Filter
Exclude
Time range
-
Near
Truly important work happening at @arcinstitute. And all this talk of emergence and open collaborative networks in the service of such noble aims is thrilling to see for me personally.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
10
Exceedingly cool AI science applications with real world impacts
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
3
Dr. Yusuf Roohani, currently a Group Lead in Machine Learning at the @arcinstitute, has a history of collaboration with $RXRX Recursion Pharmaceuticals. Notably, he spent time as a Visiting Scholar at Recursion’s headquarters in Salt Lake City in 2023. His previous roles include positions at GlaxoSmithKline and Genentech, indicating a strong background in AI-driven drug discovery
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
World should be more about WHOLLY ("...never-before-seen-by-nature genomes"), than about WOOLLY (...mice)! 😀😀😀 Congrats, @patrickc, @arcinstitute and the stellar people there!
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
I love the fact that someone with a conscience is working on this.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
if you’re in shrimp welfare, pivot to E. coli welfare
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
6
Incredible achievements. I love seeing people explore and create things that could only be dreams before. Ai is a great assistant and performer in the field of biology, he analyzes, designs, creates, CREATES new genomes with new characteristics, it's impressive. The possibility of such a strong development and improvement of our health, the ability to change genomes and at the same time maintain health (just my past article on the topic of ai+ genomes). Thank you for this research and teaching Ai in these areas, it is helping humanity in very important aspects. This is a development at a crazy level. And this is a very good training for ai, which will contribute to scaling and development in other areas.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
I think Arc is OpenAI circa 2016, and will have a similarly interesting governance arc as they run away with the compbio ball. IE, they’re open and collaborative today, but in a few years their tools will have terrifying power and value, will be irresponsible to disclose, etc
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
3
This is the type of AI work we should all be proud of and cherish. There’s enough in this list already that could make a country say “this is our new national mission”.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
Amazing
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
this souunds really cool "They experimentally synthesized these genomes and showed that these AI-generated phages actually work" what does it mean to exp synth an AI genome? build it base by base and put it in a cell to be turned into protein?
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
2
This 👇❤️❤️❤️ "With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation."
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
I've spent the past decade working on a *single* effort at @ezrainc – early cancer detection, using a single approach (MRI & AI). Incredible to see how much @arcinstitute has managed to accomplish in 1/3 of that time.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
2
Oh you retards stop right now
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
We're living in the future @arcinstitute!
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
AI shaping the frontiers of science:
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
1
What would you change about how you lead your life if you found out you were going to live forever? A question people should start asking themselves. The younger you are, the more seriously you should consider it.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
2
2
Exciting times ahead for new scientific institutions! Looking forward to see what other pioneering works come from the Arc Institute.
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
3
advancing science is arguably the single best way to make humans happy, healthy, and free. incredibly impressive to see this - especially given it's been driven largely by private individuals
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
1
We have had a good run in the last week. Some zoomed out thoughts on why we started Arc, how we did it, and where we’re going
Over the past week, @arcinstitute published three new discoveries that I’m very proud of. • The world's first functional AI-generated genomes. Using Evo 2 (the largest biology ML model ever trained, which Arc released in partnership with @nvidia in February), Arc scientists took advantage of the fact that Evo 2 is a generative model to produce completely new sequences for complete phage genomes. That is, they used AI to produce wholly new, never-before-seen-by-nature genomes. They experimentally synthesized these genomes and showed that these AI-generated phages actually work, killing E. coli bacteria with high efficacy. • Germinal, an AI system for creating new antibodies. Antibody design is one of the great problems of medical biology given their obvious importance and usefulness for creating therapeutics. (Antibodies are tiny particles that help the immune system identify pathogens and other harmful intruders. See also the recent Works in Progress article on this topic: [1].) Today, designing effective antibodies is very expensive and slow. Germinal is a cheap and fast way to produce drug candidates, with success rates of up to 22%. This means that one can go from having to screen thousands of candidates in the lab to screening perhaps a few dozen. It's early, but I suspect that better methods for designing antibodies will be a very big deal for disease treatment in the coming years. • Today, we published a paper showing that “bridge editing”, which Arc scientists first introduced last year, can make precise edits in human cells that are up to 1 million base pairs long, and without relying on intrinsically unpredictable cellular repair machinery (which CRISPR requires, often leading to editing mistakes). They showed that it’s possible to use this editing to cut out the DNA repeats that cause Friedreich’s ataxia (a neurological disease), an approach which should also be relevant to Huntington’s and other similar disorders. One particularly cool thing about it is that it’s possible to specify every nucleotide within the extended editing window, meaning that recursive bridge edits could potentially be a powerful way to reprogram even biological traits that are caused by many genetic mutations. (Genetic therapies today target single mutations.) Arc is pretty new. Its doors opened in mid 2022, and it's now 300 people. I’m excited about these discoveries because they show that a number of our hopes in starting Arc are starting to pay off: • AI/ML and computation are at the center of all three. That is obviously true for the first two, but the mobile genetic element behind bridge editing was also discovered as a result of a complex computational search. One of our premises in starting Arc was the belief that the intersection of software/AI and experimental wet lab biology should enable great things. (And besides requiring great computational work, all three of these also required strong wet lab work, tightly coordinated under a single physical roof.) • We’ve been toying with the idea that a handful of technologies are enabling a new kind of “Turing loop” in biology: sequencing advances (including single-cell sequencing) give us new ways to read; transformers and AI gives us new ways to think; and functional genomics (such as bridge editing) give us new ways to ways to write. This trio of discoveries span each part of this loop, and we’re hopeful that there’ll be compounding returns in improving each part. • Arc is a non-profit, which we hoped would make collaborating with others easier, since we can avoid worries about financial return. This is indeed proving important, and all three of these projects involved close partnership with others. Germinal was done in partnership with @SynBioGaoLab at Stanford; Evo 2 was trained in partnership with Nvidia. Bridge editing was jointly published with a structure from the @HNisimasu Lab at the University of Tokyo. Arc tries to make its discoveries useful (see the Evo 2 Designer[2]) for others, and the code behind the computational projects is open source, hopefully making it easy for others to spot new opportunities for collaboration and partnership in the future. Most of all, Arc itself is an ongoing collaboration with @UCSF, @UCBerkeley, and @Stanford. • With Arc, we wanted to enable better bottom-up and top-down work. With the fully flexible, no-strings-attached funding that we provide to investigators, we want to enable completely unexpected discoveries and avenues of investigation. With our institute initiatives (around creating a virtual cell and curing Alzheimer’s), we want to bring to bear a scale and level of coordination that’s usually difficult in basic science. Germinal is a “surprise” discovery that didn’t involve top-down coordination, whereas Evo 2 is the result of ambitious high-level planning and funding. • Humanity has never cured a complex disease (a category that includes most neurodegenerative diseases, most cancers, and most autoimmune diseases), and my hope is that Arc can help change this. It’s also clear that AI will revolutionize biology, and I hope that Arc can effectively aggregate the ingredients needed to fully capitalize on its promise. I’m biased, but I think some of the coolest biology in the world is currently being done at Arc. (They’re always hiring if you’re interested.) While I’m a cofounder of Arc, I spend almost all my time on Stripe, where we spend our time building economic infrastructure for the internet. All credit for Arc’s progress should go to the remarkable scientists and staff who’ve made Arc their home or who’ve chosen to collaborate with us. (You can read more about these particular discoveries in these threads: [3], [4], [5].) I’m also very grateful to the amazing Stripe employees who’ve built the company that makes Arc’s ongoing work possible, and to the millions of customers who’ve chosen to partner with Stripe. John and I feel fortunate to be able to support Arc’s work to the extent that we do. Maybe this is reading too much into it, but I sometimes feel that there’s a commonality between @arcinstitute and @stripe. Both biology and economic infrastructure involve reasoning about complex systems with many levels of emergent effects, and in both cases building the right tools can have almost unboundedly large benefits. Even though progress in both tends to take a long time, it also feels like the next five years in both will be some of the most interesting in living memory. (If economic infrastructure is your jam, we have a whole slew of fantastic announcements coming up at Stripe Tour in New York next week. Tune in!)
5
18
1
267