Bookmarked Selective pressures on genomes in molecular evolution by Charles Ofria, Christoph Adami, Travis C. Collier (arXiv.org, 15 Jan 2003)
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.
To be published in J. theor. Biology 222 (2003) 477-483
DOI: 10.1016/S0022-5193(03)00062-6

Synthetic Biology’s Hunt for the Genetic Transistor | IEEE Spectrum

Read Synthetic Biology's Hunt for the Genetic Transistor (spectrum.ieee.org)
How genetic circuits will unlock the true potential of bioengineering 
This is a great short article on bioengineering and synthetic biology written for the layperson. It’s also one of the best crash courses I’ve read on genetics in a while.

Reply to Mythbusters | The Sheridan Libraries Blog

Replied to Mythbusters by Margaret Burri (The Sheridan Libraries Blog)

Ever walk past a campus tour and wonder how much of it is true? While most of it is, and we love the plug for “your own librarian,” there are a couple of long-standing inaccuracies that we’d like to put to rest:

“No building on campus can be taller than Gilman Hall because that’s what’s in Gilman’s will.” Wrong. Decisions about buildings’ heights, including that of the library, have been made based on the scale of the campus and the architecture of Homewood House. Stand at the middle of the lower part of the beach, and look through the glass windows of MSEL. Notice anything? That’s right–Gilman Hall is beautifully framed in the center.

Gilman died in 1908, and mentioned nothing in his will about buildings. In 1912, the Trustees began to plan a new “Academic Building.” This was completed in 1915, and formally named after Gilman in 1917.

“The library sank three inches when they put the 2.5 million books in it in 1964.” Wrong again. I often wonder how many parents, when they hear this, would like to end the tour right there. First, there weren’t 2.5 million books in 1964; we didn’t reach that milestone until the 1990s. When the new library opened on November 15, 1964, there were just over 1.1 million books on the shelves.

Second, no sinking occurred. The weight of the thousands of shelves and books had been calculated into the plan, and the foundation was, and remains, more than adequate to hold the weight.

One thing that is true about the library is that when the hole was dug, an underground stream was discovered, and had to be rerouted before work on the building could continue. John Berthel, the library director at the time, poses in the recently dug hole with some of the books that would later grace the shelves.

Did Winston go down into the new hole for the BLC while they were digging and take a similar photo with a pile of books? The two photos would make great “book ends!”

Dictionary: A Malevolent Literary Device

Ambrose Bierce (), American editorialist, journalist, short story writer, fabulist, and satirist
in The Devil’s Dictionary

 

IPTV primer: an overview of the fusion of TV and the Internet | Ars Technica

Read IPTV primer: an overview of the fusion of TV and the Internet by Iljitsch Van Beijnum (Ars Technica)

Profound as it may be, the Internet revolution still pales in comparison to that earlier revolution that first brought screens in millions of homes: the TV revolution. Americans still spend more of their non-sleep, non-work time on watching TV than on any other activity. And now the immovable object (the couch potato) and the irresistible force (the business-model destroying Internet) are colliding.

For decades, the limitations of technology only allowed viewers to watch TV programs as they were broadcast. Although limiting, this way of watching TV has the benefit of simplicity: the viewer only has to turn on the set and select a channel. They then get to see what was deemed broadcast-worthy at that particular time. This is the exact opposite of the Web, where users type a search query or click a link and get their content whenever they want. Unsurprisingly, TV over the Internet, a combination that adds Web-like instant gratification to the TV experience, has seen an enormous growth in popularity since broadband became fast enough to deliver decent quality video. So is the Internet going to wreck TV, or is TV going to wreck the Internet? Arguments can certainly be made either way.

This brief overview of IPTV is about as concise as they get. It’s recommended for entertainment executives who need to get caught up on the space as well as for people who are contemplating “cutting the cable cord.” There’s still a lot of improvement the area can use…

Bill Davenhall at TEDMED 2009 on Geomedicine: How Your Environment May Affect Your Health

Watched TEDMED 2009 on Geomedicine: How Your Environment May Affect Your Health by Bill Davenhall from TEDMED
Does where you live have an impact on your overhall health? Bill Davenhall believes that the location of our homes is critical to our medical history.
This is a great thing to think about the next time your doctor asks for your medical history. Perhaps with more data and a better visualization of it, it may bring home the messages of pollution and global warming.

‘The Information’ by James Gleick – Book Review by Janet Maslin | New York Times

Reposted ‘The Information’ by James Gleick - Review (nytimes.com)
“The Information,” by James Gleick, is to the nature, history and significance of data what the beach is to sand.
This book is assuredly going to have to skip up to the top of my current reading list.

“The Information” is so ambitious, illuminating and sexily theoretical that it will amount to aspirational reading for many of those who have the mettle to tackle it. Don’t make the mistake of reading it quickly. Imagine luxuriating on a Wi-Fi-equipped desert island with Mr. Gleick’s book, a search engine and no distractions. “The Information” is to the nature, history and significance of data what the beach is to sand.

In this relaxed setting, take the time to differentiate among the Brownian (motion), Bodleian (library) and Boolean (logic) while following Mr. Gleick’s version of what Einstein called “spukhafte Fernwirkung,” or “spooky action at a distance.” Einstein wasn’t precise about what this meant, and Mr. Gleick isn’t always precise either. His ambitions for this book are diffuse and far flung, to the point where providing a thumbnail description of “The Information” is impossible.

So this book’s prologue is its most slippery section. It does not exactly outline a unifying thesis. Instead it hints at the amalgam of logic, philosophy, linguistics, research, appraisal and anecdotal wisdom that will follow. If Mr. Gleick has one overriding goal it is to provide an animated history of scientific progress, specifically the progress of the technology that allows information to be recorded, transmitted and analyzed. This study’s range extends from communication by drumbeat to cognitive assault by e-mail.

As an illustration of Mr. Gleick’s versatility, consider what he has to say about the telegraph. He describes the mechanical key that made telegraphic transmission possible; the compression of language that this new medium encouraged; that it literally was a medium, a midway point between fully verbal messages and coded ones; the damaging effect its forced brevity had on civility; the confusion it created as to what a message actually was (could a mother send her son a dish of sauerkraut?) and the new conceptual thinking that it helped implement. The weather, which had been understood on a place-by-place basis, was suddenly much more than a collection of local events.

Beyond all this Mr. Gleick’s telegraph chapter, titled “A Nervous System for the Earth,” finds time to consider the kind of binary code that began to make sense in the telegraph era. It examines the way letters came to treated like numbers, the way systems of ciphers emerged. It cites the various uses to which ciphers might be put by businessmen, governments or fiction writers (Lewis Carroll, Jules Verne and Edgar Allan Poe). Most of all it shows how this phase of communication anticipated the immense complexities of our own information age.

Although “The Information” unfolds in a roughly chronological way, Mr. Gleick is no slave to linearity. He freely embarks on colorful digressions. Some are included just for the sake of introducing the great eccentrics whose seemingly marginal inventions would prove to be prophetic. Like Richard Holmes’s “Age of Wonder” this book invests scientists with big, eccentric personalities. Augusta Ada Lovelace, the daughter of Lord Byron, may have been spectacularly arrogant about what she called “my immense reasoning faculties,” claiming that her brain was “something more than merely mortal.” But her contribution to the writing of algorithms can, in the right geeky circles, be mentioned in the same breath as her father’s contribution to poetry.

The segments of “The Information” vary in levels of difficulty. Grappling with entropy, randomness and quantum teleportation is the price of enjoying Mr. Gleick’s simple, entertaining riffs on the Oxford English Dictionary’s methodology, which has yielded 30-odd spellings of “mackerel” and an enchantingly tongue-tied definition of “bada-bing” and on the cyber-battles waged via Wikipedia. (As he notes, there are people who have bothered to fight over Wikipedia’s use of the word “cute” to accompany a picture of a young polar bear.) That Amazon boasts of being able to download a book called “Data Smog” in less than a minute does not escape his keen sense of the absurd.

As it traces our route to information overload, “The Information” pays tribute to the places that made it possible. He cites and honors the great cogitation hives of yore. In addition to the Institute for Advanced Study in Princeton, N.J., the Mount Rushmore of theoretical science, he acknowledges the achievements of corporate facilities like Bell Labs and I.B.M.’s Watson Research Center in the halcyon days when many innovations had not found practical applications and progress was its own reward.

“The Information” also lauds the heroics of mathematicians, physicists and computer pioneers like Claude Shannon, who is revered in the computer-science realm for his information theory but not yet treated as a subject for full-length, mainstream biography. Mr. Shannon’s interest in circuitry using “if … then” choices conducting arithmetic in a binary system had novelty when he began formulating his thoughts in 1937. “Here in a master’s thesis by a research assistant,” Mr. Gleick writes, “was the essence of the computer revolution yet to come.”

Among its many other virtues “The Information” has the rare capacity to work as a time machine. It goes back much further than Shannon’s breakthroughs. And with each step backward Mr. Gleick must erase what his readers already know. He casts new light on the verbal flourishes of the Greek poetry that preceded the written word: these turns of phrase could be as useful for their mnemonic power as for their art. He explains why the Greeks arranged things in terms of events, not categories; how one Babylonian text that ends with “this is the procedure” is essentially an algorithm; and why the telephone and the skyscraper go hand in hand. Once the telephone eliminated the need for hand-delivered messages, the sky was the limit.

In the opinion of “The Information” the world of information still has room for expansion. We may be drowning in spam, but the sky’s still the limit today.

2011 USC Viterbi Lecture “Adventures in Coding Theory” by Elwyn Berklekamp

Bookmarked 2011 Andrew Viterbi Lecture Ming Hsieh Department of Electrical Engineering (USC - Viterbi School of Engineering)

"Adventures in Coding Theory"

Professor Elwyn Berlekamp
University of California, Berkeley

Gerontology Auditorium, Thursday, March 3, 4:30 to 5:30 p.m.

>> Click here for live wedcast

Abstract
The inventors of error-correcting codes were initially motivated by problems in communications engineering. But coding theory has since also influenced several other fields, including memory technology, theoretical computer science, game theory, portfolio theory, and symbolic manipulation. This talk will recall some forays into these subjects.

I wish I could be at this lecture in person today, but I’ll have to live with the live webcast.

Confessions of David Seidler, a 73-year-old Oscars virgin

Read Confessions of David Seidler, a 73-year-old Oscars virgin by David Seidler (LA Times)
My first realization I was hooked on Oscar was when I seriously began pondering one of mankind's most profound dilemmas: whether to rent or buy a tux. That first step, as with any descent down a...
This is a great (and hilarious) story by and about the writer of THE KING’S SPEECH.

Amplify’d from www.latimes.com

Confessions of David Seidler, a 73-year-old Oscars virgin

The screenwriter, whose first nomination was for ‘The King’s Speech,’ ponders his formalwear options for the big night, his standing in Hollywood and much more.

The Response of the Schoolmaster

This must certainly be the quote of the week from English author Alan Bennett’s play Forty Years On:

Foster: I’m still a bit hazy about the Trinity, sir.
Schoolmaster: Three in one, one in three, perfectly straightforward.  Any doubts about that see your maths master.