Letter in response to "Spam + Blogs = Trouble" -- Wired

Here's a letter I wrote in response to the article below (which was never published):
I read with great interest the recent Wired article relating to spam
blogs (dubbed splogs). The article obviously took a critical tone
towards this new nuisance. However, when the idea of manipulating
search engine rankings through creating patterns of links arose,
people initially thought it was rather humorous. It first entered the
public consciousness during the 2004 presidential election, when
manipulation of links referencing "miserable failure" brought up pages
related to George W Bush as a top-ranked item on a search (see, for
instance, http://news.bbc.co.uk/2/hi/americas/3298443.stm). Now,
search-engine rankings are taken more seriously and, through the
mechanism of blogs, it's possible to automatically create deceiving
link patterns. It seems that on the internet, when there's an
important, interactive service, where it's possible for people to
rapidly and anonymously create content, there's going to be a problem
-- whether it's in the form of spam e-mail, spam blogs, or
manipulation of other web 2.0 services, such as wikis. Unfortunately,
this appears to be a general aspect of the web that needs to be dealt
with more robustly.

---

http://www.wired.com/wired/archive/14.09/splogs.html
Spam + Blogs = Trouble
Splogs are the latest thing in online scams – and they could smother the Internet.
By Charles C. Mann
I am aware that spending a lot of time Googling yourself is kind of
narcissistic, OK? But there are situations, I would argue, when it is
efficiently – even forgivably – narcissistic. When I published a book last year,
I wanted to know what, if anything, people were saying about it. Ego-surfing was
the obvious way to do that. Which is how I stumbled across Some Title....
[L2E]

Climbing Ratings - Climbing With Mike

Climbing Ratings - Climbing With Mike: Climbing Ratings - from 5.0 to Spiderman
Understand how climbs are rated and learn more about the Yosemite Decimal Rating System.

For me:

5.6 is easy yellows, up easy flat wall.
5.7 is very overhung, but with big, black holds
5.8+ is green holds, in crevice, with very hard start and end
5.8++ is xmas tree

think big, ask big, want big, do small!

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays -- Molecular & Cellular Proteomics

Interesting work that does network analysis on top of phosphorylome data set. (Mentioned in recent talk by J Fang.)

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http://www.mcponline.org/cgi/content/full/M600240-MCP200
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=16982674&dopt=Abstract
Molecular & Cellular Proteomics 5:2263-2278, 2006
doi:10.1074/mcp.M600240-MCP200 on September 18, 2006
A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays
Nazila Salamat-Miller, Jianwen Fang... and C. Russell Middaugh,
The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization. 
[x29is]

Brain Man -- 60 minutes

Amazing ability (suggested by RB).....

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60 minutes
Brain Man
http://60minutes.yahoo.com/segment/44/brain_man
Wednesday, February 28, 2007
Meet Daniel Tammet, a 27 year-old math and memory wizard. He can do things with numbers that will truly amaze you. He is a savant. . . with a difference. Unlike most savants, he shows no obvious mental disability, and most importantly, he can describe his own thought process. Join correspondent Morley Safer as he explores the extraordinary life and mind of Daniel Tammet.

Of mice and men: cancer gene discovery using comparative oncogenomics -- Cancer Cell

Thought the comparative angle of these two studies (mouse to human) was interesting.

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16843259&dopt=Abstract
Cancer Cell. 2006 Jul;10(1):2-4.Click here to read  Links
Of mice and men: cancer gene discovery using comparative oncogenomics.
Tomlins SA,
Chinnaiyan AM.
With the proliferation of high-throughput technologies to profile the cancer genome, methods to distinguish causal from bystander genetic events are needed. Two recent reports by Zender et al. and Kim et al. in Cell use genetically defined mouse models to serve as biological filters to mine the human cancer genome. Integration of high-resolution copy number profiles of mouse tumor models and human tumors identified cIAP1 and Yap as oncogenes in human hepatocellular carcinoma, while NEDD9 was identified as a metastasis gene in human melanoma. Together, these reports demonstrate that a comparative oncogenomics approach can identify genes causally involved in oncogenesis and metastasis.

Look wise, say nothing, and grunt. Speech was given to conceal thought. [quote]

Thought it'd be nice to post this quote:
Look wise, say nothing, and grunt. Speech was given to conceal thought.
- Sir William Osler

Letter in response to "Unhappy Meals" -- NY Times

Here's the final text of letter I wrote in response to the article below (which was never published):
I was impressed by Michael Pollan's recent article on the American
diet and "nutritionism" ("Unhappy Meals"). I also enjoyed reading the
letters that commented on this article in last Sunday's magazine
(February 12th issue). That being said, I felt that, taken as a
whole, the letters offered a single take on Pollan's piece. Here I try
to offer a somewhat different perspective. Pollan's central thesis --
that Americans should move away from a science-based diet and toward
eating traditional, more natural foods -- is grounded in the
underlying idea that our bodies are carefully adapted to process
nutrients in the context of whole foods. These biochemical
adaptations stem from our development in Africa millions of years
ago. Note, however, that our bodies are adapted to thrive to the age
of reproduction -- not to old age -- on natural foods. The fact that
people are living so long now is as unnatural for the human species as
Pollan's notion of artificial foods, and a number of natural foods
beneficial to the young and growing are, in fact, completely unhealthy
from a longevity perspective. Moreover, many of the traditional foods
that Pollan extols are actually products of man's manipulation; that
is, many of staples of a traditional European diet ("Mom's food") are
not foods that our ancestors would have found grazing on the African
savanna, but rather are products of the later agricultural and
industrial revolutions. In particular, milk and dairy products
obviously relate to the domestication of animals. Many of the crops
that we routinely eat, such as corn, have effectively been genetically
engineered by thousands of years of breeding to be completely
different from what they first were. Thus, the original diet that
people were biochemically designed for is a far cry from what today's
vegetarian or adherent of the Mediterranean diet would eat. Thus, can
we really claim that it is imperative to move away from the human
manipulation of food?

---

http://www.nytimes.com/2007/02/11/magazine/11letters.t-1.html
http://www.nytimes.com/2007/01/28/magazine/28nutritionism.t.html?ex=1327640400&en=a18a7f35515014c7&ei=5090&partner=rssuserland&emc=rss
http://www.nytimes.com/2007/01/28/magazine/28nutritionism.t.html?ex=157680000&en=ec2685fd6c213846&ei=5124&partner=permalink&exprod=permalink
Unhappy Meals
By MICHAEL POLLAN
Published: January 28, 2007
Eat food. Not too much. Mostly plants.
That, more or less, is the short answer to the supposedly incredibly complicated
and confusing question of what we humans should eat in order to be maximally
healthy. I hate to give away the game right here at the beginning of a long
essay, and I confess that I'm tempted to complicate matters in the interest of
keeping things going for a few thousand more words....
[L2E ]

Letter in response to "Commercial Break" -- Wired

Below is a letter I wrote in response to the article at bottom (which was never published). Might be interesting in relation to magazine advertising. Viz:
I read with great interest the article about the innovative way that
Chevrolet decided to advertise its Tahoe SUV -- by trying to stimulate
lots of user generated content, some of it not so favorable. Taken to
the extreme, the logical extension of this strategy would be that
advertising should aim not so much to create a positive message as to
create buzz for its own sake. Thus, a successful advertising campaign
would simply result in an article such as the one I just read --
describing a new phenomenon, loosely associated with a product,
irrespective of its merits or demerits.

---

Issue 14.12 - December 2006
http://www.wired.com/wired/archive/14.12/tahoe.html
Commercial Break
In a risky experiment, Chevrolet asked Web users to make their own video spots
for the Tahoe. A case study in customer generated advertising.
By Frank Rose
Commercial Break
The thinking went something like this: Chevrolet is all about being
revolutionary, right? (That's debatable, but since Chevy's tagline is "An
American Revolution!" this is where all discussion starts at its ad agency.) And
if Chevrolet is revolutionary, then its advertising ought to be, too. Ergo, the
Chevy message needed to escape the tightly controlled, painstakingly monitored,
woefully predictable confines of the 30-second TV spot and roam the online
jungle. But everybody's doing that now. So, Chevy marketers thought, let's take
this thing a notch further – let's have an online contest to see who can create
the best TV ad for the new Tahoe. The wikification of the 30-second spot – what
could be more revolutionary than that?
[L2E]

New Weapon in Web War Over Piracy -- NY Times

Doesn't mention that directly image collections (e.g. flickr or artstor) but this is potentially quite relevant to that.

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New Weapon in Web War Over Piracy
By BRAD STONE and MIGUEL HELFT
Published: February 19, 2007
Content-recognition software could address a major entertainment industry concern— songs and videos being posted on the Web without permission.
http://www.nytimes.com/2007/02/19/technology/19video.html?ex=1329541200&en=ac662a919b4ff2cb&ei=5124&partner=permalink&exprod=permalink

Freedom for Prisoners of Voice Mail -- NY Times

Looks interesting... wonder if it's worth a try

---

State of the Art

Freedom for Prisoners of Voice Mail

By DAVID POGUE

Published: February 15, 2007

If you're tired of spending time and cellphone minutes listening to the voice-mail lady, try new tools that convert voice messages to text and deliver them by e-mail.

http://www.nytimes.com/2007/02/15/technology/15pogue.html?ex=1329282000&en=0a077798a213507c&ei=5124&partner=permalink&exprod=permalink
https://simulscribe.com/

ihop-net.org

Perhaps nice to interface with LinkHub, pubnet... .

---

http://www.ihop-net.org/UniPub/iHOP

www.levity.com/digaland/whitman

Liked the very interesting Whitman images, which make up one from many. These are similar in some respects to the cover of Nature for the sequencing of the genome (also, linked below).

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http://www.levity.com/digaland/whitman/index.html
http://bioinfo.mbb.yale.edu/~mbg/dom/fun3/nature-cover/
http://www.nature.com/nature/supplements/collections/humangenome

The Invisible Enemy -- Wired

Interesting pop science article that highlighted the new problem Acinetobacter baumannii has become from the war in Iraq.

---

http://www.wired.com/wired/archive/15.02/enemy.html
The Invisible Enemy
Issue 15.02 - February 2007
The Pentagon created the perfect machine for saving the lives of soldiers wounded in Iraq. But then GIs started getting sick. The culprit: a drug-resistant supergerm infecting the military's evacuation chain.
By Steve Silberman
A homemade bomb exploded under a Humvee in Anbar province, Iraq, on August 21, 2004. The blast flipped the vehicle into the air, killing two US marines and wounding another - a soft-spoken 20-year-old named Jonathan Gadsden who was near the end of his second tour of duty. In previous wars, he would have died within hours. His skull and ribs were fractured, his neck was broken, his back was badly burned, and his stomach had been perforated by shrapnel and debris....
But he still had mysterious symptoms that he couldn't shake, like headaches, rashes, and intermittent fevers. His doctors gave him CT scans, laxatives, methadone, beta-blockers, Xanax, more surgery, and more antibiotics. An accurate evaluation of his case was difficult, however, because portions of his medical records never arrived from Bethesda. If they had, they would have shown a positive test for a kind of bacteria called Acinetobacter baumannii. In the taxonomy of bad bugs, acinetobacter is classified as an opportunistic pathogen. Healthy people can carry the bacteria on their skin with no ill effects - a process known as colonization. But in newborns, the elderly, burn victims, patients with depressed immune systems, and those on ventilators, acinetobacter infections can kill. The removal of Gadsden's spleen and the traumatic nature of his wounds made him a prime target....

www.eia.doe.gov

Might be nice to correlate with insulation and other durables over time.

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http://www.eia.doe.gov/emeu/steo/pub/contents.html

Gene Themes

EMINENT DOMINION -- New Yorker

Interesting re-evaluation, coupled with three exhibitions that might be nice to see.

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http://www.newyorker.com/critics/skyline/
http://www.newyorker.com/printables/critics/070205crsk_skyline_goldberger
http://www.learn.columbia.edu/moses/
EMINENT DOMINION
Rethinking the legacy of Robert Moses.
by PAUL GOLDBERGER
Issue of 2007-02-05
Posted 2007-01-29
For a generation, the standard view of Robert Moses has been that he transformed New York but didn't really make it better. This view was shaped by Robert Caro's epic biography "The Power Broker"—published in 1974 and in print ever since. (Parts of it initially ran in this magazine.) Caro portrays Moses as a brilliant political operative who perpetuated his power by means of grand public works....Moses is clearly due for a reëvaluation, and this week sees the opening of "Robert Moses and the Modern City," a huge exhibition that surveys his impact on New York. Organized by Hilary Ballon, an architectural historian at Columbia, the exhibition extends over three institutions. The broadest installation, at the Museum of the City of New York, is called "Remaking the Metropolis," and presents Moses's highway system and the big institutions, like Lincoln Center and the United Nations, that he helped build. "The Road to Recreation," at the Queens Museum of Art, documents Moses's new parks, playgrounds, and swimming pools; and "Slum Clearance and the Superblock Solution," at Columbia's Wallach Art Gallery, shows his inventive mastery of the federal government's Title I slum-clearance programs, and the results, both good and bad.
[cached]

Data bleach

Total information awareness for worm genetics -- Science

Some relevant worm data integration papers. Integration methods are fairly simple from a computational standpoint.

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16527956&query_hl=2&itool=pubmed_docsum
Science. 2006 Mar 10;311(5766):1381-2. 
Genetics. Total information awareness for worm genetics.Eddy SR.

http://www.sciencemag.org/cgi/content/full/311/5766/1481
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16527984&itool=pubmed_AbstractPlus
Science 10 March 2006:
Vol. 311. no. 5766, pp. 1481 - 1484
DOI: 10.1126/science.1123287
Genome-Wide Prediction of C. elegans Genetic Interactions
Weiwei Zhong and Paul W. Sternberg*

http://www.nature.com/nature/journal/v436/n7052/abs/nature03876.html
Nature 436, 861-865 (11 August 2005) | doi:10.1038/nature03876
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
Kristin C. Gunsalus et al.

What is biophysics ?

Structures, interactions and functions of biological molecules studied and
understood through the application of quantitative methods based on
physics and chemistry.

Is this the end of the scholarly journal? -- Christian Science Monitor

An interview based on article in the Scientist.

---

Is this the end of the scholarly journal?
http://www.csmonitor.com/2007/0124/p14s02-stss.html
Publishing research to blogs and e-books is so easy, some are wondering if peer-reviewed journals are on their way to obsolescence.
By Gregory M. Lamb | Staff writer of The Christian Science Monitor
Scientific advances sometimes come as lightning flashes of inspiration. But when scientists sit down to record and take credit for what they've found, they still use much the same method they have for decades – an article published in a scholarly journal.
But science's hidebound traditions are changing. The Internet has opened up new forms of publishing in which anyone in the world can find and read a scientific paper. And papers themselves are becoming more interactive, leading readers to the underlying data, videos, and discussions that augment their value. With blogs and e-books providing easy means of self-publishing, some observers are speculating that scholarly journals and their controversial system of peer reviews may not be needed at all.
"The traditional journal publishing medium we've grown used to really needs to evolve and change because that's not the way people are accessing information," says Mark Gerstein, a professor of biomedical informatics at Yale University in New Haven, Conn. Dr. Gerstein cowrote an article, "The Death of the Scientific Paper," which appeared last year on The-Scientist.com, an online science magazine....
Already, an online database called arXiv (www.arXiv.org), hosted by Cornell University in Ithaca, N.Y., contains more than 400,000 scientific papers posted by their authors without peer review. (The papers often appear later in peer-reviewed journals). Its comprehensiveness makes arXiv (pronounced "archive") a valuable tool, Gerstein, the Yale researcher, says. If someone claims to make a new discovery, anyone can search this database and say, "No, you didn't. It's in the arXiv."
Nonetheless, Gerstein says he thinks scientific journals, and some kind of peer review, will be around for a long time. Publishing in prestigious journals is "deeply intertwined with [scientists'] reputations and their promotions," he says. "You still want to get the stamp of approval of a journal."

Don’t Call. Don’t Write. Let Me Be -- NY Times

Lots of advice to remove oneself from spam communication.

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Business

Don't Call. Don't Write. Let Me Be.

By DAMON DARLIN

Published: January 20, 2007

How to get your name off lists, so sales people won't call, junk mail won't come, and spam won't clog the in-box.

http://www.nytimes.com/2007/01/20/business/20money.html?ex=157680000&en=896f28ce9e43bcc0&ei=5124&partner=permalink&exprod=permalink
http://www.the-dma.org/consumers/offmailinglist.html
http://donotcall.gov/
http://www.optoutprescreen.com/
http://www.doubleclick.com/us/about-doubleclick/privacy/dart-adserving.asp
http://www.lexisnexis.com/terms/privacy/data/remove.asp

Some random interesting reads in 2005

8-Jan-05 times.com Two Studies Suggest a Protein Has a Big Role in Heart Disease

8-Jan-05 sciencenews.org What's Wrong with This Picture?

5-Jul-05 TechnologyReview.com The Fading Memory of the State

28-Jul-05 sciam.com Nanobodies by Wayt Gibbs

28-Jul-05 wired.com The Birth of Google

Thoughts on Yale Podcasts

Yale Press Podcast -- http://yalepress.yale.edu/yupbooks/podcast.asp

Nice episode #1. Liked description of The Yale Book of Quotations and Caesar Life of a Colossus (particularly the Addendum on the later). These were good because they gave to easy to understand overviews of well-worked out existing media (i.e. the books). However, it'd be nice if each podcast could have a brief summary and it's own episode page -- e.g. like http://www.sciencefriday.com/pages/2005Publish/Jul/hour2_072905.html

Yale OPA podcast -- http://www.yale.edu/opa/podcast

The web page of this is a bit more confusing. Again it'd be nice, if each podcast could have a brief summary and it's own episode page, so you could refer to (and blog) an individual podcast. Some thoughts on specific ones: The podcast "American Foreign Policy: Multilateralism or Unilateralism. From the Yale Tomorrow campaign launch, recorded Sept. 30, 2006." was good but it'd be nice if it were connected with some specific textual material. Likewise for "Nutrition and Cancer Prevention: How diet can prevent cancer. Part of the Yale Cancer Center Healthline Series, recorded May 21, 2006." Again, however, I don't know where to go for more -- a paper, the professor's site, etc. The Tian Xu podcast is engaging. Liked the vision at end of a series of all possible mouse knockouts with high-res MRI to show which cells they affect. The Salzman talk gives a nice vision of developing a community of biomedical engineering. Both of these suffer from the lack of visuals referred to and some context given at the beginning. They are just bare recordings.

Subcompact Camera comparison

Some random stats and links related to finding the optimal subcompact camera.

http://docs.google.com/View?docid=ddpspxzw_26fdkpfw

Some flowery text on what Synthetic Biology is

Synthetic biology is a natural outgrowth of systems biology in the same way that molecular biotechnology was a natural outgrowth of molecular biology. That is, the molecular biology revolution (in the 1950s and 1960s) led to the discovery of the main molecular actors, thus paving the way for the fields of genetic and molecular engineering in the late 1970s and early 1980s (Goujon, 2001). At present, biology is undergoing another transition, first defining molecular and cellular systems in the context of systems biology and then using these to build new functionalities in the framework of synthetic biology (Arkin & Fletcher, 2006; Endy, 2006; Cassman, 2005; Vidal, 2001; Ge et al., 2003; Kitano, 2002a,b). One the main issues in early synthetic biology is developing sets of standard, interoperable, composable biological parts for manipulation (parts.mit.edu; Endy, 2005).

from wikipedia :

Systems biology is an academic field that seeks to integrate high-throughput biological studies to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system (e.g. metabolic pathways, organelles, cells, physiological systems, organisms etc.) it is hoped that eventually an understandable model of the whole system can be developed.

from wikipedia :

Synthetic biology aims to create novel biological functions and tools by modifying or integrating well-characterized biological components (i.e. genes, promoters) into higher order genetic networks using mathematical modeling to direct the construction towards the desired end product.

Letter in response to "Open-Source Spying" -- NY Times

Here's a letter I wrote in response to the article below (which was never published):
I was very impressed by the recent article in the magazine section about how the
intelligence community could use collective intelligence in the form of wikis
and blogs to help combat potential threats. I think the idea of using collective
intelligence is a great one. However, I was very surprised that the article did
not mention the recent and public episode where it was suggested that Defense
Advanced Research Projects Agency (DARPA) establish a Policy Analysis Market to
help predict terrorist threats. In the framework of magazine article, this
proposal appears to be quite prescient. Given the clear incentive of profit,
efficient markets are an even better idea for harnessing collective intelligence
than wikis and blogs. However, this proposal was strongly criticized in the
press and this lead to the resignation of DARPA department head John Poindexter.

---

http://www.nytimes.com/2006/12/03/magazine/03intelligence.html
Open-Source Spying
By CLIVE THOMPSON
Published: December 3, 2006
When Matthew Burton arrived at the Defense Intelligence Agency in January 2003,
he was excited about getting to his computer. Burton, who was then 22, had long
been interested in international relations: he had studied Russian politics and
interned at the U.S. consulate in Ukraine, helping to speed refugee applications
of politically persecuted Ukrainians. But he was also a big high-tech geek
fluent in Web-page engineering...
[L2E]

Letter in response to "A Cryptologist Takes a Crack at Deciphering DNA’s Deep Secrets" -- NY Times

Here's a letter I wrote in response to the article below (which was never published):
I read with great interest the recent "Scientist at Work" piece in Science Times focusing on Nick Patterson. I work in a similar area to Dr. Patterson and liked the way the piece developed the concept of a "Data Analyst". In particular, I thought it important that it showed that in seemingly disparate fields such as Military Intelligence, Finance, and Genomics, there was a common thread of having to grapple with and analyze large amounts of data. Increasingly, the modern world is being transformed by vast sea of social and commercial information being tracked on the internet and by the huge amounts of data being generated by high-throughput scientific experimentation. Because of this, we are increasingly being confronted with large data sets in many fields. The challenge is how to mine them as Dr. Patterson does. A related issue is how we should educate a new generation of ace analysts who can take a more straightforward path to their problem than Dr. Patterson has.

---

http://www.nytimes.com/2006/12/12/science/12prof.html
Scientist at Work | Nick Patterson
A Cryptologist Takes a Crack at Deciphering DNA's Deep Secrets
By INGFEI CHEN
Published: December 12, 2006
Thirty years ago, Nick Patterson worked in the secret halls of the Government
Communications Headquarters, the code-breaking British agency that unscrambles
intercepted messages and encrypts clandestine communications. He applied his
brain to "the hardest problems the British had," said Dr. Patterson, a
mathematician. Today, at 59, he is tackling perhaps the toughest code of all —
the human genome...Genomics is a third career for Dr. Patterson, who confesses
he used to find biology articles in Nature "largely impenetrable." After 20
years in cryptography, he was lured to Wall Street to help build mathematical
models for predicting the markets. His professional zigzags have a unifying
thread, however: "I'm a data guy," Dr. Patterson said. "What I know about is how
to analyze big, complicated data sets." In 2000, he pondered who had the most
interesting, most complex data sets and decided "it had to be the biology
people."...
[L2E]

Letter in response to "Entrepreneurs See a Web Guided by Common Sense" -- NY Times

Here's a letter I wrote with Andrew Smith in response to the article below (which was never published):
We read with great interest John Markoff's 11/12/2006 article "Entrepreneurs See a Web Guided by Common Sense." We agree with the excitement surrounding the emerging Web 3.0 but we feel that the article did not go enough into the controversy between today's highly unstructured version of the web, where documents are essentially disseminated in natural language free-text lightly marked up with HTML for display, and the more recent and contrasting semantic web being propelled by the World Wide Web Consortium (W3C) which allows web information to be expressed and cross-referenced in fine-grained structured ways so applications can more readily and precisely extract key facts and information without having to worry about disambiguating meaning from natural language texts as is necessary in the current web. The article seemed mostly to suggest that the new Web 3.0 would emerge primarily from complex data mining of the current web to extract important entities (people, businesses, places, etc.) and relationships among them. Unfortunately, this problem is very difficult and is basically the artificial intelligence problem that many researchers have been working hard on for a long time with limited progress. This fact that it is extremely difficult to automatically extract fine-grained data, information, and relationships from today's web (and the best we can practically do is to support coarse-grained topical queries with search engines) is one of the primary motivations of the semantic web. It is noteworthy that the perfect, personalized "travel agent" scenario given in Markoff's article was basically the same as the primary running example from a 2001 Scientific American article by Tim Berners-Lee (the inventor of the web and semantic web) which introduced the semantic web to a wider audience.

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http://www.nytimes.com/2006/11/12/business/12web.html
Entrepreneurs See a Web Guided by Common Sense
By JOHN MARKOFF
Published: November 12, 2006
SAN FRANCISCO, Nov. 11 — From the billions of documents that form the World Wide Web and the links that weave them together, computer scientists and a growing collection of start-up companies are finding new ways to mine human intelligence....

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ooo[L2E]ooo

quickonlinetips.com/archives/2005/02/absolutely-delicious-complete-tools-collection

Thought this was a nice collection of del.icio.us tools, particularly: SlashLinks, sid.vicio.us, From Del.icio.us to WordPress, DiggLicious, and Diggdot.us .
However, couldn't find a tool that would interconvert between Digg and del.ico.us...

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http://www.quickonlinetips.com/archives/2005/02/absolutely-delicious-complete-tools-collection

Taking Control of Electric Bill, Hour by Hour -- NY Times

Availability of continuous pricing of power looks to be a useful feature in new dwellings...

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http://www.nytimes.com/2007/01/08/business/08power.html?ex=157680000&en=ce5fbf661c20579d&ei=5124&partner=permalink&exprod=permalink
Taking Control of Electric Bill, Hour by Hour
By DAVID CAY JOHNSTON
Published: January 8, 2007
A pilot project in Chicago allows residents to save money by shifting their use of power.

Midnight Run Timings

Lap	Wall clock	Delta	Time (min)	Mile	Minutes/mile
	12:00:00	0:02:46	0:19:47	0 to 2	0:09:54
1	12:02:46	0:17:01
2	12:19:47	0:10:15	0:10:15	2 to 3	0:10:15
3	12:30:02	0:08:12	0:09:13	3 to 4	0:09:13
	12:38:14	0:01:01
	12:39:15
Total		0:39:15

Graphs of the times with heart rates are here

The Energy-Drink Buzz Is Unmistakable. The Health Impact Is Unknown -- NY Times

280 mg caffeine/8oz > 2 * amt. in cup of coffee

---

http://select.nytimes.com/search/restricted/article?res=FA0C15F93F550C718DDDAB0994DE404482
THE CONSUMER; The Energy-Drink Buzz Is Unmistakable. The Health Impact Is Unknown.
By MICHAEL MASON
Published: December 12, 2006
Meet Jamey Kirby. If you're young enough, and hip enough, he'd like to sell you some Cocaine... Each 8.4-ounce can of Cocaine contains 280 milligrams of caffeine, more than twice the amount in a cup of coffee, and a throat-numbing blend of fiery spices.... This year, in a study published in the Journal of Analytical Toxicology, a team of researchers analyzed the caffeine content of 10 popular energy drinks and found concentrations as high as 141 milligrams per 16-ounce can. While the Food and Drug Administration does not regulate the amount of caffeine in soft drinks, agency guidelines for colas suggest no more than 68 milligrams per 12-ounce serving....

So Many Advances in Medicine, So Many Yet to Come -- NY Times

Thought this was a great overview in simple terms of the advances in medicine in the last half century

---

http://www.nytimes.com/2006/12/26/health/26docs.html?ex=157680000&en=f5c21ae48e834d42&ei=5124&partner=permalink&exprod=permalink
So Many Advances in Medicine, So Many Yet to Come
By LAWRENCE K. ALTMAN, M.D.
Published: December 26, 2006
Technology and treatments have come a long way, but the gains have led to new challenges.

Tennis Venues

Crosstown Tennis, 14 W. 31st St., New York
East River Tennis Club, 44-02 Vernon Blvd., Long Island City
Eastside Tennis Club, 220 E. 76th St., New York
Forest Hills Tennis Stadium, 69th Ave. And Burns Rd, Forest Hills
Hrc Tennis, South St., Piers 13 And 14, New York
Midtown Tennis Club, 341 Eighth Ave., New York
New York Health And Racquet Club - Village Tennis Courts, 110 University Place, New York
Prospect Park Tennis Center, 305 Coney Island Ave., Brooklyn
Randall's Island Indoor Tennis, Randall's Island Tennis Field House, New York
Tennis Club Grand Central, 15 Vanderbilt Ave., New York
Tower Tennis Courts, 1725 York Ave., New York
U.S.T.A. National Tennis Center, Flushing Meadows-Corona Park, Flushing
Van Cortlandt Park - Stadium Tennis Courts, W. 241st St. And Broadway, Bronx

Lucrative store locations pinpointed by new model -- New Scientist

Interesting "geo" (realestate) mining

---

http://www.newscientist.com/channel/fundamentals/mg19225724.900-lucrative-store-locations-pinpointed-by-new-model.html
Lucrative store locations pinpointed by new model
07 October 2006
>From New Scientist Print Edition.
The old mantra about the three most important factors for a shop's success - location, location and location - has been borne out by a new mathematical model. It could help retailers pinpoint lucrative sites for their stores....

A Letter in response to "Cyber-Neologoliferation" -- NY Times

Here's the letter I wrote in response to this article (which was never published):
I was struck by the recent article on the development of the third edition of the Oxford English Dictionary. I was impressed by the degree to which the curators of this dictionary are embracing modern, computerized search in addition to manual annotation. The parallels between making a lexicon of all the English words and the way scientists are annotating the genes in many genomes being sequenced are quite striking. In both cases, people are looking for where it (word or gene) first appeared and how it's varied in usage across many different contexts. One crucial difference, however, is in the gene annotation business, researchers are very interested in how often a gene is duplicated or how common it is. I feel that people should probably do the same in relation to the OED, tabulating words by their frequency of usage. In a rough fashion, this can simply be done by looking at some statistics, such as the number of "Google hits" for a given term.

---

http://www.nytimes.com/2006/11/05/magazine/05cyber.html
Cyber-Neologoliferation
By JAMES GLEICK
Published: November 5, 2006
When I got to John Simpson and his band of lexicographers in Oxford earlier this
fall, they were working on the P's. Pletzel, plish, pod person, point-and-shoot,
polyamorous — these words were all new, one way or another. They had been
plowing through the P's for two years but were almost done (except that they'll
never be done), and the Q's will be "just a twinkle of an eye," Simpson said. He
prizes patience and the long view. A pale, soft-spoken man of middle height and
profound intellect, he is chief editor of the Oxford English Dictionary and sees
himself as a steward of tradition dating back a century and a half....

ooo[clip]ooo

ooo[general]ooo

ooo[L2E]ooo

Oenology: Red wine procyanidins and vascular health -- Nature

Looks like I should shift from California Reds to those from département of Gers in the Midi-Pyrenees in southwest France and those from Nuoro province, Sardinia.

---

http://www.nature.com/nature/journal/v444/n7119/abs/444566a.html
Nature 444, 566 (30 November 2006) | doi:10.1038/444566a; Received 29 August 2006; Accepted 9 November 2006; Published online 29 November 2006
Oenology: Red wine procyanidins and vascular health
R. Corder1, W. Mullen2, N. Q. Khan1, S. C. Marks2, E. G. Wood1, M. J. Carrier1 and A. Crozier1
Regular, moderate consumption of red wine is linked to a reduced risk of coronary heart disease and to lower overall mortality1, but the relative contribution of wine's alcohol and polyphenol components to these effects is unclear2. Here we identify procyanidins as the principal vasoactive polyphenols in red wine and show that they are present at higher concentrations in wines from areas of southwestern France and Sardinia, where traditional production methods ensure that these compounds are efficiently extracted during vinification. These regions also happen to be associated with increased longevity in the population....We used the 1999 census data to identify unusual patterns of ageing in France (see supplementary information) and found that there are relatively more men aged 75 or over in the département of Gers in the Midi-Pyrenees in southwest France.Wines from Nuoro and the Gers area have 2–4-fold more biological activity and OPC content than other wines (Fig. 1c, d). This difference remains (P < 0.001) when OPC measurements are extended to a wider selection of wines from the Gers area (2.9 0.1 mM, n = 58), from France (1.8 0.1 mM, n = 61) and from other parts of the world (1.5 0.04 mM, n = 227)....

American Culture’s French Connection -- NY Times

Why isn't there an AmericanCulture.org? The answer from France.

---

http://www.nytimes.com/2006/12/26/books/26martel.html?ex=157680000&amp;amp;en=a4db9732c27a057e&ei=5124&partner=permalink&exprod=permalink

American Culture's French Connection

By ALAN RIDING

Published: December 26, 2006

In "Culture in America," Frédéric Martel challenges the view that (French) culture financed by the government is good and that (American) culture shaped by market forces is bad.... Reviewing the book in Le Monde, Michel Guerrin and Emmanuel de Roux also said its strength lay in its emphasis on investigation over opinion. And another article in Le Monde took the American cultural statistics collected by Mr. Martel and compared them with similar figures for France. Its unexpected conclusion was that measured per capita the cultural infrastructures in the two countries were roughly similar... The first half of "Culture in America" — the title echoes Tocqueville's own "Democracy in America" — is built around a question that puzzles some French: Why doesn't the United States have a Culture Ministry?...He seemed to be looking forward to a fight. "That's why my book is about France," he said, "while being about America."

Route to LGA over Queensboro

http://maps.google.com/maps?f=d&hl=en&saddr=40.757,-73.89&daddr=25th+Avenue,+Queens,+NY+to:40.756,-73.88+to:40.757,-73.9205&sll=40.760905,-73.88115&sspn=0.022364,0.039525&ie=UTF8&om=1&z=13&ll=40.747907,-73.889065&spn=0.089474,0.1581
over queensboro bridge
* Northern Ave
* 51 St.
* 32 Ave.
* somehow get to 25 Ave.
* enter highway near 60T

"Everything before the but is a lie" -- anonymous quote

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts -- PNAS

Interesting analysis of some yeast pseudogenes. However, omits reference to Harrison et al. (2002) JMB.

---

http://www.hhmi.org/bulletin/spring2005/upfront/yeast.html
Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14144-9. Epub 2004 Sep 20.
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15381776&query_hl=20&itool=pubmed_docsum

Literature mining for the biologist: from information retrieval to biological discovery -- Nat. Rev. Genetics

Good review... but doesn't mention pubnet!

---

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16418747&query_hl=15&itool=pubmed_docsum
Nat Rev Genet. 2006 Feb;7(2):119-29. 
Literature mining for the biologist: from information retrieval to biological discovery.Jensen LJ, Saric J, Bork P.

Co-evolution of transcriptional and post-translational cell-cycle regulation -- Nature

Regulatory network evolution

---

Co-evolution of transcriptional and post-translational cell-cycle regulation
Nature. 2006 Oct 5;443(7111):594-7. Epub 2006 Sep 27.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&dopt=AbstractPlus&list_uids=17006448&query_hl=10&itool=pubmed_docsum

www-cse.ucsd.edu/~rik

some bio textmining

---

http://www-cse.ucsd.edu/~rik/
Richard K. Belew
"Literature and its referents: Analyzing PubMed citations across PFAM", Richard K. Belew, Robert Finn, Alex Bateman, Poster at ISMB02
http://www-cse.ucsd.edu/~rik/papers/pfam-pubmed-ismb02.pdf

Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics -- J Mol. Biol.

Datamining the struc. genomics pipeline

---

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=16211521
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15544807&query_hl=5&itool=pubmed_DocSum
J Mol Biol. 2004 Dec 3;344(4):977-91.
Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics.
Canaves JM, Page R, Wilson IA, Stevens RC

Good Fats, Bad Fats, and Trans Fats -- sciencefriday.com

For the podcast listener: Thought this was a particularly good one. Nice discussion of different types of fats: good (monounsaturated and polyunsaturated, particularly from plants) and bad (saturated, trans-, from partially hydrogenated vegetable oil)

---

http://www.sciencefriday.com/pages/2006/Nov/hour2_110306.html
Restrictions on Trans Fats - SciFri Podcast - 2006110324
Good Fats, Bad Fats, and Trans Fats
A sizzling steak with a pat of butter on top. Tuna, trout, or herring. A pile of crispy french fries. A flaky biscuit or delicate pie crust. Sure, all have some fat in them - but which fats are good, which are bad, and which are somewhere in between?...

from http://en.wikipedia.org/wiki/Trans_fat
Trans fatty acids (commonly termed trans fats) are a type of unsaturated fat (and may be monounsaturated or polyunsaturated)...
Chemically, trans fats are made of the same building blocks as non-trans fats, but have a different shape. In trans fat molecules, the double bonds between carbon atoms (characteristic of all unsaturated fats) are in the trans rather than the cis configuration, resulting in a straighter, rather than a kinked shape. As a result, trans fats are less fluid and have a higher melting point than the equivalent cis fats.

Slow Is Beautiful -- NY Times

Turtles! living up to 250 years on a very sparse diet.

---

http://select.nytimes.com/search/restricted/article?res=F40611F93F550C718DDDAB0994DE404482
Slow Is Beautiful
By NATALIE ANGIER
Published: December 12, 2006
This was no euphemistic brushoff, no reptilian version of ''Sorry, I'll be busy that night washing my hair.'' Paddling around in a tropically appointed pool at the National Aquarium in Baltimore, the husky female Gibba turtle from South America made all too palpable her disdain for the petite male Gibba that pursued her....''The tale of the tortoise and the hare is the turtle's life story,'' said Mr. Cover, who calls himself a card-carrying member of the ''turtle nerds'' club. ''Slow and steady wins the race.'' With its miserly metabolism and tranquil temperament, its capacity to forgo food and drink for months at a time, its redwood burl of a body shield, so well engineered it can withstand the impact of a stampeding wildebeest, the turtle is one of the longest-lived creatures Earth has known. Individual turtles can survive for centuries, bearing silent witness to epic swaths of human swagger. Last March, a giant tortoise named Adwaita said to be as old as 250 years died in a Calcutta zoo, having been taken to India by British sailors, records suggest, during the reign of King George II....

The Man on the Table Devised the Surgery -- NY Times

Thought this was a great medical, human interest story....

---

http://www.nytimes.com/2006/12/25/health/25surgeon.html?ex=157680000&en=b49710b1b9497c07&ei=5124&partner=permalink&exprod=permalink

The Man on the Table Devised the Surgery

By LAWRENCE K. ALTMAN

Published: December 25, 2006

Dr. Michael DeBakey, one of the first surgeons to perform a coronary bypass operation, is its oldest survivor

stratbridge.com

Interesting niche data mining for sports.

---

http://www.stratbridge.com/news/WSJ-091606.asp
http://money.cnn.com/magazines/fsb/fsb_archive/2006/12/01/8395130/index.htm
Discounting NBA tickets like airline seats
An entrepreneur helps pro sports teams fill stadiums more efficiently, using new technology that tracks ticket sales.
FORTUNE Small Business Magazine
By Maggie Overfelt, FSB Magazine
December 11 2006: 10:06 AM EST
(FSB Magazine) -- As the NBA season gets underway, experts predict a tough slog for the Boston Celtics. Last year's team finished with 33 wins and 49 losses, and the roster this season is filled with younger players and few big names. The bottom line? Senior management has to rely on something else to help attract fans: StratBridge, a 15-person firm based in Cambridge, Mass.....

NIH in the Post-Doubling Era: Realities and Strategies -- Science magazine

Thought this was an interesting article on where NIH is going for the year.

---

http://www.sciencemag.org/cgi/content/full/314/5802/1088
Elias A. Zerhouni

Some notes from Data Mining 2006 (cs545)

Data mining lecture slides for courses based on reference text books

---

Ian Witten and Eibe Frank:
http://books.elsevier.com/us//mk/us/subindex.asp?maintarget=companions/defaultindividual.asp&isbn=0120884070&country=United+States&srccode=&amp;ref=&subcode=&amp;head=&pdf=&basiccode=&txtSearch=&SearchField=&operator=&order=&community=mk

Margaret Dunham:
http://engr.smu.edu/~mhd

Pang-Ning Tan, Michael Steinbach, and Vipin Kumar:
http://www-users.cs.umn.edu/%7Ekumar/dmbook/index.php#item4

Jiawei Han and Micheline Kamber:
http://www.cs.uiuc.edu/class/fa05/cs412/schedule.htm

http://twiki.med.yale.edu/twiki/bin/view/Lessons/SlidesFall04

==
Markov Blankets

Market Blankets (MB) are a promising, relatively new, set of datamining techniques for handling feature selection and related issues on Bayesian networks. Learn about MBs, read about different algorithms for implementing them , try them out for some typical problems (especially ones with many features), and write a short review paper.

References:
http://dbpubs.stanford.edu:8090/pub/1996-77
http://citeseer.ist.psu.edu/koller96toward.html
http://citeseer.ist.psu.edu/xing01feature.html
http://discover1.mc.vanderbilt.edu/discover/public/Presentations/HITON_amia_2003.pdf
http://reports-archive.adm.cs.cmu.edu/anon/cald/CMU-CALD-04-102.pdf

Those Inflatable Santas: Eyepoppers to Eyesores -- NY Times

Seems to be an expensive new fad

---

http://www.nytimes.com/2006/12/22/nyregion/22inflate.html?ex=157680000&amp;en=149d00bec3b33dc9&ei=5124&partner=permalink&exprod=permalink
Those Inflatable Santas: Eyepoppers to Eyesores
By PAUL VITELLO
Published: December 22, 2006
Whatever else Christmas in America means, it now also includes inflatable outdoor decorations.... But the inflatables have brought the notion of Christmas self-expression to another plane. Now, the Macy's Thanksgiving Day Parade, that televised triumphal march that inaugurates the season, can live on in miniature for weeks at a time, swaying and bobble-heading across the front lawn of anyone willing to pay the electric bill — maybe a thousand dollars if you keep them inflated all the time, less if you leave the skins of your Christmas characters sprawled on the ground most of the day, their crumpled faces staring blankly at the sky or the sod, depending....The inflatables sell off the shelf for $69 to $300, and Gemmy Industries Corporation of Coppell, Tex., which claims to produce the majority of the large figures sighted this year on lawns, porches, terraces and roofs from Long Island to Los Angeles, is not shy about the product's corner-cutting appeal.

Dosage sensitivity and the evolution of gene families in yeast -- Nature

Interesting in relation to copy number. (Also, other papers by Hurst.)

---

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12853957&query_hl=4&itool=pubmed_docsum
Nature. 2003 Jul 10;424(6945):194-7.Click here to read  Links
Dosage sensitivity and the evolution of gene families in yeast.
Papp B,Pal C, Hurst LD.

Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations -- J Comput Biol.

structure and covariation angle looks interesting

---

http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.929
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16761919&query_hl=1&itool=pubmed_docsum
J Comput Biol. 2006 May;13(4):929-45.
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
Gunewardena S, Jeavons P, Zhang Z.

A particular only bacterial fold

A particular only bacterial fold -- beta-lactamases and D-Ala carboxypeptidases.
These enzymes perform functions associated with the unique structure of the bacterial cell wall (i.e. antibiotic resistance and cleavage of D-Ala peptides).

A Scientist's Nightmare: Software Problem Leads to Five Retractions -- Science

Computer bugs mess up membrane protein structures... Could this have been seen ahead of time? (Also note use of Google scholar by Science to find citations.)

---

http://www.sciencemag.org/cgi/content/full/314/5807/1856
Until recently, Geoffrey Chang's career was on a trajectory most young scientists only dream about. ...His lab generated a stream of high-profile papers detailing the molecular structures of important proteins embedded in cell membranes....Then the dream turned into a nightmare. In September, Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang's group had described in a 2001 Science paper. When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure. Unfortunately, his group had used the program to analyze data for other proteins. As a result, on page 1875, Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures....Chang's MsbA structure was the first molecular portrait of an entire ABC transporter, and many researchers saw it as a major contribution toward figuring out how these crucial proteins do their jobs. That paper alone has been cited by 364 publications, according to Google Scholar.

A impressionists view of Connecticut

"Road to the Land of Nod" 1910 by Frederick Childe Hassam
was painted in the Weir farm in CT
http://www.nps.gov/wefa
http://www.thechronicle.us/print_active.php?id=1341
http://maps.google.com/maps?q=735+Nod+Hill+Road,+Wilton,+CT+06897
The image -- http://mylifestream.net/photostream/2006/12/c-hassam-road-to-land-of-nod-20dec06.html]

http://metnet.vrac.iastate.edu/browser -- pubmed assistant

Perhaps worth a download...

---

http://metnet.vrac.iastate.edu/browser/manual.htm

Some random but interesting quotes and tidbits

Some random but interesting quotes and tidbits I've been accumulating.... might find them interesting.

---

"This will be a better world when the power of love replaces the love of power."

"Ontology = Specification of a conceptualization"

"REST = random episodic silent thought"

"The 'four M's', measurement, mining, modeling and manipulation" -- D Lauffenburger.

"When easter is: 1st Sunday after 1st full moon after Vernal equinox"
(difficult to place because involves joining solar & lunar calendars)

"The more choices we are presented with, the more likely it is we'll become a "maximizer" and cease being a "sufficer", (to use the terminology psychologist Barry Schwartz uses in The Paradox of Choice), meaning we're more likely to be unsatisfied with anything less than perfection. "
(from http://www.popmatters.com/pm/columns/article/6668/freedom-from-choice)

loranya.com

Being born with a website! -- http://www.loranya.com

‘Sonic Hedgehog’ Sounded Funny, at First -- NY Times

Interesting article on gene names in the same spirit as "What's in a name?"

---

http://www.nytimes.com/2006/11/12/weekinreview/12schwartz.html
'Sonic Hedgehog' Sounded Funny, at First
By JOHN SCHWARTZ
Published: November 12, 2006
"Lunatic fringe," "head case" and "one-eyed pinhead" might sound like insults from the schoolyard or talk radio. But these are actually examples of the kind of oddball names that scientists give to genes they discover....

Listing of Statistical Software, besides R

Made up this listing of Statistical Software, besides R -- thought it might be useful

---

http://www.JMPdiscovery.com/
Splus -- http://www.mathsoft.com/webstore
SAS -- http://www.sas.com/software/products.html
statview -- www.statview.com (mac only?)
statistica ??
sigma plot -- www.spss.com
sigma stat --
SPSS -- www.spss.com
MatLab statistics -- http://www.mathworks.com/
    http://www.eng.yale.edu/Matlab/
NAG excel add ins -- http://www.nag.com/
atlantis -- http://sigmasoftc.com/atlantis/
Good listing of software at
http://statlab.stat.yale.edu/statlab/software.html
http://www.eng.yale.edu/Mathematica/

nextgencode.com

Perhaps (!) a promising biotech startup, as featured in the 16 Nov. WSJ

---

http://nextgencode.com

The Artist and the Mathematician -- Science Friday

"Chris" lives!

---

http://www.sciencefriday.com/pages/2006/Nov/hour2_111706.html
http://www.amazon.com/o/ASIN/1560259310/sciencefriday/
Science Friday > Archives > 2006 > November > November 17, 2006, Hour Two:
The Family that Couldn't Sleep / The Artist and the Mathematician
Starting in the 1930s, Nicolas Bourbaki published dozens of papers, becoming a famous mathematician. There was just one problem: he didn't exist. Join Ira in this hour on Science Friday for a conversation with Amir Aczel about the genius mathematician who never existed.

KT event

According to Wikipedia, mice and men diverged 75 million years ago and then we had the major KT event 10 million years later.

---

http://www.ucmp.berkeley.edu/diapsids/extinction.html
http://en.wikipedia.org/wiki/Dinosaur_extinction
http://en.wikipedia.org/wiki/Timeline_of_evolution#_note-20
http://en.wikipedia.org/wiki/Timeline_of_evolution#_ref-20

Cycling Around NYC

Top of Manhattan

Route on Google maps

Summary Data
Total Time (h:m:s)	3:41:08	10:46 pace
Moving Time (h:m:s)	2:33:33	7:28 pace
Distance (mi )	20.53
Moving Speed (mph)	8.0 avg.	24.5 max.
Elevation Gain (ft)	+7,875 / -8,006
Avg. Heart Rate	74 bpm	Zone 0.8
Temperature (°F)	50.4°F avg.	51.8°F high
Wind Speed ( mph)	S 3.7 avg.	S 5.8 max.

Central Park to Prospect Park

Route on Google maps
http://www.onnyturf.com/subway and http://monkeyhomes.com/map/nycsubway.php have matching subway maps giving connections back.

Summary Data
Total Time (h:m:s)	5:09:31	11:24 pace
Moving Time (h:m:s)	4:02:56	8:57 pace
Distance (mi )	27.14
Moving Speed (mph)	6.7 avg.	49.2 max.
Elevation Gain (ft)	+2,803 / -2,833
Avg. Heart Rate	84 bpm	Zone 0.9
Temperature (°F)	63°F avg.	64.4°F high
Wind Speed ( mph)	SSE 6.2 avg.	SSE 8.1 max.

Up West Side to NJ

Route on Google maps

Summary Data
Total Time (h:m:s)	3:12:13	16:19 pace
Moving Time (h:m:s)	1:38:16	8:20 pace
Distance (mi )	11.78
Moving Speed (mph)	7.2 avg.	17.6 max.
Elevation Gain (ft)	+4,407 / -4,375
Avg. Heart Rate	83 bpm	Zone 0.9
Temperature (°F)	45.8°F avg.	46.4°F high
Wind Speed ( mph)	N 1.9 avg.	N 5.8 max.

Metcalfe's Law is Wrong -- IEEE Spectrum

Thought this social networking analogy gave some nice intuition about the power-law network structures.

---

Metcalfe's Law is Wrong
http://spectrum.ieee.org/jul06/4109
By Bob Briscoe, Andrew Odlyzko, and Benjamin Tilly
Communications networks increase in value as they add members—but by how much? The devil is in the details

Of all the popular ideas of the Internet boom, one of the most dangerously influential was Metcalfe's Law. Simply put, it says that the value of a communications network is proportional to the square of the number of its users....The foundation of his eponymous law is the observation that in a communications network with n members, each can make (n–1) connections with other participants. If all those connections are equally valuable—and this is the big "if" as far as we are concerned—the total value of the network is proportional to n(n–1), that is, roughly, n^2.... We propose, instead, that the value of a network of size n  grows in proportion to n log(n)....To understand how Zipf's Law leads to our n log(n) law, consider the relative value of a network near and dear to you—the members of your e-mail list. Obeying, as they usually do, Zipf's Law, the members of such networks can be ranked in the same sort of way that Zipf ranked words—by the number of e-mail messages that are in your in-box. Each person's e-mails will contribute 1/k to the total "value" of your in-box, where k is the person's rank. The person ranked No. 1 in volume of correspondence with you thus has a value arbitrarily set to 1/1, or 1. (This person corresponds to the word "the" in the linguistic example.) The person ranked No. 2 will be assumed to contribute half as much, or 1/2. And the person ranked kth will, by Zipf's Law, add about 1/k to the total value you assign to this network of correspondents. That total value to you will be the sum of the decreasing 1/k values of all the other members of the network. So if your network has n members, this value will be proportional to 1 + 1/2 + 1/3 +… + 1/(n–1), which approaches log(n). More precisely, it will almost equal the sum of log(n) plus a constant value. Of course, there are n-1 other members who derive similar value from the network, so the value to all n of you increases as n log(n). Zipf's Law can also describe in quantitative terms a currently popular thesis called The Long Tail.....

To Probe Further
David P. Reed argues for his law in "The Sneaky Exponential" on his Web site at http://www.reed.com/Papers/GFN/reedslaw.html.
Several additional quantitative arguments are made for the n log(n) value for Metcalfe's Law on the authors' Web sites at http://www.cs.ucl.ac.uk/staff/B.Briscoe and http://www.dtc.umn.edu/~odlyzko.
Chris Anderson's article "The Long Tail" was featured in the October 2004 issue of Wired. Anderson now has an entire Web site devoted to the topic at http://www.thelongtail.com.
An article in the December 2003 issue of IEEE Spectrum, "5 Commandments," which can be found at http://www.spectrum.ieee.org/dec03/5com, discusses Moore's and Metcalfe's laws, as well as three others: Rock's Law ("the cost of semiconductor tools doubles every four years"); Machrone's Law ("the PC you want to buy will always be $5000"); and Wirth's Law ("software is slowing faster than hardware is accelerating").

cycling fast loops in Central Park

4 fast (for me) loops in Central Park. Some stats and images below.

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route on Google Maps
http://gerstein.info/gps/cycling-fast-loops-in-Central-Park-heartrate.jpg
Total Time (h:m:s) 2:08:16 5:08 pace
Moving Time (h:m:s) 1:55:04 4:36 pace
Distance (mi ) 24.96
Moving Speed (mph) 13.0 avg. 30.9 max.
Avg. Heart Rate 133 bpm
Temperature (°F) 53.6°F avg. 53.6°F high
Wind Speed ( mph) WNW 8.0 avg. WNW 12.6 max.

Cycling Around New Haven

Route on Google Maps [static cached image]
Elevation Profile
http://textstream.blogspot.com/2006/11/how-to-get-on-farmington-canal-heritage.html

Total Time (h:m:s)	7:36:51	10:54 pace
Moving Time (h:m:s)	4:52:57	6:59 pace
Distance (mi )	41.91
Moving Speed (mph)	8.6 avg.	20.0 max.
Elevation Gain (ft)	+3,583 / -3,586
Avg. Heart Rate	88 bpm	Zone 1.0
Temperature (°F)	48°F avg.	57.2°F high
Wind Speed ( mph)	SSE 5.1 avg.	SSE 8.1 max.