29 January 2007

27 January 2007

Total information awareness for worm genetics -- Science

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

Science. 2006 Mar 10;311(5766):1381-2. 
Genetics. Total information awareness for worm genetics.Eddy SR.

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*

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?
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."

13 January 2007

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.


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.

12 January 2007

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.

Open-Source Spying
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...

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.

Scientist at Work | Nick Patterson
A Cryptologist Takes a Crack at Deciphering DNA's Deep Secrets
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

10 January 2007

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.

Entrepreneurs See a Web Guided by Common Sense
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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09 January 2007


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...

08 January 2007

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...

Taking Control of Electric Bill, Hour by Hour
Published: January 8, 2007
A pilot project in Chicago allows residents to save money by shifting their use of power.

07 January 2007

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



Graphs of the times with heart rates are here

02 January 2007

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

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

THE CONSUMER; The Energy-Drink Buzz Is Unmistakable. The Health Impact Is Unknown.
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

So Many Advances in Medicine, So Many Yet to Come
Published: December 26, 2006
Technology and treatments have come a long way, but the gains have led to new challenges.