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.

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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.

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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.

Marshall's IT Plan for Janelia Farm -- Bio IT World

Might be useful to think about in terms of future high-performance computing purchases. See extracted snippets below.

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http://www.bio-itworld.com/issues/2006/oct/janelia-farm/
Oct. 2006 
Marshall's IT Plan for Janelia Farm
By  Kevin Davies
Oct. 16, 2006 |  Driving north from Washington Dulles Airport towards the Potomac River, it's easy to miss Janelia Farm. The only road sign faces the opposite direction, belatedly guiding lost taxi drivers retracing their route in search of the campus. Outside a makeshift hut in the middle of a construction site, the security guard waves a visitor's taxi down a long, winding dirt road appropriately named Helix Drive. Around a corner, however, the scene changes dramatically.....
The data center is completely fiber and boasts a multi 10-Gb network. "That's a constant question," says Peterson. "Am I going to get the data to my desktop fast? If I can't, then I'm going to start having people buying their own supercomputers and sliding it under their desk. I don't want that - it's not cost effective, and you can't manage it." He adds: "We're going to have very high-resolution graphics, and people are going to see it very fast. Just one set of microscopes will be generating 500 GB data/day. 24x7x365."....
With some 1,200 64-bit Intel Xeon processors in all, cooling was a major concern. Peterson explains: "We ended up going with Dell and Xeons, which are hot, but we did a calculation: given the price we got with them and given the increased power requirements, it still came in price effective. Having said that, we're very interested in the new generation of Intels and obviously AMD." ...
Everything in the data center is designed to be ripped out and replaced if needed. "The idea is to design infrastructure that is cost effective and easy to replace. We try to be open source - everything is Linux-based, low stress. It helps hugely with the maintenance."....
Peterson selected three tiers and 150 TB of spinning disk storage from EMC. "We started small... seriously!" Peterson smiles. Tier 1 is 30 TB of SAN. Tier 2 is 70 TB of NAS. Tier 3 - the archive - consists of more NAS on disk plus tape. Peterson wants to expand tier 3. "We have capability of over 1 PB of tape," says Peterson. "I can grow to multi petabytes without adding another cabinet." He opens one of a long row of EMC cabinets to show rows of vacant racks....

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements -- Nature Biotech

Might be good to use as benchmark to judge tiling arrays and protein chips

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16964229&query_hl=5&itool=pubmed_docsum
Nat Biotechnol. 2006 Sep;24(9):1151-61.
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Great Example of Spring Minimization

http://java.sun.com/applets/jdk/1.4/demo/applets/GraphLayout/example2.html

original URL
http://www.javasoft.com/applets/jdk/1.0/demo/GraphLayout/example2.html

How to get on the Farmington Canal Heritage Trail in Hamden

How to get on the Farmington Canal Heritage Trail in Hamden

Official Info.
http://www.ct.gov/dot/cwp/view.asp?a=1390&q=259678
Hamden – Farmington Canal Heritage Trail
http://www.ct.gov/dot/LIB/dot/documents/dbikes/024.pdf
Cheshire – Farmington Canal HeritageTrail
http://www.ct.gov/dot/LIB/dot/documents/dbikes/026.pdf
http://www.railserve.com/jump/jump.cgi?ID=8240

Useful maps
Looking at map on
http://www.farmingtoncanal.org/
Looks like approximate entry point is at:
http://maps.google.com/maps?q=41.365182,-72.917729&spn=0.025348,0.05446

Some Distances
Farmington Canal Greenway:
Simsbury-Avon section; 8 mi
Avon-Farmington section; 2.3 mi
Hamden-Cheshire section; 8 mi

Global variation in copy number in the human genome -- Nature

Assume everyone has seen this. Might be nice to start using this data.

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http://www.nature.com/nature/journal/v444/n7118/abs/nature05329.html
Nature 444, 444-454 (23 November 2006)
Global variation in copy number in the human genome
Richard Redon1, Shumpei Ishikawa2,3, Karen R. Fitch4, Lars Feuk5,6, George H. Perry7, T. Daniel Andrews1, Heike Fiegler1, Michael H. Shapero4, Andrew R. Carson5,6, Wenwei Chen4, Eun Kyung Cho7, Stephanie Dallaire7, Jennifer L. Freeman7, Juan R. González8, Mònica Gratacòs8, Jing Huang4, Dimitrios Kalaitzopoulos1, Daisuke Komura3, Jeffrey R. MacDonald5, Christian R. Marshall5,6, Rui Mei4, Lyndal Montgomery1, Kunihiro Nishimura2, Kohji Okamura5,6, Fan Shen4, Martin J. Somerville9, Joelle Tchinda7, Armand Valsesia1, Cara Woodwark1, Fengtang Yang1, Junjun Zhang5, Tatiana Zerjal1, Jane Zhang4, Lluis Armengol8, Donald F. Conrad10, Xavier Estivill8,11, Chris Tyler-Smith1, Nigel P. Carter1, Hiroyuki Aburatani2,12, Charles Lee7,13, Keith W. Jones4, Stephen W. Scherer5,6 and Matthew E. Hurles

Machine Over Man: Stock Pickers' Woes -- WSJ

Appears indexing maybe back in fashion....

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Machine Over Man: Stock Pickers' Woes
By IAN MCDONALD
November 6, 2006; Page R1
Stock pickers' recently healed egos are about to be battered anew....
http://online.wsj.com/article/SB116276713084613902.html

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The Word on Warranties: Don’t Bother -- NY Times

What I always thought...

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http://www.nytimes.com/2006/11/01/technology/circuits/01warr.html
After the Sale
The Word on Warranties: Don’t Bother
By DAVID S. JOACHIM
Published: November 1, 2006
IT may be tempting to buy extended warranties with all those high-tech gadgets on your holiday list, but the experts say they are almost always a waste of money.

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Gaming the Search Engine, in a Political Season -- NY Times

Interesting article pointing to the future of misinformation

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http://www.nytimes.com/2006/11/06/business/media/06link.html
Gaming the Search Engine, in a Political Season
By TOM ZELLER Jr.
Published: November 6, 2006
A GOOGLE bomb — which some Web gurus have suggested is perhaps better called a link bomb, in that it affects most search engines — has typically been thought of as something between a prank and a form of protest. The idea is to select a certain search term or phrase (“borrowed time,” for example), and then try to force a certain Web site (say, the Pentagon’s official Donald H. Rumsfeld profile) to appear at or near the top of a search engine’s results whenever that term is queried.....

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A loss-of-function RNA interference screen for molecular targets in cancer -- Nature

Interesting datasets related to cancer and phenotypes

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16572121&query_hl=6&itool=pubmed_docsum
Nature. 2006 May 4;441(7089):106-10. Epub 2006 Mar 29.
A loss-of-function RNA interference screen for molecular targets in cancer.
Ngo VN, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, Lam LT, Dave S, Yang L, Powell J, Staudt LM.

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The Connectivity Map: using gene-expression signatures to connect

Interesting dataset related to cancer and phenotypes

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17008526&query_hl=4&itool=pubmed_docsum
Science. 2006 Sep 29;313(5795):1929-35.
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP,
Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ,
Clemons PA, Wei R, Carr SA, Lander ES, Golub TR.

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Letter ("Programming Pedigrees") responding to "The Semicolon Wars" -- American Scientist

Resurrected one of my favorite letters, which might be good to follow up on. Viz: :
I read with great interest Brian Hayes's recent column "The Semicolon Wars" on the genealogy of computer languages (Computing Science, July-August). I was struck by the first figure that shows how many well-known languages are related to each other in a tree-like structure. Mr. Hayes carefully compared the development of computer languages to that of spoken languages. This is, of course, quite appropriate. However, another illuminating comparison is to the development and evolution of genomes in biology.
The genome has often been compared to an organism's operating system, and in this sense, its underlying genetic coding is the ultimate computer language. The triplet codons in the literal genetic code have not changed much over time. However, the specific features they encode in different genomes have changed dramatically since life first appeared.
One of the nice things about biology, moreover, is that the main mechanisms underlying this evolution can be studied experimentally. It is believed that the genome evolves through a variety of processes duplicating and copying chunks of DNA, and then further variation happens to these copies. One also sees, most often in bacteria, whole genetic elements horizontally transferred from one organism to another.
The parallels to computer languages in the operation of these mechanisms are quite strong: In a specific lineage of languages (such as that for Algol60, C and Java) one sees the duplication and variation of basic control structures for such items as loops and subroutines, and horizontal transfer of new structures (such as the object-oriented constructions from Simula67).

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Citation of Letter:
Programming Pedigrees
http://www.americanscientist.org/template/AssetDetail/assetid/54089
Volume 94, Number 6 (November-December 2006)
Mark Gerstein
Yale University
New Haven, CT

Article Commented on:
http://www.americanscientist.org/template/AssetDetail/assetid/51982
The Semicolon Wars
Every programmer knows there is one true programming language.
A new one every week
Brian Hayes
American Scientist, July-August 2006
If you want to be a thorough-going world traveler, you need to learn 6,912 ways to say "Where is the toilet, please?" That's the number of languages known to be spoken by the peoples of planet Earth, according to Ethnologue.com. If you want to be the complete polyglot programmer, you also have quite a challenge ahead of you, learning all the ways to say: printf("hello, world\n") ;.....
[L2E]

The Thin Pill -- Wired

Interesting article on how medicines are labelled and targeted

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Issue 14.10 - October 2006
WIRED magazine
The Thin Pill
http://wired.com/wired/archive/14.10/thin.html
FOR PATIENTS, disease puts a name to an affliction. It answers that question we all face at one time or another: What's the matter with me? If there is a clear and precise explanation for what's wrong, then surely there is an equally clear way to get better.....

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A limited universe of membrane protein families and folds -- Prot Sci

Yang Liu et al. part II

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=16815920&dopt=Abstract
Protein Sci. 2006 Jul;15(7):1723-34. 
A limited universe of membrane protein families and folds.
Oberai A, Ihm Y, Kim S, Bowie JU.

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Cyberface: New Technology That Captures the Soul -- NY Times

Thought this was an interesting fusion of science and art -- biophysicists go to Hollywood.  Got to check out the video.

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http://www.nytimes.com/2006/10/15/movies/15waxm.html
Cyberface: New Technology That Captures the Soul
By SHARON WAXMAN
Published: October 15, 2006
THERE’S nothing particularly remarkable about the near-empty offices of Image Metrics in downtown Santa Monica, loft-style cubicles with a dartboard at the end of the hallway. A few polite British executives tiptoe about, quietly demonstrating the company’s new technology....

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Structural biology: proteins flex to function -- Nature

Nice cartoon of protein motions, related to order-disorder transitions. Might be useful in expanding classification.

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16267540&query_hl=2&itool=pubmed_docsum
Nature. 2005 Nov 3;438(7064):36-7.
Structural biology: proteins flex to function.

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http://zoho.com

Zoho might be nice in a similar way to Google Spreadsheet.

A Letter in response to "Inspired by the Cell, With Mitochondrial

Here's the letter I wrote in response to this article (which was never published):
I read with great interest the recent article in Science Times about the new biomedical research center in China with architecture inspired by the cell. It's a great thing having man-made creations inspired by fundamental molecular and cellular architecture. It's ironic that this hasn't happened to a greater degree. Many of the shapes in scientific structures are particularly interesting. Good examples would be the famous double helix of DNA and lipid bilayer of the cell membrane. Moreover, a key aspect of post-modern architecture is referring to and playing with evocative shapes and forms borrowed from non-architectural contexts. Thus, the irony in why famous pieces of post-modern architecture -- such as the AT&T building in New York, which makes reference to a grandfather clock or a Chippendale highboy -- seem to ignore the fundamental designs of nature.

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http://www.nytimes.com/2006/09/12/science/12find.html
FINDINGS; Inspired by the Cell, With Mitochondrial Pools
Article Tools Sponsored By
By JOHN SCHWARTZ
Published: September 12, 2006
The blob is coming to Chengdu. A biomedical research institute in Chengdu,
China, is planning to show true commitment to scientific principles by erecting
an innovative building inspired by cells. Bulges on the surface are meeting
rooms and are intended to represent the proteins embedded in a cell membrane.
The interior pools, shaped like mitochondria, border on the surreal....

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Connecting the Dots -- Am. Sci.

Nice social network analogies. In particular, discussion of Granovetter paper relates nicely to ‘socio-affinity’ index in Gavin et al. (2006) [http://www.nature.com/nature/journal/v440/n7084/abs/nature04532.html]

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September-October 2006
Connecting the Dots
Can the tools of graph theory and social-network studies unravel the next big plot?
Brian Hayes
http://www.americanscientist.org/template/AssetDetail/assetid/53062
In the five years since that wrenching Tuesday morning when hijacked aircraft sliced into the World Trade Center and the Pentagon, Americans have been living with a new undercurrent of worry and mistrust. Naturally, there's fear of further attacks. But there's also concern that measures taken to forestall such attacks could erode traditional rights and liberties. In recent months, controversy has erupted over reports that government agencies are monitoring Internet and telephone communications as well as financial transactions. Some of the surveillance programs are said to be sifting through gigantic data sets, scanning for patterns that might reveal criminal intent or activity....

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http://babyadenine.blogspot.com/

A baby named for a nucleic acid -- http://adenine.org/
Based on http://en.wikipedia.org/wiki/Adenine , there are many potential
derivative names here: AMP, Deoxyadenosine, &c.

Scenic Routes Bike Routes -- NY Magazine

Thought this was interesting... includes bike trip to Bear Mountain and a route through DUMBO.

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Brooklyn Waterfront
http://newyorkmetro.com/nymetro/urban/strategist/everything/bikes/12336/index1.html
Approximately 24 miles
1. Start at City Hall. Head across Park Row onto the bridge.
2. Take first right off the bridge onto Tillary Street.
3. Left on Cadman Plaza West, quick right on Clark Street. Left on Henry Street, down about a mile.
4. Right on Sackett Street, three blocks.
5. Left on Van Brunt Street, down to the end.
6. Walk bike at Beard Street Warehouse.
7. Go back up Van Brunt Street a block, then left on Van Dyke Street to the end.
8. Take sidewalk to avoid cobblestones.
9. Walk bike down Valentino Pier. Exit on Coffey Street, two blocks.
10. Left on Van Brunt Street.
11. Right on Union Street, quick left on Columbia Street.
12. Right on Congress Street, two blocks.
13. Left on Hicks Street, parallel to highway.
14. Left on Montague Street, to the Promenade.
15. Right on Promenade, walk bike to end.
16. Left on Columbia Heights, down the hill to Fulton Landing.
17. First left on Water Street, two blocks against traffic.
18. Left on Washington Street, quick right on Plymouth Street.
19. Enter park on left for a block, under the Manhattan Bridge.
20. Left back onto Plymouth Street.
21. Right on Hudson Avenue, then merge onto Navy Street for a block.
22. Right on Sands Street, down toward Manhattan Bridge.
23. Follow signs to the bridge entrance across the street on the left.
24. Coast down to the Manhattan exit, cross onto Canal Street.
25. Take Canal Street down to the Broadway subway station.

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Which Was Painted by a Child? -- NY Times

Stumbled on this old article... the pictures are very evocative. It really does call into question what is art.

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Which Was Painted by a Child?
http://www.nytimes.com/2004/10/03/weekinreview/03kimm.html
By MICHAEL KIMMELMAN
Published: October 3, 2004
A 4-YEAR-OLD in Binghamton, N.Y., whose splattery paintings have been selling for $6,000, is the latest child to raise the question: What is art?
The painter is Marla Olmstead. Her preferred medium is acrylic on canvas. She gives titles like "Dinosaur" to cheerful smears of blue and red with dark squiggles on top. Her break came at 3 when a family friend hung her art in a local coffee shop. Now collectors are lapping it up....

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And if You Liked the Movie, a Netflix Contest May Reward You Handsomely -- NY Times

Might be nice to download this huge dataset for comparison in some mining applications.

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http://www.netflixprize.com/
http://www.nytimes.com/2006/10/02/technology/02netflix.htm
And if You Liked the Movie, a Netflix Contest May Reward You Handsomely
By KATIE HAFNER
Published: October 2, 2006
Netflix, the popular online movie rental service, is planning to award $1 million to the first person who can improve the accuracy of movie recommendations based on personal preferences. To win the prize, which is to be announced today, a contestant will have to devise a system that is more accurate than the company’s current recommendation system by at least 10 percent. And to improve the quality of research, Netflix is making available to the public 100 million of its customers’ movie ratings, a database the company says is the largest of its kind ever released....

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http://www.ncbi.nlm.nih.gov/WGA

looks interesting

Meet the Life Hackers -- NY Times

Thought this interesting in relation to computer UI design...

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http://www.nytimes.com/2005/10/16/magazine/16guru.html
Meet the Life Hackers
By CLIVE THOMPSON
Published: October 16, 2005
In 2000, Gloria Mark was hired as a professor at the University of California at Irvine. Until then, she was working as a researcher, living a life of comparative peace. She would spend her days in her lab, enjoying the sense of serene focus that comes from immersing yourself for hours at a time in a single project. But when her faculty job began, that all ended. Mark would arrive at her desk in the morning, full of energy and ready to tackle her to-do list - only to suffer an endless stream of interruptions. No sooner had she started one task than a colleague would e-mail her with an urgent request; when she went to work on that, the phone would ring. At the end of the day, she had been so constantly distracted that she would have accomplished only a fraction of what she set out to do. "Madness," she thought. "I'm trying to do 30 things at once."...Lots of people complain that office multitasking drives them nuts. But Mark is a scientist of "human-computer interactions" who studies how high-tech devices affect our behavior, so she was able to do more than complain: she set out to measure precisely how nuts we've all become.

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Hungry Workers, Tied to Desks, Clicking to Get Culinary Delights -- the New York Times

web food

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http://www.nytimes.com/2006/09/17/jobs/17seamless.html
Hungry Workers, Tied to Desks, Clicking to Get Culinary Delights
By JENNIFER 8. LEE
Published: September 17, 2006
EVERY weekday, when they are hungry, thousands of the most highly paid workers in New York City will log on to the same Web site. Finding food while they work requires just a few clicks of the mouse, and fits neatly into their multitasking, desk-bound work lives. Few of those employees will ever see the bill or pay a tip when their food is delivered. Instead, their orders are processed, and billed to their employers, through a single company: SeamlessWeb.....

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Metal Mouth: What You Should Know About the Mercury in Dental Fillings -- WSJ

I have Hg fillings and have worried about this hidden diet additive as well...

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Metal Mouth: What You Should Know About the Mercury in Dental Fillings
Wall Street Journal
September 12, 2006
http://www.healthdecisions.org/Dental/News/default.aspx?doc_id=82399
Whether you have a mouthful of silver teeth or just a few cavities, new questions about the safety of mercury fillings have made many of us nervous about our dental work. Last week, an expert panel for the Food and Drug Administration rejected an agency report that had concluded mercury dental fillings are safe. In a 13-7 vote....

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Where Do Rivals Draw the Line? - New York Times

New Haven appears to be near the border of Red Sox country...
What is a person who wears a Yankees cap and a Red Sox shirt!

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Where Do Rivals Draw the Line? - New York Times
New Britain, Connecticut is where Yankees country ends and Red Sox nation begins...
www.nytimes.com/2006/08/18/sports/baseball/18fans.html
http://mylifestream.net/scrapbook/2006/09/yankees-redsox-border-from-nytimes.html
http://mylifestream.net/photostream/2006/09/yankees-cap-and-redsox-shirt-18sep06.html

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Reimagined Math -- NY Times

Thought these were quite pretty from a mathematical perspective

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http://www.nytimes.com/slideshow/2004/12/02/magazine/20041205_PORTFOLIO_SLIDESHOW_1.html  
It's hard to imagine that these plaster forms, so starkly beautiful, were originally used to teach advanced students trigonometry. ...Last year, the Japanese photographer Hiroshi Sugimoto shot each object, the tallest of which is less than a foot high, from below at close range so that they appear monumental. His series of photographs, ''Mathematical Forms,'' reimagine these scientific models as things of wonder. ...

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industrial-landscape.com

Really liked the photos in the Industrial Landscape book by Brian Hayes. Kind of similar in spirit to those in those in my photostream.

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http://industrial-landscape.com/FG-image-gallery/index.html
http://americanscientist.org/other/BPH.html

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Maureen Hillenmeyer

Interesting image morph

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e-mail bankruptcy -- Wired

Perhaps email bankruptcy would be good for me as well....

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http://www.wired.com/news/culture/0,1284,63733,00.html
Call It the Dead E-Mail Office
By Michael Fitzgerald|
02:00 AM Jun, 07, 2004
If you've been waiting for internet legal visionary Lawrence Lessig to reply to your e-mail, forget about it.
In a script-driven note sent out last week, Lessig wrote: "Dear person who sent me a yet-unanswered e-mail, I apologize, but I am declaring e-mail bankruptcy.".....

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A Letter in response to "Homo Conexus" -- Tech Review

A letter of mine commenting on trust in technology was just published in TR. Thought it was interesting how it was edited.

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Published Version of the Letter:
http://www.technologyreview.com/read_article.aspx?id=17417&ch=biztech&sc=&pg=2
Friday, September 08, 2006 (Sept./Oct. '06 issue)
"Homo Conexus"

I read with interest James Fallows's piece on the new wave of Web-based
applications sometimes called Web 2.0 ("Homo Conexus," July/August 2006). In
using these new programs, he sometimes found that while a new online service was
impressive, he was just too old to enjoy it. Unfortunately, I often feel quite
the same way. I enjoy reading about exciting technological innovations,
but--nose pressed to glass--cannot really participate.

I also liked Fallows's observation that trust, in general, is important to Web
2.0, but would like to add that Web 2.0 demands a specific kind of trust between
a given application's makers and users. Desktop software, such as Microsoft Word
and the Thunderbird e-mail ­client, is the same day-to-day. Not so with Web 2.0.
One can log on to Gmail or Yahoo Mail and find that the interface has radically
changed and that the arrangement and filtering of one's e-mail has been altered.
Mark Gerstein
New Haven, CT

The Original Version of My Letter (which I submitted):
I read with great interest James Fallow's article on Web 2.0. I
empathize with his initial statement about "Dodgeball truth" --
realizing that while a new computational service was impressive, he
had outgrown its potential utility. Unfortunately, I often feel this
way with regards towards many technological innovations. I enjoy
reading about them but -- eyes pressed to glass -- can not really
participate. I also liked Mr. Fallow's emphasis on trust as being
important to Web 2.0. However, I felt he could have elaborated on this
further, discussing the degree to which Web 2.0 requires an explicit
element of trust between users and providers. If one is using a
standard piece of desktop software, such as Microsoft Word or the
Thunderbird email client, one correctly assumes that it is going to be
the same day to day and that the structure of one's creations will
also remain static (unless, of course, we opt to upgrade). Likewise,
when one builds a website in the old Web 1.0 paradigm we can assume
that it will look the same going into the future. This is not the
case with Web 2.0 content. One can suddenly log on to Gmail or Yahoo
Mail and find that the interface has radically changed and that the
arrangement and filtering of one's email has been altered. Likewise,
when one posts content into an online review services, such as Amazon,
one is trusting that the presentation of an opinion will remain the
same going into the future. Of course, the Amazon can easily change
the way its reviews are presented without anyone's consent. Thus,
there really is an additional element of trust in Web 2.0.

Article Commented on:
http://www.technologyreview.com/read_article.aspx?id=17061&ch=infotech
Tuesday, July 25, 2006
Homo Conexus
A veteran technology commentator attempts to live entirely on Web 2.0 for two weeks.
By James Fallows
Sooner or later, we all face the Dodgeball truth. This comes at the moment when you realize that one of life's possibilities -- a product, an adventure, an offer, an idea -- is really meant for people younger than you. This bitter revelation is named for the relatively new Web-based service Dodgeball.com. This is a social networking site, and it represents most of what is supposed to be advanced and exciting about the current wave of "Web 2.0" offerings. Dodgeball's goal is to help you figure out, at any moment of the day or night, whether your friends or people who might be friendly are nearby... Dodgeball is light, mobile, interactive. And for the life of me, I can't imagine when I would use it....

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How Human Cells Get Their Marching Orders -- NY Times

John Rinn in the News !

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http://www.nytimes.com/2006/08/15/science/15skin.htm
How Human Cells Get Their Marching Orders
By NICHOLAS WADE
Published: August 15, 2006

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The references to ppts on PCA

pca-1 - black ---> www.astro.princeton.edu/~gk/A542/PCA.ppt
by Professor Gillian R. Knapp gk@astro.princeton.edu

pca-2 - yellow ---> myweb.dal.ca/~hwhitehe/BIOL4062/pca.ppt
by Hal Whitehead.
This is the class main url http://myweb.dal.ca/~hwhitehe/BIOL4062/handout4062.htm

pca.ppt - what is cov. matrix ----> hebb.mit.edu/courses/9.641/lectures/pca.ppt
by Sebastian Seung. Here is the main page of the course
http://hebb.mit.edu/courses/9.641/index.html

from BIIS_05lecture7.ppt ----> www.cs.rit.edu/~rsg/BIIS_05lecture7.ppt
by R.S.Gaborski Professor

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Gaussian split Ewald: A fast Ewald mesh method for molecular simulation -- J. Chem. Phys.

A new career path: a PhD, then Wall St. millions followed by a return to academia

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http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000122000005054101000001&idtype=cvips&gifs=yes
J. Chem. Phys. 122, 054101 (2005)
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, and David E. Shaw
D. E. Shaw Research and Development, New York, New York 10036

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An RNA gene expressed during cortical development evolved rapidly in humans -- Nature

Interesting article... results of a straightforward computational screen to find conserved elements with accelerated recent evolution and then a detailed focus on the biology of one of the regions found.

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http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05113.html
An RNA gene expressed during cortical development evolved rapidly in humans
Nature advance online publication 16 August 2006
Katherine S. Pollard.... and David Haussler
The developmental and evolutionary mechanisms behind the emergence of human-specific brain features remain largely unknown. However, the recent ability to compare our genome to that of our closest relative, the chimpanzee, provides new avenues to link genetic and phenotypic changes in the evolution of the human brain. We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal–Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks......
Using alignments produced by MULTIZ (http://www.bx.psu.edu/miller_lab/), we identified
34,498 conserved regions of the chimpanzee genome that are >100 bp long
and >96% identical with mouse and rat. Each conserved region was evaluated
for acceleration in the human lineage using a likelihood ratio test .....

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New York Law School: Professors Emeriti

Listing for E Donald Shapiro - authority on law and medicine

"Reclusive Genius," a Letter in response to "The Math Was Complex,

Below (#1) is the letter to the editor of the NY Times on the reclusive mathematician Perelman that was actually published (!). It comments on the week in review article (#2). It was also based on reading a long article in the New Yorker (#3).

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#1
http://www.nytimes.com/2006/09/03/opinion/l03math.html
Reclusive Genius (1 Letter)

Published: September 3, 2006

Re “The Math Was Complex, the Intentions, Strikingly Simple” (Week in Review, Aug. 27):
I read with great interest your article about Grigory Perelman, the Russian mathematician who refused to accept the highest honor in mathematics, the Fields Medal.
Whatever Dr. Perelman’s true motivations are, it has certainly made him something of a hero in the scientific community; he apparently puts deep thought and seeking knowledge ahead of personal accolades and career recognition in marked contrast to many of his prominent colleagues.
One cannot help but wonder whether the way that Dr. Perelman sequestered himself from the minutiae of academic life and from e-mail and correspondence altogether is a principal reason he has been able to think so deeply about a problem.
Perhaps tranquil reclusion is a prerequisite for brilliant thought, as evident in other legendary geniuses like Newton and Darwin.
Mark Gerstein
New Haven, Aug. 28, 2006
The writer is a professor of biomedical informatics and molecular biophysics at Yale.

#2
http://www.nytimes.com/2006/08/27/weekinreview/27johnson.htm
The Math Was Complex, the Intentions, Strikingly Simple
By GEORGE JOHNSON
Published: August 27, 2006
LONG before John Forbes Nash, the schizophrenic Nobel laureate fictionalized
onscreen in “A Beautiful Mind,” mathematics has been infused with the legend of
the mad genius cut off from the physical world and dwelling in a separate realm
of numbers. In ancient times, there was Pythagoras, guru of a cult of geometers,
and Archimedes, so distracted by an equation he was scratching in the sand that
he was slain by a Roman soldier. Pascal and Newton in the 17th century, Gödel in
the 20th — each reinforced the image of the mathematician as ascetic, forgoing a
regular life to pursue truths too rarefied for the rest of us to understand....

#3
http://www.newyorker.com/fact/content/articles/060828fa_fact2
MANIFOLD DESTINY
A legendary problem and the battle over who solved it.
by SYLVIA NASAR AND DAVID GRUBER
Issue of 2006-08-28
Posted 2006-08-21
On the evening of June 20th, several hundred physicists, including a Nobel
laureate, assembled in an auditorium at the Friendship Hotel in Beijing for a
lecture by the Chinese mathematician Shing-Tung Yau. In the late
nineteen-seventies, when Yau was in his twenties, he had made a series of
breakthroughs that helped launch the string-theory revolution in physics and
earned him, in addition to a Fields Medal—the most coveted award in
mathematics—a reputation in both disciplines as a thinker of unrivalled
technical power. ... When a member of a hiring committee at Stanford asked him
for a C.V. to include with requests for letters of recommendation, Perelman
balked. “If they know my work, they don’t need my C.V.,” he said. “If they need
my C.V., they don’t know my work.”... Mikhail Gromov, the Russian geometer, said
that he understood Perelman’s logic: “To do great work, you have to have a pure
mind. You can think only about the mathematics. Everything else is human
weakness. Accepting prizes is showing weakness.” Others might view Perelman’s
refusal to accept a Fields as arrogant, Gromov said, but his principles are
admirable. “The ideal scientist does science and cares about nothing else,” he
said. “He wants to live this ideal. Now, I don’t think he really lives on this
ideal plane. But he wants to.”

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Thoughts on sunscreens

According to
http://www.consumersearch.com/www/family/sunscreen/index.html
it appears that Avobenzone also known as Parasol 1789, confers UVA protection.

I like
http://www.amazon.com/gp/product/B00027CR4S/ref=pd_sim_hpc_2/002-5543058-9208048?ie=UTF8
and
http://www.amazon.com/gp/product/B00008IHO4/ref=pd_sim_hpc_1/002-5543058-9208048?ie=UTF8
, which appear to be good in this regard.

The below contain titanium & zinc oxide, physical sunblocks:
http://911skin.com/orsuspf30.html
and
http://www.amazon.com/gp/product/B000FRUHN8/sr=1-1/qid=1156282164/ref=sr_1_1/002-5543058-9208048?ie=UTF8&s=hpc

Thoughts??
--
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A Product Endorsement, Courtesy of the Revolution -- NY Times

Seems to be the ultimate product endorsement... by the ultimate non-capitalist

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http://www.nytimes.com/2006/08/21/business/media/21adidas.html
http://mylifestream.net/scrapbook/2006/08/castro-in-adidas-from-nytimes.html

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Raging Hormones -- NY Times

HGH is perhaps a substitute for dieting, albeit an illegal one...

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http://www.nytimes.com/2006/08/20/sports/playmagazine/20hgh.html
Raging Hormones
By GRETCHEN REYNOLDS, Published: August 20, 2006

Six years ago, Dr. Paul Savage was a pudgy mess. A 38-year-old emergency-room director in Waukegan, Ill., he weighed 267 pounds, suffered from high blood pressure and shortness of breath and had sallow skin that drooped in wattles around his chin. Today, at 44, he’s a new, unrecognizable man. Almost 100 pounds lighter, he boasts 12 percent body fat, a superhero jaw line and skin tone that seems almost incandescent. Savage says he owes much of his transformation to the self-administration of human growth hormone (H.G.H.).....

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I, Admin: 004 dk.eos.net.FtpError: Login incorrect.

Very useful post

Phone, Web Conferencing, Webinar and Webcasting Services

for setting up conference calls

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Spy’s-eye View -- the Atlantic

Nice guide to things one can do with Google Earth

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http://www.theatlantic.com/doc/prem/200603/google-earth
The Atlantic Monthly | March 2006
Spy’s-eye View
Google Earth and its rival programs offer (civilians) a new way to look at the world
by James Fallows
A s best I can figure, I have spent 35,000 to 40,000 hours of my life sitting at a computer. This knowledge does not improve my mood or self-esteem. But it brings into sharp relief the handful of moments at the keyboard I can distinctly remember, each involving a time when I realized that the computer had just done something important and new....

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Mr. Ratner’s Neighborhood -- New York Magazine

Another financial analysis related to a NY sports team, highlighting the tricky politics of  development.

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http://newyorkmetro.com/news/features/18862
Mr. Ratner’s Neighborhood
Manipulative developers, shrill protesters, and a sixteen-tower glass-and-steel monster marching inexorably forward. What the battle for the soul of Brooklyn looks like—from right next door.
By Chris Smith, New York Magazine
Jim Stuckey is clearly having trouble containing his excitement. As he waits for the small scrum of reporters to get ready, he adjusts his light-purple tie. He smooths his shock of white hair. He suppresses a smile....

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Don't Eat This Book: Fast Food and the Supersizing of America (Hardcover)

Enjoying reading this book. It contains links to websites listing Farmer's markets and also a nice listing of all the fad diets in the last century.

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http://www.amazon.com/gp/product/0399152601/ref=si3_rdr_bb_product/002-5543058-9208048?ie=UTF8
www.ams.usda.gov/farmersmarkets/map.htm
localharvest.org
Fad Diet History:
"Another liquid diet, the vinegar diet, was a fad in Europe in the ...  up one of the most boring diets in history, the Bland Diet. He believed that rich and spicy foods not only ... the cereal guy, was a big fan of Fletcherizing [diet]) The grapefruit diet, huge for a while in the 1920s, advocated massive ... and more disgusting diets, also from the 1920s, was the tapeworm diet. Apparently no one actually swallowed live tapeworms, but there were diet pills on the market that claimed to contain ....Since 1970, as Americans' weight has ballooned, the diet fads have been coming hot and heavy: Dr. Robert Atkins come out with his low-carb diet in 1972. it faded, ... high-protein Scarsdale diet swept the land in 1978. The low-fat Pritikin diet was all the rage in 1979. Judy Mazel's Beverly Hills diet... life Choice diet was big in the early nineties. The Zone plan had people loading up on lean meat, egg whites, fish and chicken in the late 1990s. And more recently, the Southbeach diet...Not to mention the cabbage soup diet, the boiled egg diet, the Abs diet ... It's no big surprise that the Fatkins diet is popular again. ..."

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Give attachment names more room in Thunderbird » Chris Ilias’ Blog

Useful blog post to fix problem in new Thunderbird.

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A Trader’s Train to Wall Street, Conn. -- NY Times

Appears to be a reverse commute to CT.

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http://www.nytimes.com/2006/08/04/business/04reverse.html
A Trader’s Train to Wall Street, Conn.
By MICHAEL S. SCHMIDT, Published: August 4, 2006
Inga Shchipanova does some reading on her Metro-North commute from Manhattan to Connecticut. But many are not on their way to offices on Wall Street or in Midtown. Instead, they are crowded into trains for Greenwich, Conn., which has emerged as the home of the ballooning hedge fund industry... The trains leaving Grand Central between 7 and 8:30 a.m. are packed. Most seats are taken and conversation is sparse. Unlike Wall Street commuters, many are not wearing suits. Yet like the Wall Street crowd, some are working furiously on their BlackBerrys and laptops...

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ARE YOU LISTENING? (podcasts) -- the-scientist.com

An interesting review of science podcasts. For fun, my personal rankings follow.
Top tier (best to worst): Nature, Science, NY Times Sci. Times, New Scientist (scipod), Security Now!
Middle tier: NOVA, Science Friday, Naked Scientist
Bottom tier: The Scientist, Scientific American, NEJ Med. , This Week in Science

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http://www.the-scientist.com/2006/6/1/28/1/
ARE YOU LISTENING?
For some, science podcasts are time-savers that open their minds to new fields. For others, they're just another fad. What's the future?
By Ishani Ganguli

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Top 20 NIH grants of 2005 -- the-scientist.com

Eric Lander's single NIH grant with >$50M for 2005!

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http://www.the-scientist.com/article/table/24101/1/
Top 20 NIH grants of 2005
from the-scientist.com/2006/8/1/26/1/
Volume 20 | Issue 8 | Page 26
The Inequality of Science
BY ALISON MCCOOK

1 - Lander, Eric S AT Massachusetts Institute of Technology, $53.4 million TO Generate high-quality genome sequence
2 - Wilson, Richard K AT Washington University, $46.1 million TO Improve informatics tools, produce genome sequence
3 - Gibbs, Richard AT A Baylor College of Medicine, $32.7 million TO Produce draft sequences of the rhesus macaque and bovine genomes
4 - Hirst, Kathryn AT George Washington University, $31.1 million TO Coordinate clinical trials of type 2 diabetes in adolescents and children
5 - Reaman, Gregory H AT National Childhood Cancer Foundation, $28.5 million TO Reduce deaths from childhood cancer by 20% and increase 5-year disease-free survival rates to >85%
...

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Search Beyond Google -- Technology Review

Resurrected an old letter that I wrote to TR to post on my blog. (It was never published.) Thought it was still relevant. Here it is:

I was very intrigued by the recent article in Technology Review about
"Search beyond Google." The article mentioned various ways people are
trying to subvert and spoof Google and how Google is fighting back. I
thought I would add something to this, a practice I have observed that
people call "anti-googling." Now that Google is so prevalent when two
people meet who have not met before, they tend to Google each other
immediately afterwards and then peruse a variety of interesting facts
and tidbits about each other. If one wants to be a bit annoying -- or
downright mean -- one can create a number of web pages (using weblogs
or free sites such as geocities) implicting someone in various silly
acts or even in a crime. These reside on the web and will often be
picked up by Google. Once they spring into existence it is very hard
to make them disappear or to combat their veracity. Thus, one can be
smeared in a very unfortunate way, using Google.

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http://www.technologyreview.com/read_article.aspx?id=13505&ch=infotech
Search Beyond Google -- Technology Review
March 2004, By Wade Roush

Google reigns supreme as the search engine of choice-but for how long? A pack of startups-and Microsoft-are developing technologies to find what you want, faster. If employees at Google are anxious about the future, you wouldn't know it from a visit to the company's headquarters. Since last fall, when talk of an initial public offering got investors salivating, the organization has been under unusual scrutiny: some observers have called it "the hottest company on the planet," while others claim it's a business in leaderless disarray, with competitors crowding in and major customers on the verge of defection. But the Google complex in Mountain View, CA, is as outwardly carefree as any college campus....

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http://www.cisred.org

Interesting in relation to binding sites.

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http://www.cisred.org

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