Cavalcade of Mammals

Nanobots are miniature molecular machines. So far they are just an idea as no one knows how to design or build one. But there is discussion of them, and certain properties be considered. For example, how big is a nanobot?

A ‘simple’, dumb miniature machine could be quite small, for example an antibody attached to a viral-like particle that binds to particular cells, get absorbed by the cell and opens to release the DNA into the cell. But that’s not a very interesting machine, the really interesting nanobots are miniature robots with sensors, computer logic to make decisions, and hands to grab or manipulate things.

So what’s the minimum size for a smart nanobot? It has 100,000 bytes of memory, 1,000,000 bits, and 10 atoms/bit. Let’s figure the same number of atoms for the computer logic. Add an equivalent number for energy storage and generation, structure, sensors, and manipulators. Thirty million atoms in total.

If it is mostly carbon, atoms will be 1 Å apart. Assume a spherical shape, and look at protein structures to estimate packing of atoms in a compact structure. From this, the core of the nanobot will be an estimated 1000 Å or roughly 100 nm.

An E. coli is roughly 1 &#181m long, so a nanabot would be a about a 1/10 the size of a bacteria. This is small, about the size of an average virus particle, small enough to exist inside cells. A nanobot is large enough to be recognized and engulfed by immune cells, and to need a specific mechanism to enter cells.

I’ve always wondered how sea level is measured so accurately. Global sea level changes are measured to high accuracy. The global yearly sea rise averaged over many years is measured to a fraction of a mm. There are two ways sea level is measured. The old system uses tidal gauges, and satellites were launched in 1992 (TOPEX/Poseidon) and 2005 (Jason-1).

Here’s a page explaining how the tidal gauges work: Univ. of Colorado. Ah, stilling well!

I’m always looking for good books, so I sorted through other people’s lists of 10 most influential books and consolidated them. The notes I included are mostly notes from the original lists.

Philosophy & Political philosophy
The Federalist Papers, by Alexander Hamilton, James Madison, and John Jay.
Democracy in America by Alexis de Tocqueville.
The Open Society and its Enemies by Karl Popper.
John Stuart Mill, Autobiography. (This got me thinking about how one’s ideas change, and should change, over the course of a lifetime. Plus Mill is a brilliant thinker and writer more generally.)
Bertrand Russell (my addition, not on anyone’s list)

Plato, Dialogues.
Thucydides, History of the Peloponnesian War.
The Meditations by Marcus Aurelius (Hay’s translation).
Letters from a Stoic by Seneca.
Niccolò Machiavell’s The Prince.
The Discovery and Conquest of Mexico by Bernal Diaz del Castillo.
On War by Carl Von Clausewitz.
more George Orwell–Homage to Catalonia, The Road to Wigan Pier.
Churchill’s history of the Second World War.
The Art of Memory by Frances A. Yates. (History of an ancient mental technique for orators, up to its graphical importance for pre-science in the early modern period.)

History
Battle Cry Of Freedom by James MacPherson.
Lincoln at Gettysburg: The Words that Remade America by Garry Wills. (Presented a way of thinking about “liberalism” and “conservatism” in the American context that I don’t think anyone has yet been able to refute. More than that, it’s also a tour de force, linking the history of America, the nature of rhetoric, and the meaning of democracy and constitutionalism together into a single, succinct argument.)

The Presence of the Past: Essays on the State and the Constitution by Sheldon S. Wolin. (Like a deeply planted time bomb, this book’s various observations and arguments (mostly about Tocqueville and the Federalists and Anti-Federalists) kept coming to me, suddenly making sense, while thinking about community or politics or government or religion or philosophy or just about anything else, years and years after my advisor first recommended it to me.)

The Power Broker by Robert Caro.
Fear and Loathing: On the Campaign Trail ’72, by Hunter S. Thompson.
Before the Storm, by Rick Perlstein. (The rise of Barry Goldwater and movement conservatism in the early 60s).

Economics
Wealth of Nations by Adam Smith.
The Communist Manifesto by Karl Marx.
The General Theory of Employment, Interest, and Money by John Maynard Keynes. (Keynes is one of the greatest thinkers of economics and there are new ideas on virtually every page.)
Micromotives and Macrobehavior by Thomas Schelling.
The Undercover Economist by Tim Harford.
The Incredible Bread Machine, by Susan Love Brown, et.al.

A Farewell to Alms by Gregory Clark.
Economics in One Lesson by Henry Hazlitt.
The Long Tail by Chris Anderson. (There is not much that needs to be said about this book other than it defines current net economics. There’s the head of the tail which is the stuff you find in Borders, and the tail, which is the infinite inventory on Amazon.)

Modern
How to Lie with Statistics by Darrell Huff.
Mathematics in the Modern World: Readings from Scientific American by Morris Kline
Visualizing Data by William S. Cleveland. (This book presents a set of graphical methods for displaying data. Does it ever. Cleveland shows you how it’s done in practice and wrote the software that lets you code it yourself.)

The Quark and the Jaguar by Murray Gell-Mann. (QM and modern physics).

Why Buildings Fall Down by Matthys Levy and Mario Salvadori.
How Buildings Learn by Stewart Brand.
Death and Life of Great American Cities by Jane Jacobs.

Rebel Without a Crew: Or How a 23-Year-Old Filmmaker With $7,000 Became a Hollywood Player by Robert Rodriguez.

Code Complete by Steve McConnell.
The Cathedral and the Bazaar: Musings on Linux and Open Source by Eric S Raymond. (me–I might have already read this, and certainly absorbed the ideas.)

Vagabonding: An Uncommon Guide to the Art of Long-Term World Travel by Rolf Potts.

Life’s Devices by Steven Vogel. (This is a book about biomechanics but also, and more importantly, a terrific introduction to what is means to do science.)
Ravens in Winter by Bernd Heinrich. (Heinrich follows ravens around in Vermont, trying to figure out why the hell they would share carrion they find. I’d recommend this book to anyone.)
The Chimpanzees of Gombe, In the Shadow of Man, by Jane Goodall.
Plagues and Peoples by William McNeill.

Boyd: The Fight Pilot who Changed the Art of War by Robert Coram.

Silent Spring by Rachel Carson. (me–Heard enough about it, and it’s been absorbed into the culture, that it doesn’t feel urgent to read it. But seeing the details and situation when she wrote would be interesting.)

The Omnivore’s Dilemma by Michael Pollan.
Hell’s Angels by Hunter S. Thompson.

Biography
My Bondage and My Freedom by Frederick Douglass.
The Autobiography of Malcolm X by Malcolm X and Alex Haley.
Alexander Hamilton by Ron Chernow.
Thomas Moody by Michael Davitt (Biography of an Irish patriot).

Business/Self-help
The Four Hour Workweek by Tim Ferriss.
The Ropes to Skip and the Ropes to Know by Richard Ritti and G. Ray Funkhouser.
How To Win Friends And Influence People by Dale Carnegie. (It’s a timeless classic–highly recommend it.)

Fiction
One Thousand and One Nights.
Don Quixote by Miguel de Cervantes.
Dracula by Bram Stoker.
Jonathan Swift. (me–Not sure which book.)
Leaves of Grass by Walt Whitman.
The Big Sleep by Raymond Chandler.
Mother Night by Kurt Vonnegut.
The Handmaid’s Tale by Margaret Atwood.
The Caves of Steel by Isaac Asimov.

Other
The Dark Knight Returns by Frank Miller.
The Watchmen by Alan Moore and Dave Gibbons.
The Sandman series by Neil Gaiman.

Not mentioned but on my to read list:
A Vindication of the Rights of Women by Mary Wollstonecraft (1792).

Studs Terkel, The Good War: An Oral History of World War Two (Detailed ordinary peoples’ accounts of the country’s involvement in World War II). Hard Times: An Oral History of the Great Depression, Working: People Talk About What They Do All Day and How They Feel About What They Do.
The New Science of Strong Materials: Or why you don’t fall through the floor by J E Gordon.
War Before Civilization: The Myth of the Peaceful Savage by Lawrence H. Keeley.
Houdini!!! by Ken Silverman.
Military Blunders: The how and why of military failure by Saul David.

Skipped on most/all lists:
Dewey, anarchists, science, Renaissance writers, biographies, Malthus, The Origin of Species by Charles Darwin.

On multiple lists but unappealing to me:
Plutarch
philosophy
religious texts
Analects of Confucius
Thomas Aquinas
Rene Descartes
Edmund Burke
Sigmund Freud (me–a pseudoscientific fraud interesting today mainly as a historical and curtural oddity).
The History of the Decline and Fall of the Roman Empire by Edward Gibbon.
Leo Tolstoy
Dostoyevky
Charles Dickens
Ayn Rand
Milton and Rose Friedman, Free to Choose.
The Feminine Mystique by Betty Friedan.
The Structure of Scientific Revolution by Thomas Kuhn. (me–Heard the thumbnail version).
Fight Club by Chuck Palahniuk.
Animal Liberation by Peter Singer.
Joseph Campbell, The Power of Myth (me–Heard the thumbnail version, suffered through all six Star Wars movies).
Richard Herrnstein and Charles Murray’s The Bell Curve. (me–Instead I read Gould’s The Mismeasure of Man).
The Origin of Consciousness in the Breakdown of the Bicameral Mind, by Julian Jaynes. (me–wrong).
everything else written before 1800.

Update:
(5/10) How to Solve It (1945) by George Pólya. Mathematician explains how to solve problems.

Here’s my list, not ten but as short as I could make it. It’s roughly in the order I read them. Ten books gets me through high school but doesn’t include all the books that had a big influence on me.

My list:
A kid’s biography of Thomas Edison. Sparked my interest in invention.

Commodore 64: Programmer’s Reference Guide. I taught myself programming on a VIC-20 and then a Commodore 64, then picked it back up again in graduate school to analyze mouse genomic DNA.

The Boy Scout Handbook. Learned lots of useful things!

Moon is a Harsh Mistress, Stranger in a Strange Land by Robert A. Heinlein. I became a space nut by reading science fiction. Heinlein was an early favorite.

The Best and the Brightest by David Halberstam. First big book on government I read.

A stack of old Scientific American magazines. I was given a few feet of Scientific American magazines and devoured the science review articles. This is where I found out biology was much more interesting than what was covered in high school. This is also where I discovered Martin Gardner’s Mathematical Games column and from that fractals and many more wonderful things.

Sleepless Nights in the Procrustean Bed, The Glass Teat, and short story collections by Harlan Ellison. I started reading Ellison’s short stories, then found his movie reviews in the Magazine of Fantasy and Science Fiction, then found his essays. He’s a master essayist.

Slaughterhouse-Five by Kurt Vonnegut. Eye opening.

Broca’s Brain, The Dragons of Eden, The Demon-Haunted World: Science as a Candle in the Dark by Carl Sagan. Taught me all sorts of science and started my love of general science books.

G̦del, Escher, Bach РAn Eternal Golden Braid by Douglas Hofstadter. A stunning book about math, music, recursion, and cognition.

The Fractal Geometry of Nature by Benoit B. Mandelbrot. Spent a summer reading this book. I wasn’t quite up to the math, but still it was fascinating.

Chaos by James Gleick. Fractals, chaos, deterministic but unpredictable systems, like weather. Good ideas, lots of interesting examples.

Science: Good, Bad, and Bogus by Martin Gardner. Pseudoscience and skepticism.

Extraordinary Popular Delusions and the Madness of Crowds by Charles MacKay (1841). Read this early on in college. The tulip madness, the South Sea Bubble, and other incredible episodes in the history of human folly.

Other books, ones that didn’t make the top 10 or that I read later.

The Lord of the Rings by J. R. R. Tolkien.

A Connecticut Yankee in King Arthur’s Court by Mark Twain. (interestingly, the technology an everyman Connecticut Yankee knows was all new to me).

The Crystal Cave by Mary Stewart. (the first book of her Arthurian legend series. Loved me some Arthur)

Neuromancer by Wiliam Gibson (sf, cyberspace!)

Knotted Doughnuts and Other Mathematical Entertainments, The Ambidextrous Universe: Mirror Asymmetry and Time-Reversed Worlds, Mathematical Circus by Martin Gardner. (recreational mathematics, puzzles, and oddities, mainly from his Mathematical Games column in Scientific American).

The Foundation Trilogy by Isaac Asimov. (sf, sociology as a super-science)

Animal Farm by George Orwell. (this rather than 1984, hearing so much about 1984 before I read it weakened the impact of 1984).

The Hitchhiker’s Guide to the Galaxy by Douglas Adams. (sf, funny, absurdist British sf)

Dune by Frank Herbert. (sf, a great tale integrating great sweeping ideas).

Fahrenheit 451 by Ray Bradbury.

Far Frontiers edited by Jerry Pournelle and Jim Baen. (I’ll let this stand as a representative of the non-fiction I read about prospects and plans for space development in books and in Analog. Read G. Harry Stine, Pournelle, Bova, Brin, Clark. “The Earth is the cradle of the mind, but we cannot live forever in a cradle”. –Konstantin E. Tsiolkovsky, Kaluga, 1911).

Shakespeare’s plays. (I thought in iambic pentameter for a few weeks in high school. A fun way to rewire your brain!).

Ender’s Game by Orson Scott Card. (sf)

Bruce Sterling, The Hacker Crackdown: Law and Disorder on the Electronic Frontier. (the history of computer hacking and the government’s alternately clueless and thugish reactions to it).

The Best of the Nebulas (sf, the best of the best).

Surely You’re Joking, Mr Feynman! by Richard Feynman

A People’s History of the United States by Howard Zinn. (an eye opener for me).

Bully for Brontosaurus by Stephen Jay Gould. (Gould’s rich essays on biology and natural history are amazing. I think this is the collection I started with).

Churchill’s Complex Variables and Applications (complex numbers are strange and wonderful).

The News That Didn’t Make the News and Why: the Project Censored Yearbook by Carl Jensen & Project Censored. (strangely enough, not all the news is fit for print).

Manufacturing Consent: The Political Economy of the Mass Media (with Edward Herman), Deterring Democracy by Noam Chomsky. (a different view of American government policy and actions, densely written and exhaustively sourced).

The Aquatic Ape by Elaine Morgan (read this in grad school, the thesis is that humans evolved through a semi-aquatic intermediate hominid. This turns out not to be true, but I found the idea of using biological features as evidence for human evolution very interesting. I grew up during the ‘man the upright walker’ period in human paleoanthropology).

The Mismeasure of Man by Stephen Jay Gould (scientific racism, history and arguments against, read this instead of the Bell Curve).

Douglas North and Roger Miller, Abortion, Baseball and Weed. (counterintuitive economics)

Anne Rice, Interview With the Vampire. (started me reading fantasy again)

The Mythical Man-Month by Fred Brooks. (software engineering and personnel management on large software projects)

Guns, Germs and Steel by Jared Diamond. (a sweeping explanation of the large-scale pattern of human history. Not proven, but a great approach to the question).

The Voyage of the Beagle by Charles Darwin. (incredible travelogue of his around the world voyage)

Tyler Cowen at the blog Marginal Revolution posted a list of the 10 most influential books for him. Other people, mostly economists, followed up with their lists.

Cowen is an economist, and many of the early linkers were economists as well. The lists contained many economics books, of course. I was surprised at how many philosophy and political philosophy books appeared on the economists’ lists. And how few–none on most lists–science books of any field or any modern books of ideas appear. From the lists of books, their minds were untouched by the ideas and incredible gains in understanding the world that flipped society upside down several times in the 20th century.

To jump to a wild conclusion, this may be one of the reasons the field of economics is so screwed up. Economists come to field field by way of philosophy and think ideas mixed with some mathematical modeling leads to discoveries about how real societies work. And these are people without any practical knowledge–no science, no engineering, no business experience, no government experience. Not even science at an undergrad level, or a widely read enthusiast. They think philosophy contains the essential ideas, and all the more applied fields are derivative, and so they have set their economics on a sound foundation.

Also, Ayn Rand is an important influence on many, which is not surprising but good for a few giggles. Also, Fight Club by Chuck Palahniuk is gaining as the influential book for libertarian minded young men. Watch out Ayn!

This is odd and sort of funny. And a little old. In Afghanistan, the US military has been conducting an offensive in Helmand Province. Apparently the propaganda push got a head of the facts. The official accounts had the US battling to clear the Taliban out of the Marjeh, a moderate size city of 80,000 to 125,000 people.

I ran across articles saying that the city didn’t exist. BAGnewsNotes had a picture of an isolated farm in Marjah, ostensibly showing that the place wasn’t a city.

BAGnewsNotes linked to a story on the truthout.com site. But this article didn’t have any pictures at all. Now this a story that really needs a picture, and there are easy sources, Google Maps for one. Here’s the farming village of Marjeh (or Marjah, or Marja, the name can be written different ways in english):

Just a collection of farms, no city at all.

Zooming out further shows that it is the biggest town in the area, so it makes sense that news of a big military operation in the area would talk about it happening in Marjeh, but it’s certainly no city.

Mars Underground by William_Hartmann. The book was a good read. It is set on Mars, at a time when thousands of people are on the planet, second stage exploration. People are beginning to think about colonization. The book is a mystery, with an administrator, Carter, his friend the resident artist, Philippe, and a newly arrived reporter, Annie Pohaku, investigating the disappearance of a Stafford, an exobiologist who’s one of the longest serving research scientists and explorers on Mars. Stafford had discovered traces indicating microbial life on Mars billions of years in the past.

The book starts very well, but then seems to stall out in the middle. The plot is uncomplicated and feels too bare. The characterization of the protagonist, Carter, is lacking. The description of Mars and the bases on the planet and Phobos are well done.

Composite electron micrograph of the flagellum basal body and hook, produced by rotational averaging (Francis et al., 1994).

Stephen M. Barr has an article in First Things, The End of Intelligent Design?. Unfortunately, Barr is looking to rescue something from intelligent design (ID) so his criticisms are muted. His main interest is whether ID has been useful in advancing religion and theology. In a faux even-handed approach he criticizes ID for not proving it’s claims but then tosses in criticism of scientists for unspecified excesses. He also tries to win favor with a religious audience by claiming that “the ID movement has been treated atrociously and that it has been lied about by many scientists”, a judgment he doesn’t substantiate.

The readership of First Things is a strange group, many of the comments go off in philosophical directions but no one is talks about the central issue–whether ID is true or false. Is there good evidence for it? Is it likely to be true? Could it be true? Or is it known to be false?

Barr’s article starts well, it is true that there’s “not a single phenomenon that we understand better today” through ID. To restate that, there is no evidence at all for ID and that is the reason ID has been dismissed by biologists.

When the idea that certain biological structures are “irreducibly complex” was proposed several examples were given: the bacterial flagellum, the immune system, the blood clotting cascade, the vertebrate eye, the Krebs cycle, etc. In fact, biologists have evolutionary models and physical evidence of how each of these things has evolved. No “irreducibly complex” structures were proposed and then proven to be so. In truth, none of the proposed examples are even open questions, things that puzzle biologists that could possibly be shown to be “irreducibly complex” in the future.

And the case for ID is really worse that what I’ve described. It’s not that ID theorists proposed structures that biologists didn’t have good evolutionary models for, structures that could have turned out to be “irreducibly complex”. When these examples were given, there was already published research explaining the evolutionary origins of each example. For example, biologists reviewing Behe’s book were able to look up and reference the research discounting his examples. No better “irreducibly complex” examples have come to light since then.

Converting a single file:

faad -o - file.m4a | lame - file.mp3


Bash script for converting multiple files:

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#!/bin/bash

for i in *.m4a; do
    echo "Converting: ${i%.m4a}.mp3"
    faad -o - "$i" | lame - "${i%.m4a}.mp3"
done
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Copied directly from the Calculated Risk blog, but too good to pass up!

The Mortgage Bankers Association … fell victim to the collapse of the market and sold its $90 million headquarters in downtown Washington on Friday for $41 million.
…
The Mortgage Bankers Association moved into the building in 2008 just as the real estate market was crashing …

Definition of irony…