31 July 2006

A genomic code for nucleosome positioning -- Nature

Computational biology makes it to the NY Times! -- for analysis of chromatin structure. Wonder the degree to which this analysis applies to human encode data.

Nature. 2006 Jul 19;
A genomic code for nucleosome positioning.

Scientists Say They’ve Found a Code Beyond Genetics in DNA
By NICHOLAS WADE, Published: July 25, 2006
Researchers believe they have found a second code in DNA in addition to the genetic code. The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself....
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So Big and Healthy Grandpa Wouldn’t Even Know You -- NY Times

Interesting article about health... it might not be such a bad thing to eat a lot.

So Big and Healthy Grandpa Wouldn’t Even Know You
By GINA KOLATA, Published: July 30, 2006
Valentin Keller enlisted in an all-German unit of the Union Army in Hamilton, Ohio, in 1862. He was 26, a small, slender man, 5 feet 4 inches tall, who had just become a naturalized citizen. He listed his occupation as tailor....
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A New Enemy Gains on the U.S. -- NY Times

Network  War - a new concept.

A New Enemy Gains on the U.S.
By THOM SHANKER, Published: July 30, 2006
POUND for pound and pounding for pounding, the Israeli military is one of the world’s finest. But Hezbollah, with the discipline and ferocity of its fighters and ability to field advanced weaponry, has taken Israel by surprise...“We are now into the first great war between nations and networks,” said John Arquilla, a professor of defense analysis at the Naval Postgraduate School, and a leading analyst of net warfare. “This proves the growing strength of networks as a threat to American national security.”...

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24 July 2006

Population differences in the human functional olfactory repertoire -- MBE

Mol Biol Evol. 2003 Mar;20(3):307-14.
Population differences in the human functional olfactory repertoire.
Gilad Y, Lancet D.


Different noses for different people -- Nat Genet

SNPs in Pseudogenes

Nat Genet. 2003 Jun;34(2):143-4.
Different noses for different people.
Menashe I,Man O,Lancet D,Gilad Y.
Of more than 1,000 human olfactory receptor genes, more than half seem to be pseudogenes....

The House That Steinbrenner Is Building -- NY Times

A great financial history of the Yankees... Perhaps there should be a revolt against King George!

The House That Steinbrenner Is Building
Published: July 23, 2006
IT’S another June evening in baseball and the Boston Red Sox are visiting New York for the latest showdown with their archenemy, the Yankees. As it is at every meeting between the teams, the stadium is packed and crackling with energy....That perennial drive is a big reason, analysts say, that the Yankees have broken new financial ground on the field and off. Bankers, analysts and others familiar with the team’s finances say the franchise is now worth about $1 billion, nearly 70 percent more than the next most valuable team, the Red Sox, and nearly three times more than the average major league team is worth. Making the most of a winning tradition and their home in the nation’s biggest city and media market, the Yankees generate nearly $300 million in annual revenue, according to an individual with knowledge of the team’s finances. He requested anonymity because of his continuing professional relationship with the team....Set for a 2009 debut, the stadium, including building costs and debt payments, will carry a $1 billion price tag. To pay for it, the Yankees will need to generate an additional $50 million to $60 million a year in revenue, according to analysts. Mr. Levine declined to discuss how much money the team expects to earn in its new digs, though he ruled out selling the naming rights to the stadium....Even with all that spending, the Yankees haven’t always maintained a lock on winning. While it currently has a $195 million payroll, the biggest in baseball by a wide margin, and has advanced to the playoffs every year since 1995, the team has not won the World Series since 2000. In 2003, the Florida Marlins — a team with a payroll one-third the size — beat the Yankees in the World Series. Analysts also say that money alone does not explain Mr. Steinbrenner’s success. They note that he has surrounded himself with creative marketers, as evidenced by the team’s deal in 1988 to broadcast its games on cable television — a page taken from Ted Turner, who did the same with the Atlanta Braves. In 2002, an investment group that included the Yankees formed the YES Network, further leveraging the team’s brand. YES brought in $257 million last year, surpassing MSG to become the country’s top regional sports network for the first time, according to Kagan Research.
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A Bill K. accomplishment!

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TUF love for "junk" DNA -- Cell

More "What is a gene?" articles -- now in Nat. Genetics and Cell....

Nature Genetics 38, 608 - 609 (2006)
The multitasking genome
Thomas R Gingeras

Cell. 2006 Jun 30;125(7):1215-20.
TUF love for "junk" DNA.
Willingham AT, Gingeras TR.

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22 July 2006

Scientists Plan to Rebuild Neanderthal Genome -- NY Times

Wow! A lot of press for 454!

Scientists Plan to Rebuild Neanderthal Genome
Published: July 20, 2006
Researchers at the Max Planck Institute for Evolutionary Biology in Leipzig, Germany, plan to reconstruct the genome of Neanderthals, the archaic human species that occupied Europe from 300,000 years ago until 30,000 years ago until being displaced by modern humans...
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18 July 2006

USPS - Ship From Home with Click-N-Ship and Carrier Pickup


Amazon.com: More Than You Know: Finding Financial Wisdom in Unconventional Places: Books: Michael J. Mauboussin

Biologist's views on financial markets

MUTUAL FUNDS REPORT: ESSAY; Expertise in All the Wrong Places
July 9, 2006, Sunday
By JOHN SCHWARTZ (NYT); Money and Business/Financial Desk
DISPLAYING FIRST 50 OF 725 WORDS -MY investment record is, let us say, spotty. A careful evaluation of the performance of my portfolio suggests that I could have done better by shredding my cash and blowing it into my walls for insulation. So I wouldn't mind getting a little advice, but whom should I trust?...


17 July 2006

Crossing Over, Step by Step -- NY Times

Have done #1 and #3 by bike, but not sure on #2.

July 16, 2006
Weekend in New York
Crossing Over, Step by Step
At least a dozen bridges from Manhattan to the other boroughs offer pedestrian lanes — and a bit of adventure. So why do most visitors merely cross the Brooklyn Bridge, then call it a day? Here are three bridges worth the walk, especially for the (most un-Manhattan-like) neighborhoods that beckon on the other side.
This 7,308-foot suspension bridge was the longest in the world when it was completed in 1903. ...
The most human-scale of the three bridges here, with only four lanes and no trains, this is a metal truss swing bridge completed in 1895...

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Internet Help Multiplies for the Carless on the Go -- NY Times

Seems to be like a subway and train GPS.

Internet Help Multiplies for the Carless on the Go
Published: July 16, 2006
Getting from here to there using the Internet has become almost routine with Web sites like Mapquest and Google maps. Many drivers are also using satellite technology linked to computer mapping systems in their cars to guide them to their destinations. In the New York City area, where public transportation is paramount, Internet maps for subways, trains, buses and ferries in the city and the region have become a growth industry.And the competition is intensifying. These Web sites began appearing in late 2004 with HopStop.com, which provides directions throughout the city using most forms of public transit. Last year Trips123.com arrived, sponsored by a consortium of 16 public transportation and law enforcement agencies in New York, New Jersey and Connecticut and providing detailed itineraries on dozens of public and private carriers across the region, including private bus lines and commuter trains. Trips123 won instant praise for thoroughness and detail, but was criticized on ease of use and is being revamped. A simpler version is to be issued in the fall.One of the latest sites to join the fray is PublicRoutes.com, which went online in June and provides directions by knitting together various modes of public transit not just across....

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15 July 2006

Recorded Books

Science Audiobooks


13 July 2006

Unraveling Enigma of Smell Wins Nobel for 2 Americans -- NY Times

Resurrected a old letter that I wrote to the Times to post on my blog. (It was never published in the paper.) Here it is:

Tuesday October 5 was a sad day for scientists in New York. The front
page of the Times had no mention of award of the Nobel Prize in
medicine to Richard Axel, a professor at Columbia University, for
fundamental work done in New York City on the molecular basis of
smell. There was also no mention of this achievement in that Tuesday's
Science Times. There was, however, a front-page story about a
different prize for technical excellence: the ten-million dollar
Ansari X Prize, which was awarded to a consortium headed by
multi-billionaire Paul Allen for shooting a spaceship 70 miles above
the earth from Mojave, California. While this was clearly a milestone
for commercial ventures, countless rockets from many nations have long
ago surpassed this height. What is one to make of this -- an apparent
triumph of money over merit, in the coverage of science?

NYT Tuesday 5 October

Unraveling Enigma of Smell Wins Nobel for 2 Americans
Two American scientists who solved the enigma of how people can smell 10,000 different odors and recall them later were awarded the 2004 Nobel Prize in Physiology or Medicine yesterday.
The winners, who will share the $1.3 million award, were Dr. Richard Axel, 58, a professor at Columbia University, and Dr. Linda B. Buck, 57, of the Fred Hutchinson Cancer Research Center and a professor at the University of Washington in Seattle.


Private Rocket Ship Earns $10 Million In New Space Race
October 5, 2004, Tuesday
By JOHN SCHWARTZ (NYT); National Desk
Late Edition - Final, Section A, Page 1, Column 1, 1368 words
DISPLAYING FIRST 50 OF 1368 WORDS -A private rocket ship shot into space this morning and won a coveted $10 million aviation prize for its creators. SpaceShipOne, the sleek combination of rocket and glider designed by Burt Rutan and financed by the billionaire Paul G. Allen, reached a record altitude of 368,000 feet, or 69.7...

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11 July 2006

The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World

Very revealing book on the interplay between commercial and government funded research. I'd recommend it.

The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World (Hardcover)
by James Shreeve

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Bigger Houses, Longer Commutes -- NY Times

Here's the letter I wrote in response to this article (which was never published):

I read with great interest the recent real estate section article on the longer commutes people are undertaking to have bigger homes. It's amazing how much time people are spending commuting. Many of the commutes referred to involve long train trips on Metro-North and other commuter railroads. I just wanted to point out that if somehow higher speed rail could be installed in the New York City area, such as is available in Europe and Japan, many of these longer commutes would go down. For instance, one could envision the commute from New Haven, CT to midtown alluded to in the article falling from about 90 minutes to under an hour easily with higher speed rail. If this did happen, the property values of the houses served by this higher speed rail would dramatically increase given their new found proximity to Manhattan. One wonders whether somehow one could take the extra value created through the increase of property values for all of these houses and, to some degree, use it to finance the construction of the railroads.

Bigger Houses, Longer Commutes
Published: May 21, 2006
ON weekdays, Julie Kroloff sets the coffee maker for 5:45 a.m., then speeds through her kitchen in Hopewell Junction, N.Y., and grabs a cup to fortify herself for the long drive ahead. If Ms. Kroloff, a self-employed consultant, is on time, she backs out of the garage just before 6 and makes the trip from Dutchess County to her office in Midtown Manhattan in just under two hours. If traffic is heavy, Ms. Kroloff's 54-mile commute can take two and a half hours or more....
According to the latest statistics from the Census Bureau, the migration outward and the trend toward longer commutes to New York City intensified during the 1990's. In Dutchess County, for example, the number of people who commuted to the city rose 46 percent in that decade, to 5,798 from 3,975. In New Jersey, the number of people commuting from Warren County, due west of Manhattan at the Pennsylvania border, was up 39 percent, rising from 539 in 1990 to 748 in 2000. In New Haven County in Connecticut, the increase was 25 percent, from 1,797 to 2,243. But in Suffolk County, the eastern part of Long Island, the numbers increased by only 2 percent, rising to 80,003 from 78,291 in 1990....

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03 July 2006


Thought this was interesting... This is the Church CEGs on personal genomics. Note the open quality of everything, including the submitted proposal and the grant reveiws!


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Johannes Gehrke's Homepage

Interesting data miner. Gave a talk at Yale CS.

For Science's Gatekeepers, a Credibility Gap -- NY Times

Here's the letter I wrote in response to this article (which was never published):

I read with great interest the recent Science Times about problem's with the
gatekeepers in science -- journal editors and the referees they commission in
the peer-review process. This article exaggerates the problem. In my opinion,
most practicing scientists do not believe that just because something is
published in a journal, it means that it is correct. Moreover, the supposed
"quality" of the journal does not correlate with correctness of its results but
rather simply with its perceived newsworthiness. In contrast, most scientists
feel that accepted results have to pass the test of replication over time in
different laboratories and in different people's hands. That is, an idea has to
be successful in the academic marketplace, just as an everyday "meme" achieves
success in the real marketplace. Furthermore, the suggestion in the article that
we increase the stringency of the editorial process has a number of potential
negative consequences. First of all, it will invariably slow down the
publication of ideas, both good and bad. Second of all, if we increase the
severity of the review process, we potentially increase the likelihood that
papers will be rejected for a variety of non-scientific reasons, e.g. they are
not fashionable at the moment or a referee is a competitor of the author and
does not want a particular result published. What we really need to do is to
encourage scientists to constructively replicate and verify each other's work
and to report both negative and positive findings with regard to this. The
essential problem is one does not get much credit in science for doing this --
all the accolades go to the person who came up with the idea first. Thus, rather
than emphasize gatekeepers we need to provide proper incentives for careful
public replication of findings.

For Science's Gatekeepers, a Credibility Gap
Published: May 2, 2006
Recent disclosures of fraudulent or flawed studies in medical and scientific journals have called into question as never before the merits of their peer-review system....

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Scan This Book! -- NY Times

The Times article describes the idea of the Knowledge Index taken to truly grant scale.

Here's the letter I wrote in response to this (which was never published):
I read with great interest the recent article in the New York Times magazine about the future of books and publishing. I think this article illuminates how much more valuable information becomes when it's possible to link and interconnect it and how a book in isolation is of limited value. One important point to add to this is that the digitization of textual information really changes the scale and scope of what we read. A book is a convenient size for dissemination and digestion in paper form. Free of these physical constraints, authors often like to present information in differently sized bits than a whole book or a journal article. For instance, a short paragraph linked to and commenting on a longer one (i.e. like a blog entry commenting on a book) or some form of text intertwinned with another type of media such as a computer program or music. All of these things are easier to do in the digital age than in the framework of a paper book.

Scan This Book!
May 14, 2006, Sunday
By KEVIN KELLY (NYT); Magazine
DISPLAYING FIRST 50 OF 7658 WORDS -In several dozen nondescript office buildings around the world, thousands of hourly workers bend over table-top scanners and haul dusty books into high-tech scanning booths. They are assembling the universal library page by page. The dream is an old one: to have in one place all knowledge, past and...

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Wikipedia entry for the classic paper!

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Bing Ren's triangle fitting approach for ChIP-chip

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The next toy for the office....

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How do RNA folding algorithms work? -- Nature Biotechnology

Thought this was a nice overview

Nature Biotechnology  22, 1457 - 1458 (2004)
How do RNA folding algorithms work?

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The Manhattanville Project -- NY Times

Stumbled on tihs. Thought the growth of Columbia was very impressive.....

The Manhattanville Project
Published: May 21, 2006
One evening in the spring of 2004, the Rev. Earl Kooperkamp attended a presentation at a community board meeting by the celebrated architect Renzo Piano. Unveiling preliminary sketches, Piano laid out his vision for the campus he's designing for Columbia University's president, Lee Bollinger....

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Buffett Children Emerge as a Force in Charity -- NY Times

Definitely a case of money not being the root of happiness! Great quote.

Buffett Children Emerge as a Force in Charity
Published: July 2, 2006
DECATUR, Ill., June 28 — The three middle-aged children of Warren E. Buffett watched along with the rest of the country last week as their father, the celebrated investor, told the world that he would pass the bulk of his $40 billion personal fortune to the charitable foundation of Bill Gates, a fellow billionaire, and his wife, Melinda.
The investing genius's children went off to college and all three dropped out before graduating. "I had a great run in high school, academically, and then I got to college and just struggled," said Howard, who spent one year at Augustana College in Sioux Falls, S.D., and one year at University of California, Irvine. When he told his parents he was quitting school, he said, "neither of them was very happy about it."...
Susie initially majored in home economics. "If we didn't have foundations to run, Howie would farm. I would be sewing, knitting and quilting," she said.
She dropped out of the University of California, Irvine, just shy of an undergraduate degree because she was enjoying work as an administrative assistant, making $525 a month. "I thought, boy, it just doesn't get any better than this."...

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Interesting in relation to copyright.

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Nice for web search rankings....

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02 July 2006

Online methods share insider tricks -- Nature

Very interesting for lab protocols, perhaps nice to use in relation to validation and tracking DBs.

Published online: 7 June 2006; | doi:10.1038/441678a
Online methods share insider tricks
Wiki-style website allows tinkering with lab protocols.
Helen Pearson

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What is a Gene? -- Nature

Here is a letter I wrote with Mike Snyder in response to this:
(It was never published.)

We read with great interest Helen Pearson's recent article on "What is
a gene?" It underscores the fact that we need an increasing amount of
space to describe the full complexity of genes, much more so than the
simple pictures we had in the past. It is worth elaborating on one
aspect of genes -- the interplay between living and dead genes,
between gene and pseudogene. Conventionally, pseudogenes were thought
of as non-functional remains of genes; however, increasingly, people
are coming to see that they may be active in different ways. In
particular, large-scale transcriptional studies from the ENCODE
consortium and others indicate that a substantial fraction of human
pseudogenes are transcribed, and a large-scale sequence analyses have
shown that the sequences associated with pseudogenes appear to be more
conserved (and under selection) than neutrally evolving DNA,
suggesting preservation for functional reasons. Moreover, detailed
biochemical experiments have illuminated functions for a few
pseudogenes (e.g. Makorin1-p1). Finally, recent studies of
polymorphisms indicate that in some individuals, pseudogenes are
actually functional genes (and vice-versa). In summary, many findings
have shown that line between gene and pseudogene is blurred, further
increasing the complexity of fully describing "What is a gene?"

NATURE|Vol 441|25 May 2006 NEWS FEATURE
What is a Gene?
Helen Pearson

‘Gene’ is not a typical four-letter
word. It is not offensive....
Rick Young, a geneticist at the Whitehead
Institute in Cambridge, Massachusetts, says
that when he first started teaching as a young
professor two decades ago, it took him about
two hours to teach fresh-faced undergraduates
what a gene was and the nuts and bolts of how
it worked. Today, he and his colleagues need
three months of lectures to convey the concept
of the gene, and that’s not because the students
are any less bright....

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Nature Peer Review Trial and Debate -- Nature

Something to consider in future submissions to Nature, perhaps in conjuction with sending it to arxiv.org .

Journal home > Web focuses > Science and politics > Peer Review
Nature Peer Review Trial and Debate
June 2006
Nature is undertaking a trial of a particular type of open peer review. In this trial, authors whose submissions to Nature are sent for peer review will also be offered the opportunity to participate in an open peer review process...

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