diverse.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
This podcast features a discussion on the contrasting approaches of Waymo and Tesla in creating autonomous vehicles, and the role of AI in the technology industry.
1:27:16 - 1:39:02 (11:45)
Summary
This podcast features a discussion on the contrasting approaches of Waymo and Tesla in creating autonomous vehicles, and the role of AI in the technology industry.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The postdoc's favorite protein PSD 95 has components of both protein folding and protein-protein interactions contributing to the understanding of this scientific field.
1:39:03 - 1:45:34 (06:30)
Summary
The postdoc's favorite protein PSD 95 has components of both protein folding and protein-protein interactions contributing to the understanding of this scientific field.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The use of computational tools in protein design, like AlphaFold and Rosetta algorithm pioneered by David Baker, has been a prominent area of research in the field of protein science.
1:45:36 - 1:52:44 (07:07)
Summary
The use of computational tools in protein design, like AlphaFold and Rosetta algorithm pioneered by David Baker, has been a prominent area of research in the field of protein science. The question remains whether these methods can advance protein designs beyond the standard methods used currently.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The speaker argues that more openness in research from various communities like the research community, companies and governments can help us better understand the structural characterization of viruses, respond to future viruses and even aid in contact tracing purposes.
1:52:44 - 2:01:46 (09:02)
Summary
The speaker argues that more openness in research from various communities like the research community, companies and governments can help us better understand the structural characterization of viruses, respond to future viruses and even aid in contact tracing purposes.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The book, "The House of Government" by Yuri Slezkine, inspired author Masha Gessen with its unique way of combining the experience of navigating Soviet Psychiatry.
2:01:46 - 2:10:17 (08:30)
Summary
The book, "The House of Government" by Yuri Slezkine, inspired author Masha Gessen with its unique way of combining the experience of navigating Soviet Psychiatry. The dense text reads as if every paragraph is filled with ideas, and doctors have described the accounts of the patient in the book as incredibly accurate.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
The speaker discusses their personal resolution to spend more time with family while working from home and recommends a must-listen audiobook about academia and becoming a scientist.
2:10:17 - 2:16:38 (06:20)
Summary
The speaker discusses their personal resolution to spend more time with family while working from home and recommends a must-listen audiobook about academia and becoming a scientist.
Episode#153 – Dmitry Korkin: Evolution of Proteins, Viruses, Life, and AI
PodcastLex Fridman Podcast
In this podcast, Dmitry Korkin discussed his work in computational biology and how it can be applied to better understand life.
2:16:39 - 2:17:47 (01:08)
Summary
In this podcast, Dmitry Korkin discussed his work in computational biology and how it can be applied to better understand life. The conversation also touches on Korkin's love for poetry and the beauty of the Russian language.