Note: this page is in progress. I continue to read the book. This page needs to be edited but these are my preliminary notes as I read the book.
The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race, Walter Isaacson, c. 2021.
UC- Berkeley's newest supercomputer named after Jennifer Doudna: link here.
A Nobel Prize winner.
The Book
Introduction: Into the Breach.
Jennifer Doudna: superstar at Berkeley
- co-inventor of CRISPR -- gene editing technology
- her world changed: robot competition canceled for her son, Covid -- March 12, 2020
- the next day, she led a Berkeley team to decide what role they would play in the Covid outbreak
- their first meeting: sat 6 feet apart
- it would be their first and last meeting
- from now on: Zoom and Slack
CRISPR: human technology to do what bacteria have been doing for millennia to defeat viruses. Amazing. Page xvi.
CRISPR:
- the gene-editing tool that Doudna and others developed in 2012 is based on a virus-fighting trick used by bacteria, which have been battling viruses for more than a billion years.
- in their DNA, bacteria develop clustered repeated sequences, known as CRISPRs, that can remember and then destroy viruses that attack them.
- in other words, it's an immune system that can adapt itself to fight each new wave of viruses -- just what we humans need in an era that has bee plagues, as if we were still in the Middle Ages, by repeated viral epidemics.
Steps Doudna took:
- created a coronavirus testing lab;
- postdoc Jennifer Hamilton, was one of the leaders of that team/lab
- created a team to develop new types of coronavirus tests based on CRISPR
- based on lessons learned by starting a company some years earlier that used CRISPR for detecting viral disease
- settled on ten projects
Cross-country competitor: Feng Zhang
- her rival since 2012
- China-born and Iowa-raised researcher at the Broad Institute of MIT and Harvard
CRISPR:
- already science fiction becoming real
- November, 2018: a young Chinese student who had been to some of Doudna's gene-editing conferences used CRISPR to edit embryos and remove a gene that produces a receptor HIV;
- that led to the birth of twin girls, the world's first "designer babies."
A digression: is CRISPR being use in embryo research to "prevent/cure/ameliorate" sickle cell disease?
After two billion years, humans can now edit genes. Time for a discussion with ChatGPT.
Doudna:
- a graduate student in the 1990s
- other biologists were more interested in DNA
- Doudna: RNA
- wow! What a choice!
- Covid-19; seasonal flu viruses: RNA
- if I read this correctly, it was already called CRISPR when Doudna was doing her research -- but Doudna was studying "the CRISPR system" that bacteria were using in their battles against viruses;
- but now Doudna was using that same CRISPER system to edit genes;
- this reminds me of Jensen Huang pivoting with GPUs -- taking chips that were used for gaming to using those same chips for AI -- amazing!
AI prompt: The CRISPR system was already being used by bacteria to fight viruses when Doudna used the CRISPR system to edit genes. So, Doudna did not discover / invent CRISPR. She used the bacterial CRISPR system to edit genes. That was her breakthrough. Is that correct? And, of course, if accurate, that would raise issues with regard to patents. Is that accurate? Your thoughts?
Gemini:
Who discovered CRISPR if Doudna did not?
Does seasonal flu (e.g., Type A -- H1N1 -- use CRISPR CAS to target human DNA? [This was either a typo on my part or is evidence of how much I misunderstood CRISPR at this time.]
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How CRISPR Works
But looks at this. Cascade mentioned in the book, p. 111.
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By Chapter
Introduction: Into the Breach
Part One: The Origins of Life
Chapters 1 - 8
Part Two: CRISPR
Chapters 9 - 19
Part Three: Gene Editing
Chapters 20 - 31
Part Four: CRISPR in Action
Chapters 33-34
Part Five: Public Scientist
Chapters 35 - 36
Part Six: CRISPR Babies
Chapters 37 - 39
Part Seven: The Moral Questions
Chapters 40 - 43
Part Eight: Dispatches from the Front
Chapters 44 - 47
Part Nine: Coronavirus
Chapters 48 - 56
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Chapter 12: The Yogurt Makers
Page 90.
Studying CRISPR with the goal of improving ways to make yogurt and cheese:
Rudolphe Barrangou in North Carolina;
Philippe Horvath in France
apparently both worked for Danisco, a Danish food ingredient company that makes starter cultures which initiate and control the fermentation of dairy products.
Question: at this point, around 2008, Doudna was studying CRISPR at UC-Berkeley. What did they know about CRISPR at this point; I need to go back and re-read the very early part of CRISPR. Later: this was in 1987 -- need to go back and re-read that section; repeating units accidentally discovered; scientist who discovered them didn't pursue what he had found; Doudna did. She thought this bacterial immune system had to a be a big deal.
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Chapter 13: Genentech
Autumn, 2008: Jillian Banfield tells Doudna she was worried that the most important discoveries had already been made, and it was now time for Doudna to move on.
Doudna demurred. "I knew there was some kind of adaptive immunity going on and wanted to know how it worked."
So, if I'm reading this correctly, researchers understood how the system worked and how bacteria protected themselves from viruses. BUT APPARENTLY, Doudna felt there was more -- she was thinking there was too much "energy" invested in this system not to have a "deeper meaning." She thought that "deeper meaning" might be immunity of some sort; an "immune system" of some sort that would rival what eukaryotic cells have and what researchers have been able to devise.
Which raises the question: do eukaryotic cells have something similar to CRISPR?
Which leads to the next question: why doesn't RNAi protect humans from seasonal flu?
- interferon is primary mammalian response against viruses, but
- some have suggested that interferon itself may shut down the RNAi system.
Wow.
And then there's the "interferon storm" issue.
Of course this raises even more questions.
Back to the book. Chapter 13:
- Wow. Genetech. Mental breakdown for Doudna.
- Returns to Berkeley after a two-month absence while preparing her move to Genetech, which, of course, did not happen.
Chapter 14: the new team under Doudna when she "returned" to Berkeley.
After a single mention in the book, Kaihong Zhou was never mentioned again.
Chapter 15: Caribou
p. 114: Stanford and its start after WWII.
Chapter 16: Emmanuelle Charpentier
p. 119.
tracrRNA -- Cas9 -- crRNA
The process of unraveling the roles of tracrRNA began in 2010, p. 125.
Charpentier in the process of moving from Vienna to Umeå, Sweden. Thirteenth largest city in Sweden; serves as port city for northern Sweden; on the Gulf of Bothnia, the northernmost part of the Baltic Sea. Yeah, this is really far north. From wiki:
Before leaving Vienna, she found a volunteer, Elitza Deltcheva, a young student from Bulgaria, who was willing to pursue work on tracrRNA. This little team discovered the three components: tracrRNA - Cas9 enzyme - crRNA, p. 125.
Puerto Rico, March, 2011 -- Doudna and Charpentier meet! Page 127.
The foursome that made one of the most important advances in modern science:
- Doudna, UC-Berkeley
- Charpentier, Umeå, Sweden (previously Vienna where some of her researchers remained)
- Martin Jinek,
- Doudna's lab, had been working on Cas1 and Cas6
- Krzysztof Chylinski,
- Polish, in Charpentier's lab in Vienna, who had worked on Charpentier's earlier Cas9 paper
Chapter 17: CRISPR-Cas9
"fast-growing" annual CRISPR conferece, July 2011; UC-Berkeley
first time Jinek has personally met Chylinski
Chylinski did the all-important tracrRNA experiment -- solved the problem
p. 132 -- how the three-component system worked -- tracrRNA had a dual role
graphic: p. 133
the three-component system was a nice-to-know how bacteria protected themselves from viruses, but Doudna recognized immediately how Cas9 could be used as a tool to edit DNA
"call-and-response duet between basic science and translational medicine."
the eureka moment -- p. 133
sgRNA: "single-guide RNA" -- bottom of page 134
the key: middle paragraph p. 135 -- something able to patent!!!
Doudna's collaboration with Charpentier had produced two significant advances
signing the laboratory notebook!
Chapter 18: Science, 2012
the paper, sent to Science, June 8, 2012
six authors: Jinek, Chylinski, Ines Fonfara, Michael Hauer, Doudna, and Charpentier.
Again: the all-important invention -- the single-guide RNA.
Paper formally accepted Wednesday, June 20, 2012 -- p. 140.
Chapter 19: Dueling Presentations
Virginijus Šikšnys, Vilnius University, Lithuania.
Walter Isaacson really provides a nice summary of the presentations at the June 21, 2012: Šikšnys vs Charpentier.
Jinek and Chylinski made the two presentations.
Again, the crux: the single-guide technology p. 148.
Erik Sontheimer.
Many could have claims to CRISPR technology but at this point, one must seriously look at Erik Sontheimer.
Last page, chapter 19, p. 149:
Doudna, Sontheimer, Brrangou and Šikšnys went out to dinner together -- they knew it was important, but lots of important work is always being done. They knew there was something very, very important they had discovered, but probably very, very giddy, appropriately competitive, but no one thinking of a Nobel Prize.
Part Three: Gene Editing
Chapter 20: A Human Tool
"The road to engineering human genes began in 1972 when Professor Paul Berg of Stanford discovered a way to take a bit of the DNA of a virus found in monkeys and splice it to the DNA of a totally different virus."
He had manufactured what he dubbed "recombinant DNA."
Page 164, writing on Feng Zhang, Walter Isaacson writes:
Instead of pursuing computer science, however, Zhang became a forerunner of what will, I think, soon be common among aspiring geeks: his interests shifted from digital tech to biotech. Computer code was something his parents and their generation did. He became more interested in genetic code.
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