Rules for modeling signal-transduction systems -- Sci STKE

Looks like an interesting article... and perhaps also a good place to publish network ideas.

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16849649&query_hl=2&itool=pubmed_docsum
Sci STKE. 2006 Jul 18;2006(344):re6.  
Rules for modeling signal-transduction systems.
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W.
http://fontana.med.harvard.edu/WWW/Documents/Lab/publications.lab.htm

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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.

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ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16862119&query_hl=5&itool=pubmed_docsum
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
nytimes.com/2006/07/25/science/25dna.html
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.

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http://www.nytimes.com/2006/07/30/health/30age.html
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.

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http://www.nytimes.com/2006/07/30/weekinreview/30shanker.html
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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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.

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Different noses for different people -- Nat Genet

SNPs in Pseudogenes

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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....

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The House That Steinbrenner Is Building -- NY Times

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

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The House That Steinbrenner Is Building
By KEN BELSON
Published: July 23, 2006
http://www.nytimes.com/2006/07/23/business/yourmoney/23george.html
+
http://mylifestream.net/scrapbook/2006/07/yankees-attendance-from-nytimes.html
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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SCIENTISTS FIND LONG-SOUGHT KEY TO HOW BLOOD CLOTS - New York Times

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....

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Nature Genetics 38, 608 - 609 (2006)
doi:10.1038/ng0606-608
The multitasking genome
Thomas R Gingeras
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16736012

Cell. 2006 Jun 30;125(7):1215-20.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16814704&query_hl=7&itool=pubmed_docsum
TUF love for "junk" DNA.
Willingham AT, Gingeras TR.

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Scientists Plan to Rebuild Neanderthal Genome -- NY Times

Wow! A lot of press for 454!

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Scientists Plan to Rebuild Neanderthal Genome
By NICHOLAS WADE
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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USPS - Ship From Home with Click-N-Ship and Carrier Pickup

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

Biologist's views on financial markets

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http://select.nytimes.com/gst/abstract.html?res=F60E16FC3B540C7A8CDDAE0894DE404482
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?...

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Crossing Over, Step by Step -- NY Times

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

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http://travel2.nytimes.com/2006/07/16/travel/16weekend.html

July 16, 2006

Weekend in New York

Crossing Over, Step by Step
By SETH KUGEL
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.
1) WILLIAMSBURG BRIDGE
This 7,308-foot suspension bridge was the longest in the world when it was completed in 1903. ...
2) MACOMBS DAM BRIDGE
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...
3) QUEENSBORO BRIDGE...

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

Seems to be like a subway and train GPS.

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Internet Help Multiplies for the Carless on the Go
By THOMAS J. LUECK
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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Recorded Books

Science Audiobooks

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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?

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http://www.nytimes.com/2004/10/05/science/05nobel.html
NYT Tuesday 5 October
Unraveling Enigma of Smell Wins Nobel for 2 Americans
By LAWRENCE K. ALTMAN
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.

http://select.nytimes.com/gst/abstract.html?res=F30A12FA345C0C768CDDA90994DC404482
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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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.

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http://www.amazon.com/gp/product/0375406298/002-5543058-9208048?v=glance&n=283155
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.

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http://www.nytimes.com/2006/05/21/realestate/21cov.html
Bigger Houses, Longer Commutes
By ELSA BRENNER
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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http://arep.med.harvard.edu/P50_03

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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http://arep.med.harvard.edu/P50_03
http://arep.med.harvard.edu/PGP

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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.

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For Science's Gatekeepers, a Credibility Gap
By LAWRENCE K. ALTMAN, M.D.
http://www.nytimes.com/2006/05/02/health/02docs.html
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.

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http://www.nytimes.com/2006/05/14/magazine/14publishing.html
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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http://en.wikipedia.org/wiki/Alpher-Bethe-Gamow_theory

Wikipedia entry for the classic paper!

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http://www.stat.ucla.edu/~zmdl/mpeak

Bing Ren's triangle fitting approach for ChIP-chip

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http://www.ericharshbarger.org/lego/mini_dna.html

The next toy for the office....

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How do RNA folding algorithms work? -- Nature Biotechnology

Thought this was a nice overview

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http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n11/full/nbt1104-1457.html
Nature Biotechnology  22, 1457 - 1458 (2004)
doi:10.1038/nbt1104-1457
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.....

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http://www.nytimes.com/2006/05/21/magazine/21wwln.essay.html
The Manhattanville Project
By DAPHNE EVIATAR
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.

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http://www.nytimes.com/2006/07/02/business/02buffettkids.html
Buffett Children Emerge as a Force in Charity
By JEFF BAILEY
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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http://chillingeffects.org

Interesting in relation to copyright.

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http://chillingeffects.org

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http://www.google.com/trends

Nice for web search rankings....

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http://www.google.com/trends

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Online methods share insider tricks -- Nature

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

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http://openwetware.org/wiki/Main_Page
http://www.nature.com/news/2006/060605/full/441678a.html
Nature
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?"

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16724031&query_hl=3&itool=pubmed_docsum
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 .

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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...
http://www.nature.com/nature/peerreview/index.html

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740 Park : The Story of the World's Richest Apartment Building

Quite a destination! 

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http://maps.google.com/maps?f=q&hl=en&q=740+park+avenue,+ny,+ny+10021&ie=UTF8&ll=40.77064,-73.964459&spn=0.001633,0.002967&t=h&om=1
http://www.amazon.com/gp/product/0385512090/sr=8-1/qid=1151275188/ref=pd_bbs_1/002-5543058-9208048?ie=UTF8
740 Park : The Story of the World's Richest Apartment Building

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The World Is a libferris Filesystem -- Linux Journal

Might be useful to make available content in mySQL databases

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The World Is a libferris Filesystem
By Ben Martin
With libferris, the boundary of your filesystem extends to include PostgreSQL, XML, db4, RDF, the X Window System, Evolution and much more....
http://interactive.linuxjournal.com/article/8901

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THE INJUSTICE COLLECTOR -- New Yorker

Thought this article on Joyce's estate and how its supressing scholarship through copyright was very interesting. It has some very funny quotes (some of them below).

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THE INJUSTICE COLLECTOR

by D. T. MAX

Is James Joyce’s grandson suppressing scholarship?

Issue of 2006-06-19
Posted 2006-06-12
June 16th marks the hundred-and-second anniversary of Bloomsday, the date on which the events in James Joyce’s “Ulysses” take place. There will be the customary commemorative celebrations surrounding Leopold Bloom’s famous walk through Dublin: public readings and festivals in cities around the world, including Dublin, New York, Berlin, Paris, St. Petersburg, and Melbourne. In Budapest, two hundred or so academics will convene a Joyce symposium—the twentieth to be held on Bloomsday....
Academics, he declared, were like “rats and lice—they should be exterminated!”....

Stephen was funny and playful on the phone, although a subtext of anger was often evident. Acknowledging his pugnacity, he said, “It is better to be pissed off than pissed on.”
http://www.newyorker.com/printables/fact/060619fa_fact

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Solomon Lab

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Homemaker’s Helper -- NY Magazine

Has a writeup on Really Cool Foods...perhaps a bit too complicated for me! 

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http://www.newyorkmetro.com/restaurants/features/17242/
Homemaker’s Helper
By Robin Raisfeld & Rob Patronite

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Mary MacDonald - US

from A2K

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Water and life: seeking the solution -- Nature

Thought this was an interesting snippet. Wonder whether a continuous range of bond angles in water were tried about a mean of 104.5 deg. Might be useful to try with protein geometry.

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http://www.nature.com/nature/journal/v436/n7054/full/4361084a.html
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16121150&dopt=Abstract
Water and life: seeking the solution.
Ball P.
Is there any fundamental reason to be fixated on water as the universal elixir of life? Philip Ball investigates.
Where there's water, there's life. That, at least, is what our experience on Earth has taught us, and when it comes to searching for life on other worlds, NASA seems determined to follow the water. But is it right to see water as the sole medium for extraterrestrial life?

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Snap Judgments - Forbes.com

Nice guide to small cameras

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Physical Culture; A Personal Trainer, Right in Your iPod -- NY Times

Stumbled on this... interesting in trying iTrain or cardiocoach.com .

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http://www.deccanherald.com/deccanherald/Mar152006/panorama1456582006314.asp
http://select.nytimes.com/gst/abstract.html?res=F20713FA3E5B0C7A8DDDA80894DE404482
Physical Culture; A Personal Trainer, Right in Your iPod
January 19, 2006, Thursday
By CATHERINE SAINT LOUIS (NYT)
WHEN Suganthi Balasubramanian started exercising after three decades of inactivity, she found her effort worthwhile but monotonous. Like a child forced to swallow bitter medicine, she followed workout videotapes she didn't enjoy, only because they were good for her. She bought a treadmill but couldn't make herself use it....

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More Pie, Mr. President? + Our National Eating Disorder -- NY Times

Thought these two articles about the Amerian Diet were quite interesting...

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More Pie, Mr. President?
By JACK HITT
Published: October 17, 2004
Good political food -- it should be obvious -- must be democratic. The barbecue, the clambake, the chili contest, the fish fry, the hamburger cookout, the pancake social, the fried-chicken potluck, the spaghetti dinner -- these are the great entrees of American politics precisely because almost anyone can cook them and pretty much everybody likes them. Sure, the exact recipes differ from place to place, like accents, but that's the point. Political food contains the core contradiction of America, our profound differences and essential sameness all on one plate. Nothing puts a politician more at ease than being able to sing our national unity and diversity at the same time. And what says E Pluribus Unum as literally and zestily as a bowl of four-alarm chili? ....
http://www.nytimes.com/2004/10/17/magazine/17REDBLUE.html

Our National Eating Disorder
By MICHAEL POLLAN
Published: October 17, 2004
Carbophobia, the most recent in the centurylong series of food fads to wash over the American table, seems to have finally crested, though not before sweeping away entire bakeries and pasta companies in its path, panicking potato breeders into redesigning the spud, crumbling whole doughnut empires and, at least to my way of thinking, ruining an untold number of meals. America's food industry, more than happy to get behind any new diet as long as it doesn't actually involve eating less food, is still gung-ho on Low Carb, it's true, but in the last few weeks, I can report some modest success securing a crust of bread, and even the occasional noodle, at tables from which such staples were banned only a few months ago.
http://www.nytimes.com/2004/10/17/magazine/17EATING.html

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http://acg.media.mit.edu/people/fry/revisionist

Code evolution!....

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http://benfry.com/salaryper

Nice for web search rankings....

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http://benfry.com/salaryper

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Jonathan D. Blake | Quinnipiac University | Faculty Profile

Cohen Group Alumni

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Growing Wikipedia Revises Its 'Anyone Can Edit' Policy -- NY Times

Wikipedia and wiki's on the front page of the NY Times... perhaps something to take note of!

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http://www.nytimes.com/2006/06/17/technology/17wiki.html
Growing Wikipedia Revises Its 'Anyone Can Edit' Policy
By KATIE HAFNER
Published: June 17, 2006
Wikipedia is the online encyclopedia that "anyone can edit." Unless you want to edit the entries on Albert Einstein, human rights in China or Christina Aguilera....

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Now, Free Ways to Do Desktop Work on the Web -- NY Times

Google spreadsheet went all they from invitation only to front page of the Times... might be nice to try other tools.

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http://www.nytimes.com/2006/06/17/technology/17money.html
Now, Free Ways to Do Desktop Work on the Web
By DAMON DARLIN
Published: June 17, 2006

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All Ears - Information and advice on hearing loss, ear infections and other common ear disorders

Appears that Earwax is not that bad.

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George Church email

Interesting contact info. page.

Blogs to Riches -- New York Magazine

Thought this was an interesting potrait of the blog world and the popular sites. Like everything else it appears to be a very select club.

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New York Magazine, 20 Feb 06
http://www.newyorkmetro.com/news/media/15967
Blogs to Riches -- The Haves and Have-Nots of the Blogging Boom.
By Clive Thompson
http://www.newyorkmetro.com/news/media/15972
Linkology
By Stuart Luman
http://www.newyorkmetro.com/news/media/15966
Meet the Bloggers -- A smattering of local and brand-name blogs.
By Sonia Zjawinski

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Some distances for running in Central Park -- http://www.gmap-pedometer.com/?r=195461

Some distances for running in Central Park :

3.2 miles starting at 72nd, going up to reservoir, around and back to stop.
http://www.gmap-pedometer.com/?r=195461

A shorter route up to the reservoir, across to the West Side, and then back down to 72nd.
http://www.gmap-pedometer.com/?r=195605

Other sites:
http://web2.nyrrc.org/divisions/training/cpdistances.htm
http://www.nyrr.org/divisions/training/cpdistances.html

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Dipstick Caffeine Test for Coffee -- NPR

Here's the NPR reference to the caffeine test.

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Health & Science
Dipstick Caffeine Test for Coffee
Morning Edition, May 19, 2006 · A St. Louis chemist is one of many people who ask for decaf, and then wonder if it's really decaf. Jack Ladenson says he's getting more sensitive to caffeine. So he wants to test what a restaurant pours him. He's part of a research team that patented a dipstick test. Stick it in your drink and it changes color, depending on the amount of caffeine. He'd like to market it. But, so far, no company is awake to the possibilities. Maybe a cup of coffee would help.
http://www.npr.org/templates/story/story.php?storyId=5417137

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Is Economics the Next Physical Science? -- Physics Today

Wonder if this is relevant to real finance? (It appear's that Pareto's 1897 distribution was the first powerlaw.)

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http://arxiv.org/abs/physics/0506086
http://www.physicstoday.org/vol-58/iss-9/p37.shtml
Is Economics the Next Physical Science?
An emerging body of work by physicists addressing questions of economic organization and function suggests new approaches to economics and a broadening of the scope of physics — J. Doyne Farmer, Martin Shubik, and Eric Smith

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A great scientist can benefit from peer review, even while refusing to have anything to do with it. -- Physics Today

Einstein never really had to deal with a referee report !

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http://www.physicstoday.org/vol-58/iss-9/p43.html
Einstein Versus the Physical Review
A great scientist can benefit from peer review, even while refusing to have anything to do with it.
Daniel Kennefick
September 2005, page 43

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http://lib.bioinfo.pl/

Thought the display of citations was interesting.

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http://lib.bioinfo.pl/index.php?pmid=10966805

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http://www.er.doe.gov/ascr/

Heard the DOE computing budget would increase greatly next year (~36%). Perhaps this a good office to investigate.

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http://www.er.doe.gov/ascr/
http://www.medicalnewstoday.com/medicalnews.php?newsid=42009
http://www.aip.org/fyi/2006/020.html
http://content.nejm.org/cgi/content/full/354/16/1665

from http://www.aaas.org/spp/rd/prel07p.htm : The Department of Energy (DOE) would enjoy substantial increases for its energy and science R&D portfolios in 2007, an unusual turn of events for a department that has mostly seen flat budgets in recent years (see Figure 6). The DOE Office of Science (OS) would emerge as the clear winner in the 2007 budget with a 14 percent increase to $3.8 billion for its R&D portfolio centered around the physical sciences. The largest OS programs would all receive increases of 8 percent or more, including a dramatic 24 percent boost for Nuclear Physics after a decade of stagnant funding, a 36 percent increase for computing research, a 25 percent increase for Basic Energy Sciences centered around several large-scale facilities, and a 31 percent increase for the core life sciences research portfolio.

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JUNG - Java Universal Network/Graph Framework

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CSIRO's Total Wellbeing Diet book: recipes for healthy eating and weight control (Publication)

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Scientists Discover Gene Linked to Higher Rates of Prostate Cancer -- NY Times

Might be interesting to look at what this gene is....

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Scientists Discover Gene Linked to Higher Rates of Prostate Cancer
By NICHOLAS WADE
Published: May 8, 2006
http://www.nytimes.com/2006/05/08/health/menshealth/08prostate.html
A team of scientists says it has detected a variant gene associated with prostate cancer, a finding that may make possible a diagnostic test to help decide which patients are the best candidates for aggressive treatment....
The new variant, described online yesterday in the journal Nature Genetics, was first found in Icelandic men and then detected in Sweden and in two populations in the United States. David Altshuler, a medical geneticist at the Broad Institute in Cambridge, Mass., said the result was statistically convincing and, because it was tested in four populations, "a model for how these things should be done."

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Doubt Cast on Early Theory on Eye Infections - New York Times

Doubt Cast on Early Theory on Eye Infections
By BARNABY J. FEDER
Published: May 6, 2006

An outside researcher hired by Bausch & Lomb says that whatever is causing the recent outbreak of potentially blinding fungal eye infections among contact lens wearers, it is increasingly likely that consumers are not getting the microbes directly from the company's lens cleaning solution....
The findings suggest that there is no single source of contamination for the infections, which have been reported primarily in Singapore, Hong Kong and the United States among users of Bausch & Lomb's ReNu with MoistureLoc lens solution coming from a plant in Greenville, S.C..

Food and Drug Administration officials declined to comment yesterday on Mr. Geiser's assessment. But the agency's Web site posted an update saying that while it continued to confirm cases of Fusarium infections associated with products other than ReNu With MoistureLoc, "Our interest in the MoistureLoc product is based on the disproportionate number of cases of Fusarium keratitis associated with ReNu With MoistureLoc compared to the overall product market share."

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Studying Tiny Fruit Flies, and Reaping Big Rewards -- NY Times

Thought the quotes (excerpted below)  about his family were funny.

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Studying Tiny Fruit Flies, and Reaping Big Rewards
By JENNIFER MEDINA
Published: April 29, 2006
ALBANY, April 28 — A California neuroscientist and biologist whose research of fruit flies found genetic links to human behavior was awarded the $500,000 Albany Medical Center Prize in Medicine and Biomedical Research, the country's largest award in the field.....
He said he became intrigued with the topic when his second daughter was born and he noticed remarkable differences from his first daughter. "I wondered, 'Are my wife and I doing things that differently?' " Dr. Benzer said. When asked about the specific differences in the two girls, Dr. Benzer demurred. "I'd rather avoid that question — I fear the repercussions," he said with a smile. "They are not bad differences, just different."...
Similarly, Dr. Benzer said, he is coded to sleep at different times than his wife, who wakes up at 6 a.m. and typically falls asleep by 10 p.m. Dr. Benzer, on the other hand, stays awake until 4 a.m. and sleeps until noon. He routinely works in his research laboratory into the early-morning hours, he said.
"We make it a point to have dinner together," he said.
 http://www.nytimes.com/2006/04/29/nyregion/29science.html
http://benzerserver.caltech.edu/

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Studies Find Elusive Key to Cell Fate in Embryo -- NY Times

Some recent Cell papers referenced in the NY Times that seem to imply that "master regulator" TFs are themselves regulated by specific chomatin modifications. 

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Studies Find Elusive Key to Cell Fate in Embryo
By NICHOLAS WADE
Published: April 25, 2006
For three billion years, life on earth consisted of single-celled organisms like bacteria or algae. Only 600 million years ago did evolution hit on a system for making multicellular organisms like animals and plants.
http://www.nytimes.com/2006/04/25/science/25gene.html?ei=5088&en=583396425d94ee28&ex=1303617600&partner=rssnyt&emc=rss&pagewanted=all

Cell. 2006 Apr 21;125(2):315-26. 
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16630819&query_hl=5&itool=pubmed_docsum

Cell. 2006 Apr 21;125(2):301-13.   
Control of developmental regulators by polycomb in human embryonic stem cells.
Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16630818&query_hl=7&itool=pubmed_docsum

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DIMACS Workshop on Sequence, Structure and Systems Approaches to Predict Protein Function

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Proteomics and Functional Genomics Course at Rutgers -- 2006 MBB:412

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Taking the Least of You -- NY Times

Here's the letter I eventually wrote on this (incorporating suggestions):
I enjoyed the recent article describing the hidden value in biological specimens given to medical research. The article highlighted a conundrum, balancing the right of people to anything of value derived from their own tissue versus the importance of promoting research. One thing the article only alluded to was the additional complexities stemming from DNA sequencing. Sequencing the DNA of a specimen provides much information not only about the person from whom the specimen was taken but also about the parents and children of that individual. Thus, if people consent for their tissue specimens to be freely used for medical research, they are also implicitly consenting for genetic information to be revealed about their relatives. This is being given without the relatives having any direct role in the discussion. Moreover, what is possible in 2006 might be very different from what will be possible in 50 years when we might be able to glean a tremendous amount from a bit of genetic sequence -- e.g. precisely what diseases or behavior anomalies might befall someone.
--
The author appears to have her own wikipedia entry!

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http://www.nytimes.com/2006/04/16/magazine/16tissue.html
http://www.nasw.org/users/skloot/TakingTheLeast.pdf
"Taking the Least of You"
By REBECCA SKLOOT, NY Times, April 16, 2006
http://www.rebeccaskloot.com/
http://en.wikipedia.org/wiki/Rebecca_Skloot
The Tissue-Industrial Complex
Anna O'Connell couldn't find Ted. She stood bent at the waist on a frigid afternoon last December, her head and all its fuzzy red hair crammed into an old stand-up freezer that looked like something you get milk from at the corner store: tall, white with a bit of rust and a pull handle. That freezer is the first thing you see when you walk into the Fox Chase Cancer Center laboratory in Philadelphia, where O'Connell has spent decades as a staff scientist. She pushed aside vial after vial. "I know we still have him somewhere," she yelled, her head still inside the freezer. "We've got serum from, like, 450,000 people."....

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William Bialek

Very clean design

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Home Page of Steffen Möller

Like flipping picture

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Structural Bioinformatics EMBL Heidelberg

Like the rotating image

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The Scourge of Arial

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Google Maps - 41st street and 5th avenue, ny, ny 10021

convenient meeting point near Grand Central

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