The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race, Walter Isaacson, c. 2021 -- February 15, 2026

The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race, Walter Isaacson, c. 2021.

A Nobel Prize winner.

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. Did Google have a typo in the reply above? "Cas9" stands for "CRISPR associated protein 9" -- not "Cascade complex." Wow. Amazing how Google Gemini missed this. In a gazillion sites "Cas" is shorthand for "CRISPR associated protein." Apparently in some rare cases "Cas" may stand for "Cascade complex" but certainly not in this context.
 

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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 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? 
 

Wow, look at that, in mammals:
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: 

Chapter 15: Caribou

p. 114: Stanford and its start after WWII. 

A History of Israel, Third Edition, John Bright, c. 1959, 1972, 1981 -- February 15, 2026

A History of Israel, Third Edition, John Bright, c. 1959, 1972, 1981.

Maybe just the best book I've found on the history of Old Testament Israel.

Half-Price Books: $8.49. Hardcover.

Contents: seven pages. 

Index: eleven pages.

Plates (maps):

Scripture references: 

*********************
Important Dates

The dates:

• 5500 - 3500 BC: Chalcolithic Age (transitional period between the Neolithic and the Bronze Age
• 2000 BC: beginning of the Bronze Age
• collapse of the Third Dynasty of Ur due to Elamite invasion
• end of Sumerian dominance
• rise of Amorite city-states
• shift from wheat to barley
• rise of Middle Kingdom in Egypt
• increased grade in Anatolia
• 1200 BC: Trojan War; end of Bronze Age --> Iron Age 

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The Table of Contents

Prologue: the ancient Orient before circa 2000 BC

• 2000 BC: pivotal transition from stone age to bronze age
• before history: earliest stone age settlements
• Mesopotamia
• Egypt and Palestine in the 4th millenium, 3000 BC - 4000BC
• 3rd millenium: this is where the prologue ends, and we see the very first Israelites move into the area
• Mesopotamia
• Egypt and western Asia
• the ancient Orient on the eve of the Patriarchal Age 
• 1200 BC: Trojan War -- well into the future 
• 1200 BC: pivot transition from bronze age to stone age; relative decline in tin availability?

Part One: The Age of the Patriarchs

• the world of Israel's origins
• the ancient Orient: 2000- 1750 BC
• the ancient Orient: 1750 - 1550 BC
• The Patriarchs

Part Two: the Formative Period

• exodus and conquest
• the formation of the people, Israel
• late Bronze Age (before the Trojan War): the Egyptian Empire
• the Amarna Period and the end of the 18th Dynasty
• 13th century: coming up to the Trojan War; the 19th Dynasty
• Canaan in the 13th century -- coming up to the Trojan War
• Egyptian bondage and the exodus
• wandering in the wilderness -- occurring during the lead-up to the Trojan War
• the conquest of Palestine 
• the formation of the people: Israel
• early Israel: the Tribal League

Part Three: Israel under the monarchy

• from tribal confederacy to monarchy

Part Four: the monarchy -- crisis and downfall

• so, from Moses to the patriarchs to tribes to unification and monarchs
• King David: 1000 - 961 (two hundred years since the Trojan War)
• so, just prior to King David, the Greeks were going through the same stage, tribal kings
• King Solomon: united monarchy -- 961 - 922 BC
• Israel's Golden Age (compare with the Greek (Athens) Golden Age, the 5th Century)
• so:
• 10th century: Israel's Golden Age
• 5th century: Greek's (Athens') Golden Age
• divided kingdom (Israel and Judah) after death of Solomon, 922 BC
• the House of Omri, Israel's recovery, 876 BC
• Israel and Judah: mid-ninth to mid-eighth
• again, well before Greek's Golden Era
• so, again, the dates to remember
• 2000 BC: middle Bronze Age
• 1200 BC: fall of Troy; Iron Age
• 1000 BC: Israel's golden age
• 1000 - 600: monarchy 
• 500 BC: Golden Age of Greece
• Monarchy: 1000 - 600 BC, but things begin to fall apart in the 8th century
• United Monarchy: Saul, David, Solomon
• Saul: first king
• David: established Jerusalem
• Solomon: built the temple 
• Divided Israel: 900
• Northern Kingdom (Israel)
• ten tribes; capital, eventually Samaria 
• Southern Kingdom (Judah)
• two tribes, retained Jerusalem 
• reformers: Hezekiah, Josiah
• final king before Babylon exile: Zedekiah (597 - 586) 
• Eighth century: things begin to fall apart
• the Assyrian Advance, the fall of Israel and the subjugation of Judah
• Judah: a satellite of Assyria
• mid-eighth to the birth/death of Hezekiah (715 - 687)
• Old Testament prophetic period -- 850 to 400 
• pre-exilic Babylon: 
• Obadiah, Joel, Jonah, Amos, Hosea, Isaiah, Micah, Nahum, Zaphaniah, Habakkuk, Jeremiah
• Jeremiah
• the "weeping prophet" who witnessed the fall of Jerusalem  
• exilic Babylon captivity (600 - 500 BC)
• Daniel
• Ezekiel 
• post-exilic Babylon -- after return to Jerusalem
• Haggai
• Zecharia
• Malachi  (430 BC)
• Judah reigns/the end of Assyrian domination
• reign of Josiah (640 - 609)
• death of Josiah to the First Deportatioin
• Neo-Babylonian Empire / last days of Judah
• the end of the kingdom of Judah
• the developing theological emergency
• the prophets and the survival of Israel's faith

Part 5: Tragedy

• exilic periods

Part 6: Formative Period of Judaism

• the end of the Old Testament period
• from Ezra's reform to the outbreak of the Maccabean revolt

 

  

 

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Notes On The Book By Chapter

Prologue

From the ninth millennium (or even older) to the third millennium when we first see the Israelites enter the picture.

Part One
Antecedents and Beginnings
The Age Of The Patriarchs

Chapter 1
The World of Israel's Origins

 

First half of the second millennium (2000 - 1550)

Remember: 2000 -- Stone Age to Bronze Age

Father Abraham sets out from Haran to Palestine.

History of Israel cannot begin until the 13th century and later.

Canaan: a people called Israel now settled in Canaan in the 13th century, and the history of Israel legitimately begins.

Prior to this, the Israelites remember:
wandering in the desert;
prior to that, hard bondage in Egypt;
prior to that, having come from Mesopotamia

 
 

 

Genome: The Autobiography of a Species in 23 Chapters, Matt Ridley, c. 2000 -- February 15, 2026

Genome: The Autobiography of a Species in 23 Chapters, Matt Ridley, c. 2000.

Foreword:

• Craig Venter
• Human Genome Project: Jim Watson, one of three to lead the HGP
• 1999: the "moon shot"
• June 26, 2000: President Clinton and UK's Tony Blair announce that first rough draft complete
• Ridley's foreword dated July, 2000 

Introduction
how Ridley happened upon the idea for this book
chromosome 19, David Haig, "all sorts of mischievous genes"
30,000 to 80,000 genes in the human genome (wouldn't they know exactly how many now?
not precisely known, but well less than what was initially predicted
protein-coding genes: 20,000 to 25,000
total genes, including non-coding RNA genes: ~ 60,000
part of the problem: definition of a "gene."

Chapter 1: Life
life
living filaments (Charles Darwin's grandfather)
amazing how the most important non-biologic word in this book is "information" just artificial information and chatbots are all the rage
amazing serendipity: the language of life (genetic, DNA, RNA) is written linearly and in a language we can understand; a "bar code" might have worked, but imagine if the language of DNA / RNA had been analogous to a QR code.
1953: the year DNA's symmetrical structure was discovered;
1943, ten years earlier:
Francis Crick: working on the design of naval mines near Portsmouth;
James Watson, 15 years old, precocious, enrolling as an undergraduate at the University of Chicago; determined to devote his life to ornithology (bird-watching, LOL)
Maurice Wilkins: helping to design the atom bomb in the United States
Manhattan Project; University of Berkeley; focus: mass spectrometer to separate isotopes of uranium and stockpile uranium-235 for the atomic bomb
Rosalind Franklin: studying the structure of coal for the British government
to improve coal as a fuel; and, use of coal in gas masks.
Josef Mengele: his results (eugenics) are worthless for future scientists
Erwin Schrödinger: refugee from Mengele's "ilk" -- the Nazis; as a Jew forced to leave his position; in Dublin, series of lectures, on "What Is Life?"
went down a blind alley; neither quantum physics nor physics (in general) will lead to an answer
Oswald Avery: New York: 66 y/o Canadian scientist; experiment that will decisively identify DNA as the chemical manifestation of heredity
p. 15

Chapter 2: Species

Chapter 3: History

Chapter 4: Fate

Chapter 5: Environment

Chapter 6: Intelligence

Chapter 7: Instinct

X and Y: Conflict 

Chapter 8: Self-Interest

Chapter 9: Disease

Chapter 10: Stress

Chapter 11: Personality

Chapter 12: Self-Assembly

Chapter 13: Pre-Historty

Chapter 14: Immortality

Chapter 15: Sex

Chapter 16: Memory

Chapter 17: Death

Chapter 18: Cures

Chapter 19: Prevention

Chapter 20: Politics

Chapter 21: Eugenics

Chapter 21: Free Will

 

 

The Madwoman In The Attic -- Wiki Vs AI -- January 29, 2026

To get an idea how AI is different than wiki, search for The Madwoman in the Attic in wiki and the in Google Gemini.

The Quiet Americans: Four CIA Spies at the Dawn of the Cold War--a Tragedy in Three Acts, Scott Anderson; copyright, September 1, 2020 -- Posted January 24, 2026

The Quiet Americans: Four CIA Spies at the Dawn of the Cold War--a Tragedy in Three Acts, Scott Anderson (b. 1959);  copyright, September 1, 2020 by Scott Anderson. 

Act 1: This Sad And Breathless Moment

• WWII
• 1944
• Istanbul,  Turkey
• Lanning "Packy" Macfarland -- the spy; the head of the Istanbul branch of the Office of Strategic Services (OSS), America's wartime intelligence agency.
• Frank Wisner, also OSS, on the trail of Macfarland

Act 2: Hearts And Minds And Dirty Secrets

• 1948
• Czech engineer Jan Prosvic, Prague
• Johnny: an agent of the US Army's Counter Intelligence Corps, or CIC
• it had been just seven weeks since the communists seized power in Czechoslovakia
• Prosvic needed to escape to the American sector; Johnny was there to help

Act 3: Crowding The Enemy 

• 1952
• FBI director J. Edgar Hoover sent a top secret memorandum to his counterpart at the CIA, Walter Bedell Smith
• the memo concerned the CIA deputy director for plans, Frank Wisner
• questions rising again: about Wisner's wartime association with Princess Tanda Caragea of Romania. 
• began with a lengthy report out of Austria updating the situation of the exiled Princess Tanda. Caragea had led a most checkered life since the end of World War II, trading out husbands and lovers with some regularity as she flitted between various exile homes in Western Europe. Long rumored to have been a spy for a variety of intelligence agencies, both communist and non-, Tanda and her mother were now reputedly running an "intelligence shop" outof their latest exile home in the Austrian town of Dornbirn. 

The Hominin Timeline -- January 20, 2026

The timeline:

African Biomes -- Posted January 20, 2026

The biomes: 

Pathogenesis: A History of the World in Eight Plagues, Jonathan Kennedy, c. 2023.

Pathogenesis: A History of the World in Eight Plagues, Jonathan Kennedy, c. 2023. 

Chapter 7: Industrial Plagues

The first pages sound a lot like the AI revolution in the US starting around 2024. 

Nice recap of slavery, weaving, move to urban centers. The explosion -- population, industrializatio --  in the 19th century is amazing. 

With the pivot to urbanization without the sanitary conditions needed, we had tuberculosis and then cholera.

*********************
Fourth (Sixth?) Industrial Revolution

From Another Million Dollar Way Blog:

One of the best histories / summaries of the 19th century British industrial revolution is chapter 7 in Pathogenesis: A History of the World in Eight Plagues, Jonathan Kennedy, c. 2023. When you read about that industrial revolution, it sounds just like what is currently going on in the states. More on this later, perhaps. 

The world's plagues in Britain during the 19th century industrial revolution: tuberculosis and cholera. And, of the two, cholera is the much bigger story.

 

Introduction

Chapter 1: Paleolithic Plagues  

Chapter 2: Neolithic Plagues   

Chapter 3: Ancient Plagues   

Chapter 4: Medieval Plagues   

Chapter 5: Colonial Plagues   

Chapter 6: Revolutionary Plagues   

Chapter 7: Industrial Plagues -- a great chapter, the "long nineteenth century -- 1789 (French Revolution to the beginning of the First World War, 125 years later. Goes along well with recent reading on steam engine revolution; weaving; 

Chapter 8: Plagues of Poverty -- nice observations about China and sub-Saharan Africa.

Conclusion

Acknowledgments

Notes

Index 

Erie Canal

Connected the Hudson River to Lake Erie.

Completed 1825.

Circumvented Niagara Falls.

Route and lakes: 

• the route:
• origin: Cohoes, north of Troy, north of Albany.
• via: Schenectady, Utica, Syracuse, Rochester,  
• terminus: Niagara Falls / Buffalo (New York) -- Lake Erie (Lake Ontario is on north side of Niagara Falls)
• the lakes: 
• Lake Ontario, Lake Erie, Lake Huron (east side of Michigan), Lake Michigan (west side of Michigan), Lake Superior. 
• Lake Michigan is the outlier: the other four are "in line." Lake Michigan is south of the line of the other "Great Lakes." 

This is really cool.

The canal:

• from the Atlantic Ocean
• the Hudson River on the west side of NYC
• up to the capital of New York state
• several major cities grow along the canal in New York state
• ends at Buffalo, NY (co-located with Niagara Falls
• below Niagara Falls

Personal note, with relaitonship to Westfield, NJ: 

• about a 2-hour drive from Westfield, NJ, to the Poconos, northeastern Pennsylvania, north of Allentown, PA.
• from Harrisburg, PA, to Westfield, NJ, on I-78, about 2.5 hours. The route would have taken me through Allentown, just south of the Poconos.  

Pale Rider: The Spanish Flu of 1918 and How It Changed The World, Laura Spinney, c. 2017.

Pale Rider: The Spanish Flu of 1918 and How It Changed The World, Laura Spinney, c. 2017. 

Introduction: The Elephant In The Room 

Kaiser Wilhelm of Germany, November 9, 1918: À mort Guillaume! 

Same day: Guillaume Apollinaire lay on his deathbed -- the leading light of the French avant-garde movement, the man who invented the term "surrealist" and inspired such figures as Pablo Picasso and Marcel Duchamp, he had signed up to fight in 1914. Having survived a shrapnel wound to the head and the drilling of a hole into his skull, he died of Spanish flu at the age of thirty-eight, and was declared a mort pour la France."

His funeral: four days later, two days after the armistice was signed. 

Tears come to my eyes when I read that / transcribed that --  it reminds me of how much I've read over the years and how I love Europe, particularly Yorkshire. Oh, wow.

Spanish flu: 

• infected one in three people on earth;
• = 500 million human beings;
• Fauci knew that; his detractors did not;
• first recorded case, March 4, 1918 and the last sometime in March, 1920: it killed 50 - 100 million people or between 2.5 and 5 percent of the global population.
• it surpassed the First World War (17 million dead); the Second World War (60 million dead) and possibly both put together. It was the greatest tidal wave of death since the Black Death, perhaps in the whole of human history.
• broad in space; shallow in time, compared to a narrow (geographically), deep (in time, dragged on and on) war 
• most deaths occurred in the 13 weeks between mid-September and mid-December, 1918
• worldwide 

Page 9: a linear narrative won't do; what's needed is something closer to the way that women in southern Africa discuss an important even in the life of their community -- The Jewish text, the Talmud, is organized in a similar way. On each page, a colun of ancient text is surrounded by commentaries, then by commentaries on the commentaries, in ever-increasing circles, until the central idea has been woven throgh space and time, into the fabrice of communal memory. [Makes me think of Hunter S Thompson's Hell's Angels.] (There may be another reason why the African historian Terence Ranger proposed a feminised history of the Spanish flu: it was generally women who nursed the ill. They were the ones who registered the sights and sounds of the sickroom, who laid out the dead and took int he orphans. They were the link between the personal and the collective.) 

That is the theme of this book: p. 6. 

It still bothers me that Fauci was so denigrated / demeaned. 

Jinns, page 5: Jinns (or djinn/genies) are supernatural beings from Arabic/Islamic lore, created from smokeless fire, existing unseen alongside humans, possessing free will, and capable of good or evil, often depicted with powers like shapeshifting, inhabiting different realms, and influencing humanity, differing from Western "genies" by not being inherently wish-granting but by having complex roles in culture, religion, and folklore. 

It will be interesting read what Laura Spinney was writing in 2016 - 2017, years before Covid-9. 

"Part Eight, "Roscoe's Legacy," looks forward to a future battle -- the next flu pandemic --envisaging what ne weapons we will carry into it, and what is likely to be our Achilles heel. "Wow, how prescient. 

Page 8: It is often said that the First World War killed Romanticism and faith in progress, but if science facilitated inustrial-scale slaughter in the form of the war, it also failed to prevent it in the form of the Spanish flu.  

Part One: The Unwalled City

1. Coughs and Sneezes

Begins: 412 BC, Perinthus, a port city on the Sea of Marmara in what was then northern Greece. The Perinthians reported other symptoms too, sore throat, aches, difficulty swallowing, paralysis of the legs, an inability to see at night. A doctor called hippocrates jotted them all down, and the "Cough of Perinthus" became the first written description -- probably -- of influenza.  

2. The Monads of Leibniz 

Centers Of Civilization

See this post: Proto by Laura Spinney. 

AI prompt:

If western civilization as we know it (farmering, domestication, wheel, language) began on the west coast of the Black Sea (the Kurgan Theory), where were other centers of humanity at that time, around 5000 BCE?

AI Prompt: Laura Spinney's book Proto  seems to be a direct "knock-off" of David W Anthony's The Horse, The Wheel, And And Language. Is that a fair statement?

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Before All Of That