23 May 2006

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

Some distances for running in Central Park :

3.2 miles starting at 72nd, going up to reservoir, around and back to stop.

A shorter route up to the reservoir, across to the West Side, and then back down to 72nd.


Other sites:

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20 May 2006

Dipstick Caffeine Test for Coffee -- NPR

Here's the NPR reference to the caffeine test.

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

Is Economics the Next Physical Science? -- Physics Today

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

Is Economics the Next Physical Science?
An emerging body of work by physicists addressing questions of economic organization and function suggests new approaches to economics and a broadening of the scope of physics — J. Doyne Farmer, Martin Shubik, and Eric Smith
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A great scientist can benefit from peer review, even while refusing to have anything to do with it. -- Physics Today

Einstein never really had to deal with a referee report !

Einstein Versus the Physical Review
A great scientist can benefit from peer review, even while refusing to have anything to do with it.
Daniel Kennefick
September 2005, page 43
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Thought the display of citations was interesting.

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


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

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08 May 2006

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

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

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

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

Doubt Cast on Early Theory on Eye Infections
Published: May 6, 2006

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

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


07 May 2006

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

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

Studying Tiny Fruit Flies, and Reaping Big Rewards
Published: April 29, 2006
ALBANY, April 28 — A California neuroscientist and biologist whose research of fruit flies found genetic links to human behavior was awarded the $500,000 Albany Medical Center Prize in Medicine and Biomedical Research, the country's largest award in the field.....

e said he became intrigued with the topic when his second daughter was born and he noticed remarkable differences from his first daughter. "I wondered, 'Are my wife and I doing things that differently?' " Dr. Benzer said. When asked about the specific differences in the two girls, Dr. Benzer demurred. "I'd rather avoid that question — I fear the repercussions," he said with a smile. "They are not bad differences, just different."...
Similarly, Dr. Benzer said, he is coded to sleep at different times than his wife, who wakes up at 6 a.m. and typically falls asleep by 10 p.m. Dr. Benzer, on the other hand, stays awake until 4 a.m. and sleeps until noon. He routinely works in his research laboratory into the early-morning hours, he said.
"We make it a point to have dinner together," he said.
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06 May 2006

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

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

Studies Find Elusive Key to Cell Fate in Embryo
Published: April 25, 2006
For three billion years, life on earth consisted of single-celled organisms like bacteria or algae. Only 600 million years ago did evolution hit on a system for making multicellular organisms like animals and plants.

Cell. 2006 Apr 21;125(2):315-26. 
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES.

Cell. 2006 Apr 21;125(2):301-13.   
Control of developmental regulators by polycomb in human embryonic stem cells.
Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA.

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


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


Taking the Least of You -- NY Times

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

"Taking the Least of You"
By REBECCA SKLOOT, NY Times, April 16, 2006

The Tissue-Industrial Complex
Anna O'Connell couldn't find Ted. She stood bent at the waist on a frigid afternoon last December, her head and all its fuzzy red hair crammed into an old stand-up freezer that looked like something you get milk from at the corner store: tall, white with a bit of rust and a pull handle. That freezer is the first thing you see when you walk into the Fox Chase Cancer Center laboratory in Philadelphia, where O'Connell has spent decades as a staff scientist. She pushed aside vial after vial. "I know we still have him somewhere," she yelled, her head still inside the freezer. "We've got serum from, like, 450,000 people."....

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William Bialek

Very clean design


Home Page of Steffen Möller

Like flipping picture


Structural Bioinformatics EMBL Heidelberg

Like the rotating image


The Scourge of Arial


04 May 2006

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

convenient meeting point near Grand Central