Palestine / Israel and Greece -- From Tribal Chiefs To Monarchies -- March 11, 2026

IA prompt: 

n the big scheme of things, it appears civilization in Greece and civilization in Palestine/Israel was going through the same stages of moving from tribal chiefs / tribal kings to a single monarch (or a few monarchs) from 2000 BC to 1000 BC?

IA reply: 

 

The News: A User's Manual, Alain de Botton, c. 2014.

Today: The News: A User's Manual, Alain de Botton, c. 2014.

A gift from our younger daughter many years ago.

We are addicted to the news, and governed by the news cycle:

• 0400: check the overnight headlines on Fox News, x
• 0600: check Oilprice; occasionally check pre-market
• 0800: ten to thirty minutes of Jim Cramer
• 1700: ten minutes, check the weather on network television

From Botton, p. 11:

Societies become modern, the philosopher Hegel suggested, when news replaces religion as our central source of guidance and our touchstone of authority. In the developed economies, the news now occupies a position of power at least equal to that formerly enjoyed by the faiths. 

Dispatches track the canonical hours with uncanny precision: matins have been transubstantiated into the breakfast bulletin, vespers into the evening report.  

 It is clear, the author needs to write a sequel: Agentic AI: The New Writers.

Gustave Flaubert:

The noblest promise of the news is that it will be able to alleviate ignorance, overcome prejudice and raise the intelligence of individuals and nations.

But from some quarters it has intermittently been accused of a contrary capacity, that of making us completely stupid. One of the most uncompromising versions of this charge was levelled in the mid-nineteenth century by Gustave Flaubert. Flaubert belonged to a generation that had experienced the rise of mass-circulation newspapers at first hand. 

Flaubert was appalled by what, in his estimation, these newspapers were doing to the intelligence and curiosity of his countrymen. 

Quick: what novel was Flaubert best known for? 

And then there's John Hanning Speke (1827 - 1864). Remember him? I didn't think so. 

Before our time, the only way to get to Uganda was to travel for two months by sea around the perilous Cape of Good Hope bound for Dar es Salaam, then inland for another few months through bush and desert, with every likelihood that one would never return. 

In 1859, on the eve of the US Civil War, John Hanning Speke, the first European ever to enter Uganda and the man who gave Lake Inyansha its new name, Lake Victoria, made it back to Britain and gave a lecture on his travels to an almost hysterical 800-strong crowd in the Royal Geographical Society in Kensington.  

And that's just a start. 

Van Gogh: The Life, Steve Naifeh and Gregory White Smith, Pulitzer Prize winning authors of Jackson Pollock, c. 2011

Van Gogh: The Life, Steve Naifeh and Gregory White Smith, Pulitzer Prize winning authors of Jackson Pollock, c. 2011, Random House. 

• narrative: 868 pages
• appendices: 16 pages
• acknowledgments: 4 pages
• a note on  sources: 3 pages
• selected biography: 24 pages
• index: 32 pages

"liminal" -- can't remember if I first came across this word in this book; if so, early in the book. "Occupying both sides of a boundary or threshold." 

"incandescently productive" -- p. 16. A chatbot will provide a very good interpretation.

 

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

Note: Aramaic became the dominant lingua franca of the Middle East from approximately the 7th/6th centuries BCE until the 7th century CE. It gained this status under the Neo-Assyrian Empire and was later adopted as the official diplomatic language of the Achaemenid Persian Empire (559–330 BCE), spanning from Egypt to India.

AI prompt: The Dead Sea Scrolls were first discovered in 1946 and proceeded through 1956. Interestingly enough John Bright's third edition of "A History of Israel" first published in 1959 and renewed copyright as late as 1981, FAILS to mention the Dead Sea Scrolls by name. To what extent does the absence of information from the Dead Sea Scrolls throw into question some of Bright's history of Israel?

Google Gemini: 

**************************************** 
Cocktail Trivia

 Har Megiddo: Armageddon!

 

 

 **************************************** 
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. See AI note above the W.F. Albright school of thought on the history of Israel.

Half-Price Books: $8.49. Hardcover.

Contents: seven pages. 

Narrative: 463 pages -- a thick book; huge, excellent reference book; 

Index: eleven pages.

Plates (maps):

Scripture references: 

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

The dates:

• 5500 - 3500 BC: Chalcolithic Age (chalco = copper; 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
• 15th - 13th century (early / late controversy): Egyptian bondage / exodus -- 
• probably around 200 to 400 years actual bondage; 
• most likely closer to 13th century 
• 1200 BC: Trojan War; end of Bronze Age --> Iron Age 
• 922: Solomon dies (about 300 years after Trojan War)
• 722: northern state destroyed by the Assyrians; precisely 200 years after Solomon dies 
• 597 - 538: exilic period (Babylon) 
• 538 - 331: post-exilic period 

**************************
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 (~ Rameses II?)
• the exodus most likely happened around 1220 BC -- 
• placing it about the same time as the Trojan War
• certainly at the same as Greeks and Trojans were warring 
• 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
• from Trojan War (2000) to King David (see below) 

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 
• see AI prompt;
• 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 Deportation
• 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

Written history of this period greatly lacking, particularly the fourth century, 301 - 399 BCE
these centuries will be covered quickly in this book, therefore
Biblical / Jewish history 

  

 

******************************
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

 
 

 Part 1, Chapter 2, The Patriarchs

documentation:

• p. 69, start at bottom: long list of tens of thousands of tablets, etc:
• the Mari texts fo the 18th century BC (some 25,000)
• the Cappadocian texts of the 19th century (many thousands)
• thousands of documents of the First Dynasty of Babylon (19th to 16th century) 
• the Nuzi texts of the 15th century (several thousand)
• the Alalakh tablets of the 17th and 15th centuries
• the Ras Shamra tablets (ca. 14th century  but containing much earlier material)
• the Execration Texts and other documents of Egyptian Middle Kingdom (20th to 18th century
• Ebla texts from northern Syria (above 16,000) which, although they come from a still earlier period (ca the mid-third millenium) and have not yet been published an danlsyze, willundoubtedly cast much light on the question o Israel's origins 

   

  
  

 

Part 5: Tragedy and Beyond -- the exilic and post-exilic periods

Chapter 9: Exile and Restoration -- p. 343

A. The period of exile: 587- 539 -- THE CALAMITY OF 587 -- Nebuchadnezzar's Destruction of Jerusalem

• great watershed of Israel's history: destruction of Jerusalem and subsequent exile;
• almost nothing nothing from the bible
• only historical source is the concluding portion of the Chronicler's work found in Ezra-Nehemiah, supplemented bythe Apocryphal book of I Esdras (supplies a portion of the account of Ezra)
• even with other sources, so much is missing
• amazing that the Jews recovered as a people
• northern Israelites pretty much unaffected (Samaria, Galilee, and Transjordan)
• but hardly Jewish
• shot through with pagan features
• the few northern loyal adherents of the Jerusalem cult practiced Yahwism of a highly syncretistic sort (Hosea)
• Israel's true center of gravity had temporarily shifted from the homeland

• the exiles in Babylon
• the cream of their country's political, ecclesiastical and intellectual leadership -- that's why they were selected for deportation (think of Jews being selected / separated in Germay during WWII)
• most likely, only 4,600 --- amazing 4,600!
• that number probably only adult males
• total population may have been as much as 4x or around 20,000
• pretty much re-established themselves in their own way south of Babylon
• their king Jehoiachin was received as the king of Judah and became a pensioner of the court of Babylon
• later, Jehoiachin was imprisoned for unknown reasons

 

 

 

B. The restoration of the Jewish community in Palestine

 

Chapter 10: The Jewish Community of the 5th Century

A. From the completion of the Temple to the mid-fifth century

B. The reorganization of the Jewish community under Nehemiah and Ezra  ("the scribe")

 

 

 

Part 6: Formative Period of Judaism

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

Written history of this period greatly lacking, particularly the fourth century, 301 - 399 BCE
these centuries will be covered quickly in this book, therefore

Part 6, Chapter 11: The End of the Old Testament Period

 

"The Chronicler" is a modern scholarly term for the anonymous author (or group of authors/editors) responsible for compiling the biblical books of 1 & 2 Chronicles, Ezra, and Nehemiah. 

Working in the post-exilic period (likely 400–250 BC), this author retold Israel's history from Adam to the return from Babylon, focusing specifically on the Southern Kingdom of Judah, the Davidic line, and the Temple, rather than the Northern Kingdom.

Fourth century: almost total obscurity; lack of written records.

Fifth century:

• reforms of Ezra and Nehemiah were completed;
• Artaxerxes I died (424 BCE)
• then the legitimate successor, Xerxes II (assassinated by his son, Darius II Nothus 
• Darius II (423 - 404)
• the Peloponnesian War, peace, resumption, capitulation of Athens
• affairs in Judah are obscure
• the Elephantine texts
• the fortunes of the Jewish colony in Upper Egypt in this quarter century (424-400) are brilliantsly illumined by the Elephantine texts
• Jews and their syncrestistic cult (try to absorb local practices)

Language progression -- Hebrew / Aramaic -- great discussion beginning on page 411. 

Aramaic: the franca lingua from 7th century BCE to the 7th century CE. 

Aramaic is significantly closer to Arabic than to Persian. Aramaic and Arabic are both Afroasiatic languages belonging to the Semitic family (along with Hebrew), sharing similar grammar, vocabulary, and root systems. Persian is an Indo-European language with a completely different structure and origin.

The beginning of the Hellenistic Period: reminder, the difference between Hellenic and Hellenistic

• Hellenic: Helen, Classical Greece
• Hellenistic: Alexander the Great

Accession of Darius III (336 BCE) coincided with that of Alexander of Macedonia.

• five years later, Persia was gone; 
• in five short years: rapid Hellenization of the Orient -- so portentous for all its people, not least for the Jews

Alexander the great: 336 - 323.

Takes control of Palestine, including Judah and Samaria -- how Alexander took control, it is not known -- p. 413.

After an uprising in Syria, Alexander took bitter revenge and Samaria was destroyed.

Alexander's three generals take the spoils.

Three generals but only two concern us:

• Ptolemy (Lagi): Egypt: and,
• Seleucus (I): Babylonia first and then westward into Syria and eastward across Iran; the Seleucid Empire.

The spread and impact of Hellenism, p. 416.

Greek speedily becomes the lingua franca of the civilized world.

Origin of the Pharisees and Essenes, p. 423, probably from a newly formed group, the Hassidim, who were the most opposed to Seleucid / Antiochus and preferred death than being completely subjugated -- the outbreak of the Maccabean Rebellion.-- p. 422.

The Book of Daniel: the latest of the Old Testament books -- is addressed to this situation as a dire emergency. Daniel belongs to a class of literature known as apocalyptic -- p. 423 at the bottom. More later.

Daniel is the only book in the Old Testament that falls into the apocalyptic class though similar traits are observed in certain earlier writings.

Be sure to compare traditional thought that Daniel wrote the Book of Daniel during Babylonian captivity when that was impossible; Daniel describes the Macabbean Revolt and the establishment of the second temple which occurred about 160 BCE.

"Son of man" -- p. 425 -- middle of page.

Rebellion began with Mattathias (mostly likely Hassidim) but then passed to his son Judas, called "Maccabeus" -- "the hammer."

The revolt was so successful it became known as the "Maccabean War." -- p. 426.

New Jewish altar: 164 BCE. -- p. 427.

The Jews have celebrated the Feast of Hanukkah (Dedication) ever since in commemoration of this event.

This ends to the Old Testament period.

 

Part 6: Formative Period of Judaism

Chapter 12: Judaism at the end of the Old Testament Period. 

a 

 

 

 

a 

 

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.

When reading Genome, every time something interesting pops up (in context), RNA seems to be involved. When you get right down to it, DNA is like the Queen Bee and the RNA represents worker bees. 

Gene mapping: 5p15.33.

• 5: chromosome 5
• p: short arm
• 15: region 1 - band 5
• .33: sub-band 3 -- sub-sub-band 3.

The RNA world. Wiki. 

OMIM. 

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."
• Ridley rarely states "23 chromosomes." More accurately it's 23 pairs of chromosomes - "23 and me" -- 

Chapter 1: Life -- Chromosome #1
life

 

• a linear code, not a QR code -- those the code itself is quaternary -- based on four bases (A, T, C, G or A, U, C, G
• 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
• Alan Turing; 1943, Colossus, may have been the closest to solving the mystery of life than anyone else;
• Claude Shannon, New Jersey, 1943: 
• information and entropy are opposite faces of the same coin and that both have an intimate link with energy
• the less entropy a system has, the more information it contains
• low entropy: more order, concentrated energy
• high entropy: more disorder, random energy; less energy available for useful work
• "in the beginning was the word. The word was not DNA. That came later." -- p. 16

Chapter 2: Species
Chromosome #2 is a fusion of two chromosomes 

• The reason all apes, except humans, have 24 chromosomes. The non-human apes have 24 chromosomes; humans have 23 pair because two chromosomes fused, making 24 chromosomes 23.  Genes are recipes for both anatomy and behavior.
• Great ape separation (Miocene):
• orangutan-gorilla-chimpanzee-human: 12 million years ago
  gorilla-chimpanzee-human: 10 million years ago
• chimpanzee-human: 7 million years ago

Chapter 3: History
 

• 1902:  "inborn errors of metabolism"
  Richard Dawkins: incredibly computer-like; digital; 
• binary in the sense that there are two strands
• a single boring protein -- see paragraph at bottom of page 52
• both strands have correct gene: 1 - 1
• one strand with correct gene; other not: 1 - 0
• both strands with incorrect gene: 0 - 0
• very binary
• But not exactly binary like computer code
• AI prompt: DNA: both strands have correct gene: 1 - 1 one strand with correct gene; other not: 1 - 0 both strands with incorrect gene: 0 - 0. But having said that, not exactly binary like computer code because 1 - 0 still has a phenotype like 1 - 1. Thoughts?

Chapter 4: Fate

• pitiful that genes are generally known as the disease they cause (if abnormal) 
• Huntington's chorea: gene 4
• a mutated form of the gene: Huntington's chorea -- victims die later
  a complete leak of the gene: Wolf-Hirschhorn -- victims die young 
• the gene is made up of a single word (CAG) repeated over and over and over; most folks have 5 to 35 repeats; more than 35 repeats and one gets Huntington's chorea. Nancy Wexler.

Chapter 5: Environment
pleiotropy and pluralism

• See chapter 14. 
• asthma

Chapter 6: Intelligence
intelligence, chromosome 6, and Robert Plomin

Chapter 7: Instinct
chromosome 7: behavior, instinct

Noam Chomsky
William James, Henry James

X and Y: Conflict 

• reptilian: sex determined by environmental temperature of the egg (temperature of the nest during the middle third time period)
• post-reptilian: genetic determinationsexual antagonism: leading scholar is William Rice at US-Santa Cruz 

Chapter 8: Self-Interest

• reverse transcriptase -- fascinating
• no specific reason for associating this discussion with chromosome #8; there was nothing on chromosome #8 that excited Matt Ridley

Chapter 9: Disease
ABO blood type

Chapter 10: Stress
Chromosome 10: CYP17 -- protein to convert cholesterol into cortisol, testosterone, oestradiol (estradiol)

Chapter 11: Personality
D4DR -- protein -- dopamine receptor

Chapter 12: Self-Assembly
homeobox

• almost science fiction
• genes lined up in a specific order
• absolutely fascinating

Chapter 13: Pre-History
Chromosome 13

• linguistic philology and genetic phylogeny
• genetics of genealogy
• BRCA2 -- second breast cancer gene to be discovered
• [BRCA1 is on chromosome 17]
• geography

Chapter 14: Immortality
Chromosome 14

 

• gene: TEP1: telomerase
• TEP1: contains RNA; similar looking to reverse transcriptase
• TEP1: maps to chromosome 14
• gene: TERT: does the actually transcription to repair the ends of chromosomes
• 5p15.33: TERT: maps to chromosome 5
• TERT/CLPTM1L: maps very, very specifically to 15.33 on the short arm of the chromosome 5
• highly relevant / studied in cancer research 

Chapter 15: Sex
Chromosome 15

• Prader-Willi
• Angelman 
• a missing gene on Chromosome 15 

Chapter 16: Memory
Chromosome 16

• CREB gene 

Chapter 17: Death
on the short arm of Chomosome 17

• TP53 gene: possibly the most talked-about gene since its discovery in 1979.

Chapter 18: Cures
Chromosome 18

• DPP
• colon cancer
• guides the growth of spinal nerves

 

Chapter 19: Prevention
Chromosome 19

•  Fat and triglyceride

 

Chapter 20: Politics
Chromosome 20

• PRP 

Chapter 21: Eugenics
Chromosome 21

• smallest human chromosome
• Down Syndrome

 

Chapter 22: Free Will
chromosome 22 

• 1999: first chromosome to be read from beginning to end
• originally chromosome 22 was thought to be smallest chromosome but it turns out chromosome 21 is the smallest (Down syndrome) 

 

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

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.] 

***************************
How CRISPR Works

But looks at this. Cascade mentioned in the book, p. 111. 

***************************
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

*********************************
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.

 

 *********************************
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: 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.

Later, Zhang, "I was excited to discover that animals could be a programmable system. That meant human genetic coding could be programmable as well." It was more exciting than Linux. -- p. 164.

 

 

  

 

 

 a

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. 

Author's note at the beginning:

• USSR: NKVD and KGB -- two successive acronyms for same agency, but the author refers to the agency across decades as the KGB
• US: OPC and CIA are two different agencies. 
• 1948 - 1950: OPC was regarded as quite separate from the CIA, even though OPC was housed withing the CIA;
• 1950: the two agencies began their integration with each other;
• 1952: full merger; the author will us the acronyms interchangeably after the 1952 merger with some attempt to explain why one acronym is used instead of the other;

Preface:

• author spent much of his formative years with his father (and family): South Korea, Taiwan, and Indonesia; his father was attached to the American embassy
• Korea and Taiwan were both regarded as frontline states in the Cold War;
• Indonesia was just emerging from a Cold War-inspired mass bloodletting that left t least a half-million dead;
• like everyone else in his generation, his view of the world was fundamentally shaped by the Cold War
• the first few pages: wow, so incredibly depressing; I doubt I will read much of this -- starting with the Vietnam War it seems to much was lost due to "wars" based on ideological narratives spouted by old men who simply wanted to retain power in their own countries, some by force, others by "democratic" elections. It all so seems so pointless and the best years of my life, 1964 - 1993 were overshadowed / framed / whatever you want to call it by the same Cold War.

 

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: