As someone who loved collecting vintage books, I was stoked to acquire a first American edition of Francis Galton's pioneering book “Hereditary Genius” for the bizarrely low price of $25 - most copies in good condition like this one sell for an unaffordable few hundred dollars at the minimum.
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Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development3 weeks ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.3 weeks ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
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The Site is Dead, Long Live the Site2 years ago in Catalogue of Organisms
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The Site is Dead, Long Live the Site2 years ago in Variety of Life
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Does mathematics carry human biases?4 years ago in PLEKTIX
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A New Placodont from the Late Triassic of China5 years ago in Chinleana
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Posted: July 22, 2018 at 03:03PM6 years ago in Field Notes
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Bryophyte Herbarium Survey7 years ago in Moss Plants and More
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Harnessing innate immunity to cure HIV8 years ago in Rule of 6ix
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WE MOVED!8 years ago in Games with Words
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post doc job opportunity on ribosome biochemistry!9 years ago in Protein Evolution and Other Musings
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Growing the kidney: re-blogged from Science Bitez9 years ago in The View from a Microbiologist
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Blogging Microbes- Communicating Microbiology to Netizens10 years ago in Memoirs of a Defective Brain
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The Lure of the Obscure? Guest Post by Frank Stahl12 years ago in Sex, Genes & Evolution
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Lab Rat Moving House13 years ago in Life of a Lab Rat
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Goodbye FoS, thanks for all the laughs13 years ago in Disease Prone
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Slideshow of NASA's Stardust-NExT Mission Comet Tempel 1 Flyby13 years ago in The Large Picture Blog
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in The Biology Files
Galton's "Hereditary Genius" (1871)
John Polkinghorne's "Belief in God in an Age of Science"
A book I have been enjoying recently is John Polkinghorne's "Belief in God in an Age of Science." Polkinghorne who died recently was a noted theoretical physicist who was also a theologian. Unlike Polkinghorne I am an atheist, but he makes a good case for why religion, science, poetry, art, literature should all be welcomed as sources for truth about the universe and about human beings. A quote I particularly like from it:
Tolman, “The Principles of Statistical Mechanics, Chapter 1, Part 1
Survey of classical mechanics: Generalized coordinates and momenta. Lagrangian equations. Derivation of Hamilton’s equations from Lagrangian. Poisson brackets. Hamilton as representing invariant E under time for conservative systems.
“Pull quote”: Something simple and seemingly obvious but actually deep and foundational
Some notes (not checked for typos!)
100 Desert Island Books
Finally got around to making that "100 books I would want on a desert island" list. Another title would be "100 books that I consider essential reading for *my* life": thus, this is a personal selection. I don't claim to have this list cover the most important aspects of human life or the universe, nor do I expect "famous" books to be on this list (although some of them are). The list just reflects my personal traditional interests - history and philosophy of science has the most numbers, followed by science textbooks, general history, philosophy and theology and a tiny sliver of fiction (I started reading fiction seriously quite recently). One condition in listing these books was that I should have read them in their entirety: this is true of all of them except "Gödel, Escher, Bach" which I think I am going to keep soldiering through my whole life. I am very privileged to call some of the authors here my friends.
One common thread running through most of these books is that I discovered them early, when I was in high school, college and graduate school, in most cases in either the college or university library or the British Library which was a stone's throw from where I grew up. Early impressions are often the strongest, so I keep coming back to these volumes and they keep inspiring and instructing me.
I have thousands of books on my shelf and I always find it hard to give any away. There are many others I haven't listed here which I love, but if I actually had just these 100 (110 to be precise), I wouldn't be entirely depressed (just don't tell my significant other...).
HISTORY AND PHILOSOPHY OF SCIENCE (INCLUDING BIOGRAPHY AND AUTOBIOGRAPHY)
Richard Rhodes - The Making of the Atomic Bomb
Richard Rhodes - Dark Sun: The Making of the Hydrogen Bomb
Freeman Dyson - Disturbing the Universe
Freeman Dyson - Infinite in All Directions
George Dyson - Turing’s Cathedral
George Dyson - Darwin Among the Machines
Edward Wilson - Naturalist
Edward Wilson - Consilience
James Gleick - Chaos
John Horgan - The End of Science
Robert Serber - Peace and War
Jeremy Bernstein - Hans Bethe: Prophet of Energy
Silvan Schweber - In the Shadow of the Bomb
Silvan Schweber - QED and the Men Who Made It
David Kaiser - Drawing Theories Apart
Kip Thorne - Black Holes and Time Warps
Robert Kanigel - The Man Who Knew Infinity
Robert Hoffman - The Man Who Loved Only Numbers
Robert Crease and Charles Mann - The Second Creation
Douglas Hofstadter - Gödel, Escher, Bach
Alice Kimball-Smith and Charles Weiner - Robert Oppenheimer: Letters and Recollections
Peter Galison - Image and Logic
Emanuel Derman - My Life as a Quant
Kameshwar Wali - Chandra
John Gribbin - In Search of Schrödinger’s Cat
John Casti - Paradigms Lost
John Casti - The Cambridge Quintet
John Casti - Gödel: A Life in Logic
George Johnson - Strange Beauty
Roger Penrose - The Emperor’s New Mind
Roger Penrose - The Road to Reality
Richard Dawkins - Climbing Mount Improbable
Gerald Durrell - My Family and Other Animals
Konrad Lorenz - King Solomon’s Ring
Robert Laughlin - A Different Universe
Horace Freeland Judson - The Eighth Day of Creation
Peter Michelmore - The Swift Years: The Robert Oppenheimer Story
Richard Feynman - Surely You’re Joking Mr. Feynman
Stanislaw Ulam - Adventures of a Mathematician
Laura Fermi - Atoms in the Family
Werner Heisenberg - Physics and Philosophy
Ronald Clark - Einstein
Steven Pinker - The Blank Slate
David Deutsch - The Beginning of Infinity
Steven Weinberg - Dreams of a Final Theory
J. Robert Oppenheimer - The Open Mind
Stuart Kauffman - Reinventing the Sacred
Barry Werth - The Billion Dollar Molecule
Oliver Sacks - On the Move
Carl Sagan - The Demon-Haunted World
Max Perutz - I Wish I’d Made You Angry Earlier
Jonathan Allday - Quarks, Leptons and the Big Bang
Philip Ball - H2O: A Biography of Water
Philip Ball - The Self-Made Tapestry
Alan Lightman - Einstein’s Dreams
Alan Lightman - The Accidental Universe
Brown, Pais and Pippard - Twentieth Century Physics (3 volumes)
Ed Regis - Who Got Einstein’s Office?
C. P. Snow - The Physicists
TEXTBOOKS
Ira Levine - Quantum Chemistry
Peter Atkins - Molecular Quantum Mechanics
Lubert Stryer - Biochemistry
Albert Lehninger - Biochemistry
George Simmons - Introduction to Topology and Modern Analysis
George Simmons - Differential Equations
Richard Feynman - The Feynman Lectures on Physics
David Griffiths - Introduction to Electrodynamics
John Lee - Inorganic Chemistry
Samuel Glasstone - Sourcebook on Atomic Energy
Samuel Glasstone - Thermodynamics for Chemists
Arthur Beiser - Concepts of Modern Physics
Gautam Desiraju - The Weak Hydrogen Bond
Linus Pauling - The Nature of the Chemical Bond
Linus Pauling and Edward Bright Wilson - Introduction to Quantum Mechanics
Clayden, Warren, Reeves and Wothers - Organic Chemistry
Eric Anslyn and Dennis Dougherty - Modern Physical Organic Chemistry
Wells, Wells and Huxley - The Science of Life
Goodman and Gilman - The Pharmacological Basis of Therapeutics
Jerry March - Advanced Organic Chemistry
HISTORY
Barbara Tuchman - The Guns of August
William Shirer - The Rise and Fall of the Third Reich
James Swanson - Manhunt: The 12-Day Chase for Lincoln’s Killer
David McCullough - Truman
James Scott - Against the Grain
James McPherson - Battle Cry of Freedom
Gordon Wood - Empire of Liberty
John Barry - Roger Williams and the Creation of the American Soul
Bernard Bailyn - The Ideological Origins of the American Revolution
Robert Caro - The Years of Lyndon Johnson (Vols. 1-4)
Rick Atkinson - An Army at Dawn
Will Durant - Our Oriental Heritage
Russell Shorto - The Island at the Center of the World
Nick Bunker - An Empire on the Edge
Brad Gregory - Rebel in the Ranks
Cornelius Ryan - The Longest Day
PHILOSOPHY AND THEOLOGY
Sam Harris - The End of Faith
David Edmonds and John Eidinow - Wittgenstein's Poker
Plato - The Republic
Matthew Stewart - The Courtier and the Heretic
Isaiah Berlin - The Proper Study of Mankind
Bertrand Russell - Unpopular Essays
Bertrand Russell - Why I am Not a Christian
FICTION
Vasily Grossman - Life and Fate
Haruki Murakami - What I Talk About When I Talk About Running
Cormac McCarthy - Blood Meridian
Cormac McCarthy - The Road
Isaac Asimov - Asimov’s Mysteries
Cordwainer Smith - No, No, Not Rogov! (this is a single story but it is very striking in its vividness and poetry and made a deep impression)
Leo Tolstoy - War and Peace
Fyodor Dostoevsky - Notes from the Underground
William Faulkner - As I Lay Dying
H. G. Wells - The Time Machine
Chekhov - Stories
Brenner, von Neumann and Schrödinger
Erwin Schrödinger's book, "What is Life"?, inspired many scientists like Crick, Watson and Perutz to go into molecular biology. While many of the details in the book were wrong, the book's central message that the time was ripe for a concerted attack on the structure of the genes based on physical principles strongly resonated.
However, influence and importance are two things, and unfortunately the two aren't always correlated. As Sydney Brenner recounts in detail here, the founding script for molecular biology should really have been John von Neumann's 1948 talk at Caltech as part of the Hixon Symposium, titled "The General and Logical Theory of Automata". In retrospect this talk was seminal and far-reaching. Brenner is one of the very few scientists who seems to have appreciated that von Neumann's influence on biology was greater than Schrödinger's and that von Neumann was right and Schrödinger wrong. Part of the reason was that while many biologists like Crick and Watson had read Schrödinger's "What is Life?", almost nobody had read von Neumann's "General and Logical Theory of Automata".
On change
Two weeks ago, outside a coffee shop near Los Angeles, I discovered a beautiful creature, a moth. It was lying still on the pavement and I was afraid someone might trample on it, so I gently picked it up and carried it to a clump of garden plants on the side. Before that I showed it to my 2-year-old daughter who let it walk slowly over her arm. The moth was brown and huge, almost about the size of my hand. It had the feathery antennae typical of a moth and two black eyes on the ends of its wings. It moved slowly and gradually disappeared into the protective shadow of the plants when I put it down.
Later I looked up the species on the Internet and found that it was a male Ceanothus silk moth, very prevalent in the Western United States. I found out that the reason it’s not seen very often is because the males live only for about a week or two after they take flight. During that time they don’t eat; their only purpose is to mate and die. When I read about it I realized that I had held in my hand a thing of indescribable beauty, indescribable precisely because of the briefness of its life. Then I realized that our lives are perhaps not all that long compared to the Ceanothus moth’s. Assuming that an average human lives for about 80 years, the moth’s lifespan is about 2000 times shorter than ours. But our lifespans are much shorter than those of redwood trees. Might not we appear the same way to redwood trees the way Ceanoth moths or ants appear to us, brief specks of life fluttering for an instant and then disappearing? The difference, as far as we know, is that unlike redwood trees we can consciously understand this impermanence. Our lives are no less beautiful because on a relative scale of events they are no less brief. They are brief instants between the lives of redwood trees just like redwood trees’ lives are brief instants in the intervals between the lives of stars.
I have been thinking about change recently, perhaps because it’s the standard thing to do for someone in their forties. But as a chemist I have thought about change a great deal in my career. The gist of a chemist’s work deals with the structure of molecules and their transformations into each other. The molecules can be natural or synthetic. They can be as varied as DNA, nylon, chlorophyll, rocket fuel, cement and aspirin. But what connects all of them is change. At some point in time they did not exist and came about through the union of atoms of carbon, oxygen, hydrogen, phosphorus and other elements. At some point they will cease to be and those atoms will become part of some other molecule or some other life form.
Sometimes popular culture can capture the essence of science and philosophy well. In this case, chemistry as change was captured eloquently by the character of Walter White in the TV show “Breaking Bad”. In his first lecture as a high school chemistry teacher White says,
“Chemistry is the study of matter. But I prefer to think of it as the study of change. Now, just think about this. Electrons change their energy levels. Elements, they change and combine into compounds. Well, that’s…that’s all of life, right? It’s the constant, it’s the cycle, it’s solution, dissolution, just over and over and over. It’s growth, then decay, then transformation. It is fascinating, really.”
Changes in the structure of atoms and molecules are ultimately dictated by the laws of atomic physics and the laws of thermodynamics. The second law of thermodynamics which loosely states that disorder is more likely than order guarantees that change will occur. At its root the second law is an argument from probability: there are simply many more ways for a system to be disordered than to be ordered. The miracle of life and the universe at large is that complex systems like biological systems can briefly defy the second law, assembling order from disorder, letting it persist for a few short decades during which that order can do astonishing things like make music and art and solve mathematical equations enabling it to understand where it came from. The biologist Carl Woese once gave an enduringly beautiful metaphor for life, comparing it to a child playing in a stream.
“If not machines, what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow.”
Woese’s metaphor perfectly captures both the permanence and impermanence of life. The structure is interrupted, but over time its essence persists. It changes and yet stays the same.
Although thermodynamics and Darwin’s theory of evolution help us understand how ordered structures can perform these complex actions, ultimately we don’t really understand it at the deepest level. The best illustration of our ignorance is the most complex structure in the universe – the human brain. The brain is composed of exactly the same elements as my table, my cup of coffee and the fern plant growing outside my window. Yet the same elements, when assembled together to create a fern, somehow when assembled in another, very specific way, create a 3-pound, jellylike structure that can seemingly perform miracles like writing ‘Hamlet’, finding the equations of spacetime curvature and composing the Choral Symphony. We have loose terminology like ’emergence’ to describe the unique property of consciousness that arises when human brains are assembled together from inanimate elements, but if we were to be honest as scientists, we must admit that we don’t understand how exactly that happens. The ultimate example of change that makes the essence of us as humans possible is still an enduring mystery. Will we ever solve that mystery? Even some of the smartest scientists on the planet, like the theoretical physicist Edward Witten, think we may not. As Witten puts it,
“I think consciousness will remain a mystery. Yes, that’s what I tend to believe. I tend to think that the workings of the conscious brain will be elucidated to a large extent. Biologists and perhaps physicists will understand much better how the brain works. But why something that we call consciousness goes with those workings, I think that will remain mysterious. I have a much easier time imagining how we understand the Big Bang than I have imagining how we can understand consciousness…”
In other words, what Witten is saying is that even if someday we may understand the how and the what of consciousness, we may never understand the why. One of the biggest examples of change in the history of the universe may well remain hidden behind a veil.
I think about change a lot not just because I am a chemist but because I am a parent. Sometimes it feels like our daughter who is now two and a half years old has changed more in that short time than a caterpillar changes into a butterfly. Her language, reasoning, social and motor skills have undergone an amazing change since she was born. And this is, of course, a change that is observed by every parent: children change an incredible amount during their first few years. Some of that change can be guided by parents, but other change is genetic as well as idiosyncratic and unpredictable. Just like you can coax simple arrangements of atoms into certain compounds but not others, as a parent you have to make peace with the fact that you will be able to mold your child’s temperament, personality and trajectory in life to a certain extent but not beyond that. As the old alchemists figured out, you cannot change mercury into gold or gold into mercury no matter how hard you try. And that’s ultimately for the better because, just like the diversity of elements, we then get a diversity of novel and surprising life trajectories for our children.
Children undergo change but they are are also often the best instruments for causing it. Recently I finished reading Octavia Butler’s remarkable “Parable of the Sower” which is set in a 2024 California that is racked by violence and arson by desperate, homeless people who break into gated communities and burn, murder and rape. The protagonist of the story is a clear-eyed, determined 18-year-old named Lauren Olamina who, after her family is murdered, starts out by herself with the goal of starting a new religion called Earthseed amidst the madness surrounding her. Earthseed sees God as a changeable being and embraces change as the essence of living. Lauren thinks that in a world where people have to deal with unpredictable, seismic, sometimes violent change, a religion that makes the very nature of change a blueprint for God’s work can not just survive but thrive. For an atheist like myself, Earthseed seems as good a religion as any for us to believe in if we want to thrive in an uncertain world. Butler’s story tells us that just like they always have, our children exist to fix the problems our generation has created.
Change permeates the largest scales of the universe as much as it does ourselves, our children and our bodies and brains. One of the most philosophically shattering experiences in the development of science was the realization by Galileo, Brahe, Newton and others that the perfect, crystalline, quiet universe of Aristotle and other ancients was in fact a dynamic, violent universe. In the mid 20th century, astrophysicists worked out that stars go through a life sequence much like we do. When they are born they furiously burn hydrogen into helium and form the lighter elements. As they age they can go in one of several directions. Stars the size of the sun will first blow up into red giants and then quietly settle into the life of a white dwarf. But stars much more massive than the sun can turn into supernovae and black holes, ending their lives in a cosmic show of spectacular explosion or fiery gravitational contraction.
When our sun turns into a red giant, about 6 billion years from now, its outer shell will expand and embrace the orbits of Mercury, Venus and Earth. There is no reason to believe that those planets will survive that encounter. By that time the human race would either be extinct or would have migrated to other star systems; the worst thing that it could do would be to stay put. Even after that we will not escape change. The science of eschatology, the study of the ultimate fate of the universe, has mapped out many changes that will be unstoppable in the far future. At some point the Andromeda galaxy will collide with our Milky Way galaxy. Eventually the stars in the universe will run out of fuel and cease to shine; the universe will become a quieter and darker place. Soon it will only contain black holes and at a further point even black holes will evaporate through the process of Hawking radiation. And way beyond that, the laws of quantum mechanics will ensure that the proton, usually considered a stable particle, will decay. Matter as we know it will dissolve into nothingness. The accelerated expansion of our universe will ensure that most of these processes will inevitably take place. The exact fate of the universe is too uncertain to predict beyond these unimaginable gulfs of time, but there is little doubt that the universe will be profoundly different from what it is now and what it has been before.
The elements from which my body and brain are composed will one day be given back to the universe (I like to think that they will perhaps become part of a redwood tree). That fact does not fill me with a feeling of dread or sadness but instead feels me with peace, joy and gratitude. The ultimate death of the universe described above causes similar feelings to arise. Sometimes I like to sit back, close my eyes and imagine a peaceful, lifeless universe, the galaxies receding past the cosmic horizons, the occasional supernova going off. The carbon, oxygen, nitrogen and other heavier elements in my body came from such supernova explosions a long time ago; the hydrogen came from the Big Bang. Those are astounding facts that science has discovered in the last few decades. Of all the things that could have happened to those elements forged in the furnace of a far off supernova, what were the chances that they would assemble into the exact specific arrangements that would be me? While we understand now how that happens, it could well have gone countless other ways. I feel privileged to exist as part of that brief interval between supernova explosions, to be able to understand, in my own modest way, the workings of our universe. To be a tiny part of the change that makes the universe what it is.
Book Review: Chip War: The Fight for the World's Most Critical Technology
In the 19th century it was coal and steel, in the 20th century it was oil and gas, what will it be in the 21st century? The answer, according to Chris Miller in this lively and sweeping book, is semiconductor chips.