Cycling in the Bronx (BikeBx)

Into Bronx over Broadway Bridge and then to City Island
Route taken on Google Maps (kmz Color Ramped)
Associated useful links.
Summary: apx 10:30 AM-4PM, 26 miles

Jogging in Cambridge, UK (CamUK4Jogs)

Here are four slow jogs projected onto Google Maps in Cambridge radiating outwards from Trinity in four directions (in chronological order): CamWest (53:57 - 5.1km), CamNorth (34:30 - 3.8km), CamSouth (59:32 - 6.2km), CamShort (33:35 - 3.7km)

Cycling in Queens (BikeQueens)

Into Queens over Queensboro, then Roosevelt Island and Triboro to Randall's Island
Route taken on Google Maps (kml)
Summary: apx 11AM-5:30PM, 31 miles

Total Time (h:m:s)	6:40:21	12:53 pace
Moving Time (h:m:s)	4:06:06	7:55 pace
Distance (mi )	31.07
Moving Speed (mph)	7.6 avg.	231.3 max.
Temperature (°F)	53.6°F avg.	55.4°F high
Wind Speed ( mph)	SSE 3.8 avg.	SSE 6.9 max.

let. to ed. re. "Sowing Seeds Of Cures" -- C&EN

Here's a letter that wasn't published:
I read with great interest the recent article on venture philanthropy. I think
this is an interesting trend allowing philanthropic contributions to energize
the commercial process towards a good end. However, an important aspect was not
emphasized is the significant potential for conflicts of interest to arise.
Non-profits, such as medical charities, are given special status in the United
States by the tax code. However, in the scenario described in the article where
a philanthropist contributes money to making a biotech investment opportunity
more favorable for venture capital fund, he is essentially using charitable,
untaxed money towards a profitable end. This raises obvious conflicts: One could
imagine a person contributing money sheltered from taxes to a charity and then
having the charity redirect the funds to a commercial endeavor from which he
would directly benefit. Clearly, safeguards need to be developed to prevent this.

---

Letter in response to:
http://pubs.acs.org/cen/coverstory/85/8519cover.html
May 7, 2007
Volume 85, Number 19
pp. 19-26
Sowing Seeds Of Cures
As venture capitalists' priorities shift, venture philanthropists fill the gap
in funding of drug discovery by biotechs
Chemical & Engineering News (C&EN)
Lisa M. Jarvis
IN 1989, when scientists found the defective gene that causes cystic fibrosis,
it seemed that a cure, or at least an array of better treatment options, was
just around the corner. Research efforts, largely funded by the Cystic Fibrosis
Foundation (CFF), gained momentum, and by the mid-1990s, scientists had pieced
together much of the complex biology behind this debilitating and eventually
deadly disease.....

let. to ed. re. "Biology's Big Bang" -- Economist

Here's a letter to the Economist that wasn't published:
I read, with great interest the recent cover article describing biology's big
bang. I agree wholeheartedly agree with the thrust of this piece. The article
makes the point that there is a revolution in biology akin to that in early
20th-century physics. It also compares the genome to a computer operating
system. One can take these comparisons even further. The revolution in biology
is fundamentally about how a discipline once preoccupied with descriptions of
anatomy and taxonomy is now increasingly concerned with digital information
processing. We are, in fact, witnessing the fusion of parts of biology and
computer science. The new roles found for RNA are so important because of its
central place in cellular information processing.

---

Letter in response to:
http://www.economist.com/opinion/displaystory.cfm?story_id=9339752
The RNA revolution
Biology's Big Bang
Jun 14th 2007
>From The Economist print edition
What physics was to the 20th century, biology will be to the 21st—and RNA will
be a vital part of it.
NATURE is full of surprises. When atoms were first proved to exist (and that was
a mere century ago), they were thought to be made only of electrons and protons.
That explained a lot, but it did not quite square with other observations. Then,
in 1932, James Chadwick discovered the neutron. Suddenly everything made
sense—so much sense that it took only another 13 years to build an atomic bomb....

let. to ed. re. "A Challenge to Gene Theory, a Tougher Look at Biotech" -- NY Times

Here's a letter to the Times (in response to their one mention of ENCODE) that wasn't published:
As a participating scientist in the consortium cited in the July 1st Sunday
edition, I was excited that the Times covered some of the findings of our
project (ENCODE). The article discussed how the consortium's work is changing
the definition of a gene, and it was fascinating to see how scientific findings
ripple over into commercial and legal contexts. One of the interesting things
about genes is how plastic their definition has been over time. The current
definition, which is being recast by the ENCODE project's findings, derives from
the cracking of the genetic code in the 1960s. However, before that, a gene had
a more abstract definition as a unit of heredity, divorced from the physical
molecules actually encoding it. One of the amazing things about successive
redefinitions of a gene is that they have all been "backwards compatible" in a
scientific sense, still allowing old findings to apply to the current
definitions, with a bit of mental gymnastics. However, maybe we will find that
this backwards compatibility only applies in a scientific sphere and that a
redefinition of the gene will require substantial changes outside of it, in our
notions of commercially viable entities.
(Also, you might note that this subject is quite related to some recent publications, viz:
http://papers.gersteinlab.org/papers/grgenerev/
http://papers.gersteinlab.org/papers/whatisgene )

---

Letter in response to:
http://www.nytimes.com/2007/07/01/business/yourmoney/01frame.html
A Challenge to Gene Theory, a Tougher Look at Biotech - New York Times
July 1, 2007
Re:framing
A Challenge to Gene Theory, a Tougher Look at Biotech
By DENISE CARUSO
THE $73.5 billion global biotech business may soon have to grapple with a
discovery that calls into question the scientific principles on which it was
founded. Last month, a consortium of scientists published findings that
challenge the traditional view of how genes function. The exhaustive four-year
effort was organized by the United States National Human Genome Research
Institute and carried out by 35 groups from 80 organizations around the world.
To their surprise, researchers found that the human genome might not be a "tidy
collection of independent genes" after all, with each sequence of DNA linked to
a single function, such as a predisposition to diabetes or heart disease.
Instead, genes appear to operate in a complex network, and interact and overlap
with one another and with other components in ways not yet fully understood.
According to the institute, these findings will challenge scientists "to rethink
some long-held views about what genes are and what they do."...

Cycling in Brooklyn (Aborted5boro07 + BikeBeltPkwy)

Aborted 5 Boro, following course route to Brooklyn Bridge and then improvising to Verrazano after a long lunch
Route taken on Google Maps (kml)
Summary: apx 6:30AM-5PM, 46 miles

Total Time (h:m:s)	10:08:40	13:07 pace
Moving Time (h:m:s)	6:39:03	8:35 pace
Distance (mi )	46.4
Moving Speed (mph)	7.0 avg.	67.8 max.
Temperature (°F)	55.6°F avg.	62.6°F high
Wind Speed ( mph)	NE 8.5 avg.	NE 11.5 max.

Central Park to Prospect Park and then onto Belt Parkway Bikeway
Route taken on Google Maps (kml)
Summary: apx 8:30AM-5PM, 49 miles, with stops, including lunch

Total Time (h:m:s)	9:47:41	12:05 pace
Moving Time (h:m:s)	6:29:44	8:01 pace
Distance (mi )	48.55
Moving Speed (mph)	7.5 avg.	51.0 max.
Temperature (°F)	67.3°F avg.	71.6°F high
Wind Speed ( mph)	SE 5.3 avg.	SE 12.6 max.

Cycling on Northern Part of Farmington Valley Greenway (BikingCTGreenwayN)

Actuals
Route taken on Google Maps (kml)
Summary Data (apx. 11:30AM-6:30PM, with stops, 46 miles)

Total Time (h:m:s)	7:05:31	9:19 pace
Moving Time (h:m:s)	5:08:33	6:45 pace
Distance (mi )	45.67
Moving Speed (mph)	8.9 avg.	59.8 max.
Temperature (°F)	82.1°F avg.	84.2°F high
Wind Speed ( mph)	W 9.2 avg.	W 11.5 max.

Planning
Useful links: http://del.icio.us/mbgmbg/FunBikingCTGreenwayN

Great quote: “I’m an editor. I’m paid to make choices. My work still has meaning—but does it have value?”

The Rise of Craigslist and How It's Killing Your Newspaper -- New York Magazine

let. to ed. re. "A Smarter Web" -- Tech Review

Here's a letter to Technology Review that was published:
We read with interest John ­Borland's piece on the Semantic Web ("A Smarter Web," March/April 2007). We agree that this is an exciting time in the Semantic Web's development, yet we want to point out that its great degree of structure has drawbacks. As the article noted, Semantic Web users must learn complex ontology languages and structure their information and data using them. This difficulty inhibits the growth of the Semantic Web. It is thus arguable whether the Semantic Web can approach the scale of the standard Web, where anyone can easily create and publish content.
Ideally, we should combine the strengths of the Semantic Web and the normal Web. Search would be a good place to start. Today, global free-text search is the primary means of querying the whole Web, but it provides only coarse-grained access to documents. In contrast, the Semantic Web allows much more precise queries across multiple information sources (say, querying for a particular attribute, such as "street address"). However, it is on a much smaller scale, involving far fewer documents. We could imagine combining normal and Semantic Web queries--for instance, to search the free text of all real-estate Web pages written by women in Boston during the last week for the word "Jacuzzi." Taking this further, the few structured relationships currently in the Semantic Web could be used to refine the results of mainstream search engines.
Finally, as so much activity in the life sciences is focused on large-scale interoperation on the Web (as found in drug discovery), we feel that biological research could serve as a useful guide and driving force for the development of Web 3.0.

---

Citation of Letter
http://www.technologyreview.com/Infotech/18851/page2/
The Semantic Web
July/August Issue of Technology Review
Mark Gerstein and Andrew Smith
Computational Biology and Bioinformatics Program
Yale University
New Haven, CT

Letter in response to:
http://www.technologyreview.com/Infotech/18395/
Monday, March 19, 2007
Part I: A Smarter Web
New technologies will make online search more intelligent--and may even lead to a "Web 3.0."
By John Borland
Last year, Eric Miller, an MIT-affiliated computer scientist, stood on a beach in southern France, watching the sun set, studying a document he'd printed earlier that afternoon. A March rain had begun to fall, and the ink was beginning to smear....

Original Letter Text (before edit by magazine)
We read with great interest John Borland's March/April 2007 article "A Smarter
Web." We agree that this is an exciting time in the development of the semantic
web (or Web 3.0), and that it is on the cusp of more widespread acceptance and
use. A problem with the semantic web, however, is that it is not as flexible as
the free-text publishing supported by the standard web. As the article noted,
users must learn the semantic web's ontology languages and structure their
information and data using them. This presents a learning curve to users, acting
to inhibit the growth and spread of semantic web data. It is thus arguable
whether the semantic web can approach the huge size of the standard web where
almost anyone can easily create and publish web pages. The standard web will
likely still be the primary web most users see and use for the foreseeable
future, while the semantic web could remain a niche.

We thus feel that a practical direction is to investigate ways that the semantic
web and standard web can work together and leverage each other in a kind of
symbiosis. Keyword-based web search ala Google is the primary way of mining the
web for information today, but it only provides coarse-grained topical access to
documents and there are many kinds of information requests it cannot handle. For
example, queries that combine general relational information (such as provided
by the semantic web) about pages with keyword based searches are not supported.
Furthermore, one wants to be able to develop ways of leveraging small amounts of
highly structured information (as in the semantic web) as "training sets" to
better enable querying and clustering of the large bodies of unstructured, free
text information on the web; i.e. the small amount of highly structured
information could be used to bootstrap the automated organization, in support of
better querying, of the much larger unstructured information through data
mining. Since searching is widely perceived to be a crucial web application, the
semantic web's ability to improve it could be of high practical value and an
important driving force to help more fully realize the vision of the semantic
web. An important part of Web 3.0 should thus be to enumerate the kinds of
information requests that could be fruitfully made, and the kinds of information
infrastructure and data mining techniques needed to fulfill them. Finally, there
is much activity and excitement within biological research towards the goal of
truly large-scale integration and interoperation of its vast data, e.g. to aid
in more efficient drug discovery. The life sciences could thus be a useful
guide, test case, and driving force for Web 3.0.

Cycling in Southern Westchester (BikeSW)

Actuals
Riverdale into Southern Westchester, following Bronx River trailway after Bronxville
Route taken on Google Maps (kml) (Streetview works for part of the route, showing some of the Bronx River Parkway Trailway.)
With elevation information, which is too big for Google Maps but works with Earth (kml, kmz)
Summary Data: 23.7 miles, most of the day with stops

Planning
Rough google map route of lower (aborted) part of trip.
Nearby places on this route created with Google's My Maps: early and late.
Some useful links.

Cycling in Northern Westchester (BikeNW)

Actuals
Route taken on Google Maps (kml, kmz)
Bottom Southern and Northern Westchester Trails to Yorktown Heights and back with detour through Tarrytown (on old aqueduct trail)
Summary Data (apx. 9:30AM-6:10PM, with stops, 56 miles, uncorrected)

Planning
Links collections relevant to planning the trip: http://del.icio.us/mbgmbg/FunBikingNW

Hamptons Cycling (BikeHamptonsBM)

Actuals
Route taken on Google Maps (kml)
Bridgehampton to Montauk and back.
Summary Data (apx. 8AM-4PM, with stops, 53 miles)

Total Time (h:m:s)	8:11:17	9:09 pace
Moving Time (h:m:s)	5:22:45	6:01 pace
Distance (mi )	53.56
Moving Speed (mph)	10.0 avg.	23.2 max.
Temperature (°F)	69.1°F avg.	69.8°F high
Wind Speed ( mph)	SSW 12.4 avg.	SSW 13.8 max.

(51 miles without correction)

Planning
A useful reference map from ResortMaps.com
A suggested route plan and some places to stop (from Google Map's My Map)

tennis courts near CU & GWB

For reference:
For tennis courts near GWB, there appears to be only nearby bridges over tracks, with the best entry point at 165th & Riverside.
For tennis courts near CU, best entry point is near 120th and Riverside.

---

http://maps.google.com/maps?f=q&hl=en&q=W+165th+St+%26+Riverside+Dr,+New+York,+NY+10032&ie=UTF8&om=1&z=19&ll=40.847148,-73.945726&spn=0.001781,0.004227&t=h
http://maps.google.com/maps?f=q&hl=en&q=W+120th+Street+%26+Riverside+Dr,+New+York,+NY&ie=UTF8&z=18&ll=40.81132,-73.96394&spn=0.003557,0.00685&t=h&om=1

ooo[link]ooo

ooo[maps]ooo

ooo[fun]ooo

The Drive for the $1000 Genome -- BioITWorld

Interesting overview the high-throughput sequencing technologies, with quotes below from 454 people and on cost of storing a Solexa's run of data, estimated at ~$15K/run .

---

http://www.bio-itworld.com/issues/2007/may/cover-story
http://www.bio-itworld.com/issues/2007/may/cover-story-sidebar1/
http://www.bio-itworld.com/issues/2007/may/cover-story-sidebar2/
The Drive for the $1000 Genome
By Kevin Davies
May 15, 2007 | J. Craig Venter recently made his Comedy Central debut on The Colbert Report. Asked by host Stephen Colbert "What makes you think you can do a better job with life and genetics than God?" Venter shot back: "We have computers!" rendering Colbert momentarily (and uncharacteristically) speechless.....
SOLiD Storage
A potential downside of the SOLiD setup is the premium it puts on compute power and storage. The complete SOLiD system including compute and workflow pieces, could push the price above $600,000....
"No-one stores the [Sanger] images when they're small, so who's going to store them when they're large? So we want to get you past the images and into analyzing the data," says Rhodes.
By contrast, a typical 454 FLX run produces a paltry 13 GB of raw image data After data extraction, namely base calling, we're at a final of just less than 20 GB in total. That's actually quite manageable, especially nowadays with 500-GB hard drives," says Harkins. "We're looking to compress that down so potentially you could burn a DVD for one drive. You could store an instrument run for a few dollars."
Harkins notes that other next-generation sequencing platforms are talking about terabytes per run. "We're talking about pushing the science, but these other companies have a dilemma. It could cost more in computer hardware than reagents for an instrument run," says Harkins.
While Illumina's Smith agrees that, "The really big data is in the images," Illumina offers customers the opportunity to store all of their images, "because there will be people who want to do that. The issue is you get into hundreds of GB or even 1 TB [per run]." And that will only increase in the future. "The customer may decide to store a subset of the images for quality control purposes, or store images for a particularly important run and archive them to a tape backup."
The question for the market, Harkins reckons, is: Do you want to save your raw data? 454 allows users to re-evaluate their raw data. "We had one customer who re-processed his raw data using the updated GS FLX software and is seeing improvements," says Harkins. "When you're talking about 1-2% error down to 0.5%, that leads to tangible improvements for downstream analysis."
But Rhodes dismisses such criticism. With an instrument potentially pumping out 4 Megabases each second over three days, "People don't need the images, they need the data. What you really want is the result," says Rhodes.
During a panel discussion at CHI's Next Generation Sequencing conference, Rhodes said: "Back of the envelope calculations say that if you wanted to store the raw image data, it's 6 TB a week... that could require you to spend $1 million on storage, backup, and stuff. So unless you think you're going to want to go back to every image, it's cheaper to do the experiment again." Rhodes can see certain situations for storing images, say for a precious cDNA clone. "But as a routine workaday measure, no."
"Once you've got to that stage, you still have a large dataset — if you're going to generate 1 billion bases per run, you've got to have quite a lot of bytes as well as bases," says Smith. "But you're no longer in the TB of data, you're back down in the 100 GB or so. So you can reduce the data quantity by not storing the images." Smith says many customers already have the necessary compute infrastructure. ...
But Harkins says the market hasn't come to terms with the dilemma of paying $10,000-20,000 to save a single instrument run's data. "That's going to put the market into a bind," he says. "Throwing raw data away is a paradigm shift I don't think people are ready for yet."

Tetratops

Tetratops in the New York Times: "PATENTS
Geodesic Spinning Tops; Church Playhouse; Vacuum for Tiny Toys
By TERESA RIORDAN

When Kurt Przybilla was growing up in International Falls, Minn., he and his three sisters looked forward every summer to the day their father would put up the geodesic jungle gym in their back yard....
When one imagines the centers of the spheres as dots connected by lines, a cluster of four balls describes a tetrahedron, a three-dimensional shape with four triangular faces. Przybilla's tops also come in clusters of six (an octahedron, with eight triangular faces when the imaginary dots are connected), 12 (an icosahedron, with 20 faces) and 13 (a cube octahedron, which despite its extra ball has only 14 faces).

Letter in response to "A Digital Life" -- Sci. Am.

Here's the final text of letter I wrote in response to the article below (which was never published). Felt the letter and the article give one compelling vision of an information-rich future where data mining will be all important.

I read with great interest Gordon Bell's and Jim Gemmell's recent article in
Scientific American about the MyLifeBits project. The concept of recording
all the events in a person's life into a digital lifestream is fascinating.  The
logical complement of a such lifestream would be the personal genome.  Coupling
a person's genome, molecular blueprint, with the lifecourse he has taken would
potentially enable us to address one of the major questions in genetics: how
genes and the environment interrelate, or put more simply, the relationship
between nature and nurture. As the article points out, privacy is an essential
aspect of this discussion. However, one nuance that wasn't raised is the idea
that revealing personal information -- be it from your genome or your
"lifestream" -- potentially compromises not only your privacy but also that of
your friends and relatives. For example, an individual could consent to posting
his genome on the web, but what about his parents and children? Or what about a
day's worth of your videostream: did all the people that crossed your
path consent? Surely, the law needs to be revised to address these
important concerns.

---

http://research.microsoft.com/barc/mediapresence/MyLifeBits.aspx
http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=CC50D7BF-E7F2-99DF-34DA5FF0B0A22B50
FEATURE ARTICLES
March 2007 issue
INFORMATION TECHNOLOGY
A Digital Life
New systems may allow people to record everything they see and hear--and even
things they cannot sense--and to store all these data in a personal digital archive
By Gordon Bell and Jim Gemmell

Human memory can be maddeningly elusive. We stumble upon its limitations every
day, when we forget a friend's telephone number, the name of a business contact
or the title of a favorite book. People have developed a variety of strategies
for combating forgetfulness--messages scribbled on Post-it notes, for example,
or electronic address books carried in handheld devices--but important
information continues to slip through the cracks. Recently, however, our team at
Microsoft Research has begun a quest to digitally chronicle every aspect of a
person's life, starting with one of our own lives (Bell's). For the past six
years, we have attempted to record all of Bell's communications with other
people and machines, as well as the images he sees, the sounds he hears and the
Web sites he visits--storing everything in a personal digital archive that is
both searchable and secure....
[L2E]

Letter in response to "Friendster for Proteins" -- Forbes

Here's the final text of letter written by me and Philip Kim in response to the article below (which was never published):
We felt that your article "Friendster for Proteins" (Mar 12th) overlooked the
most predominant type of systems biology currently practiced in science. While
there is a growing effort in the type of bottom-up modeling described in your
article, the focus thus far has been on top-down analysis of large-scale
networks. At this point in time, our understanding of biological systems is too
tenuous to accurately simulate cellular processes -- and the recent failures at
Airbus suggest that accurate simulation is difficult to achieve even in
engineering. Current research focuses mostly on global properties of networks
and analyzing them on a more abstract level. Many new biological insights have
been gained from this type of analysis and many advances in understanding
protein function, as well as identifying new drug targets and cancer genes, have
been made in this field.

---

http://members.forbes.com/forbes/2007/0312/072.html
Forbes Mar 12, 2007
Friendster for Proteins - Robert Langreth & Matthew Herper
Understanding how the body's tiny components communicate is opening up vast
territory in drug research. Peter Sorger spent eight years developing new
laboratory gadgets and arcane mathematical theorems to explain....
[L2E]

Want to be hub rather than cog!

[quote]

Capsaicin - Wikipedia, the free encyclopedia

The molecule that makes Chili peppers hot.

Capsaicin - Wikipedia, the free encyclopedia
http://www.thinkgeek.com/tshirts/science/3813