TextStream (archived 8/10)

textstream.blogspot.com has moved to blog.gerstein.info

2010-09-06T01:51:00.001-04:00

This blog has moved to blog.gerstein.info .
The posts below are kept for simply archival purposes and to prevent broken links.

My academic genealogy, back to Newton !

2010-03-20T01:14:00.011-04:00

Link to the Mathematics Genealogy Project

Image of my academic genealogy back to Newton , with a mere 18 links ! (courtesy of C Chothia)

Text of the above (18 links to Newton)

**1.** Mark Gerstein
2. Cyrus Chothia UCL (+ R Lynden Bell)
3. Peter Pauling P 1931-2003
4. John Kendrew P 1917-1997
5. Max Perutz P 1914-2002
6. John Desmond Bernal RI 1901-1971
7. William Henry Bragg T 1862-1942
8. J. J. Thompson T 1856-1940
- - - I Lord Rayleigh T 1842-1919
9. Edward Routh P 1831-1907
10. William Hopkins T 1793-1866
- - -Augustus De Morgan (T) 1806-1871
11. Adam Sedgwich T 1785-1873
- - - William Whewell T 1794-1866
- - - John Hudson T 1773-1843
12. Thomas Jones T 1756-1807
- - - John Cranke T 1746-1816
13. Thomas Postlethwaite T 1731-1798
14. Stephen Whisson T ~ 1718-1783
15. Walter Taylor T 1700-1744
16. Robert Smith T 1689-1768
17. Roger Cotes T 1682-1716
**18.** Isaac Newton T 1643-1727
Isaac Barrow T 1630-1677
James Duport T 1606-1679

T: Trinity College; P: Peterhouse; RI Royal Institution, London; UCL: University College, London

let. to ed. re. "Empty Archives" -- Nature

2010-02-13T13:12:00.002-05:00

We read with great interest the recent article in Nature about the
difficulties in data sharing and archiving ("Empty Archives"). While the author discusses database archiving in detail, he neglects to consider the important archival role
served by academic journals. When it comes to archiving, journals are
more than disinterested third parties. They have historically been, and
continue to be, the central actors in scientific communication. As such,
journals should take the lead in devising and implementing standards
that will allow data from disparate fields to be shared and exchanged.
They should also embrace data sharing as part of the publication
process. Note that this is very much the viewpoint taken in the
companion article in the issue from the Toronto Data Release Workshop.

Although journals have historically sought to provide a permanent record
of scientific advance, many of the problems that we now face in relation
to data archiving and sharing stem from the fact that the publication
process with its varied, idiosyncratic formats often seems purposefully
divorced from this archiving role. It is time for journals to devise
universal structured versions of articles and appendices that
accommodate - and archive -- large data sets. This is no small task, and
it is no doubt larger than any one journal or editorial board. But
while daunting, such progress is necessary to preserve the value and
relevance of journals - and the fundamental service they provide - as we
move into a database-driven future.

Dov Greenbaum JD, PhD
Michael Seringhaus PhD
Mark Gerstein PhD

Above is an unpublished letter in response to:

http://www.nature.com/news/2009/090909/full/461160a.html
Published online 9 September 2009 | Nature 461, 160-163 (2009) |
doi:10.1038/461160a Data sharing: Empty archives Bryn Nelson

and

http://www.nature.com/nature/journal/v461/n7261/full/461168a.html
Nature 461, 168-170 (10 September 2009) | doi:10.1038/461168a; Published
online 9 September 2009 Prepublication data sharing Toronto
International Data Release Workshop Authors

Trips to Europe '09

2010-01-16T13:41:00.018-05:00

Here I've collected various things related to some trips to Europe in 2009.

* Pictures

Flickr photos galleries from London in Jan., Belgium in Oct., and Paris & Cambridge in Dec. (The analogous links in picasa: London, Belgium, & Paris .)

In addition to the usual tourist shots, I took some fairly abstract photos and some more general "concept" ones. My photos also added significantly to my burgeoning McDonald's photo collection.

* Tags & Routes

I tagged my photos quite extensively. Here's a listing of some of my more commonly used tags on the trips. One 'tag group' that was particularly hard to shoot were the panoramas and nighttime photos , where I was aided by my trusty new Sony. Here's an almost 360' panorama of the Louvre.

As might be expected, I geotagged many of the photos as well; thus, each of these galleries is associated with a nice map link -- e.g. here's an one for Paris . The geotagging has the side benefit of providing some tracks of where I went, viz: walking around Paris, Paris to London (via Chunnel), & walking around London (not necessarily in order).

* Links & Lectures

Here's a general collection of links of random information associated with the trips.

Some lectures that I gave during the trips: 1a, 1b, 2, 3, 4

Some of my own cryptic internal IDs with yet more links: i0wtsysbio, i0gencwinter08, i0vib

Some Interesting Quotes from "Capitalism and Financial Crashes," The New Yorker

2009-11-25T06:03:00.007-05:00

Some quotes I liked from: http://www.newyorker.com/reporting/2009/10/05/091005fa_fact_cassidy

For more see: http://delicious.com/mbgmbg/clust_bridge_keynes_quotes

Millennium Bridge

It initially closed in '00 then reopened: "The real problem was that the designers of the bridge... had not taken into account how the footway would react to all the pedestrians walking on it."

Keynes view on our "third degree" guesses

Keynes’s jaundiced view of finance reflected his own experience as an investor .... He compared investing to newspaper competitions in which “the competitors have to pick out the six prettiest faces from a hundred photographs, the prize being awarded to the competitor whose choice most nearly corresponds to the average preferences of the competitors as a whole; so that each competitor has to pick, not those faces which he himself finds prettiest, but those which he thinks likeliest to catch the fancy of the other competitors, all of whom are looking at the problem from the same point of view.... It is not a case of choosing those which, to the best of one’s judgment, are really the prettiest, nor even those which average opinion genuinely thinks the prettiest... We have reached the third degree, where we devote our intelligences to anticipating what average opinion expects the average opinion to be. And there are some, I believe, who practice the fourth, fifth and higher degrees.”

Points on the Prisoner's dilemma

Because financial markets consist of individuals who react to what others are doing, the theories of free-market economics are often less illuminating than the Prisoner’s Dilemma, an analysis of strategic behavior that game theorists associated with the RAND Corporation developed during the early nineteen-fifties....

Imagine that you and another armed man have been arrested and charged with jointly carrying out a robbery. The two of you are being held and questioned separately, with no means of communicating. You know that, if you both confess, each of you will get ten years in jail, whereas if you both deny the crime you will be charged only with the lesser offense of gun possession, which carries a sentence of just three years in jail. The best scenario for you is if you confess and your partner doesn’t: you’ll be rewarded for your betrayal by being released, and he’ll get a sentence of fifteen years. The worst scenario, accordingly, is if you keep quiet and he confesses.

What should you do? The optimal joint result would require the two of you to keep quiet, so that you both got a light sentence, amounting to a combined six years of jail time. Any other strategy means more collective jail time. But you know that you’re risking the maximum penalty if you keep quiet, because your partner could seize a chance for freedom and betray you. And you know that your partner is bound to be making the same calculation. Hence, the rational strategy, for both of you, is to confess, and serve ten years in jail. In the language of game theory, confessing is a “dominant strategy,” even though it leads to a disastrous outcome.

let. to ed. re: "Your genome isn't that precious - give it away" -- New Scientist

2009-11-10T01:53:00.009-05:00

We read Katrina Voss's article on open access to genomic information (22 August, p 22) with great interest. Summing up her argument, she quotes her father: "I'm not worried, I'm just not that important."

Narcissists aside, we can all agree that we aren't that important to the rest of the world. However, what Voss fails to account for is the small cadre of people to whom we are that important. This set includes friends, relatives, employers, potential mates, and even stalkers who already look at the wealth of information available online.

One instance where this data could be misused would be by adopted children, or even the children of sperm donors, to find parents who might not want to be found.

Similarly, certain professions could be affected from the outset. Genomics has the potential to touch all aspects of sport, from using genetic information for draft picks, to mandatory genetic testing to screen out players at all levels of the game at risk of serious and unanticipated ailments.

With the growth in understanding the links between athleticism and genetics, public disclosure of personal genomic information of athletes may be just a logical extension of what is already in place. Analysing how athletes deal with this new form of personal information will be of particular interest to the rest of society as it learns how to manage the eventual disclosure of personal physical and genetic information.

Dov Greenbaum & Mark Gerstein, New Haven, CT

Above text is a published letter . The Citation is:
"Can't run from DNA," Dov Greenbaum & Mark Gerstein
New Scientist Magazine, issue 2727 (23 September 2009), pp28-29
http://www.newscientist.com/article/mg20327270.400-cant-run-from-dna.html

It is in response to:
http://www.newscientist.com/article/mg20327224.500-your-genome-isnt-that-precious--give-it-away.html
Your genome isn't that precious – give it away
New Scientist, 24 August 2009 by Katrina Voss
GENETIC tests are becoming increasingly fashionable, and it's easy to see why: they allow people to find out all kinds of things about themselves....

Also, see commentary on magazine site:
http://www.newscientist.com/commenting/browse?id=mg20327224.500&page=5

[(Return) to Other Publications Page]

Original Submitted Text (before editing!):

We read with great interest the recent article entitled "Your genome isn't that precious - give it away" (Issue 2722, August 22, 2009).

Ms. Voss suggests that unrestricted and open access to genomic information will greatly benefit society with little lost to those who provide access. Summing up her argument she quotes her father: "I'm not worried, I'm just not that important."

Narcissists aside, we can all agree that we aren't that important to the rest of the world. However, what Ms. Voss fails to account for is the small cadre of people to whom we are that important. This set includes friends, relatives, employers, potential mates, and even stalkers who already look to Google, Facebook, Myspace, Twitter and other online sources for information about you or your close personal relatives. Further, data laid bare online could be used by adopted children (or even sperm donees) in an effort to find parents who might not want to be found. It is often these groups of people who we might especially want to limit access to our genomic information.

But sharing of genetic information raises concerns even beyond this group of close associates. In the past, people revealed private information about themselves only to close confidants – people they knew and saw regularly. Now, with the advent of social network websites (and new broader conceptions of personal boundaries and even ‘friends’), we nonchalantly reveal all forms of personal information to unfamiliar third parties.

This current laissez-faire attitude to privacy --likely to extend to personal genomic information, should be of special interest to athletes. Genomics has the potential to touch all aspects of sports, from using genetic information for real and fantasy draft picks, to mandatory genetic testing to screen out players at all levels of the game at risk for serious and unanticipated injuries, to valuation of a player worth; moreover, it is relatively easy for a scout, team manager, or an obsessed fan to surreptitiously obtain genomic information from a discarded bottle or a sweaty glove or racket, and submit it for analysis.

In fact, genetics has always played a major component in athleticism, whether its Lance Armstrong’s inhuman resting and maximum heart rates and substantially below average lactate levels, or Michael Phelps disproportionate arm span and hyperlaxic ankles. It is only a matter of time before genetics becomes an overt component in our thinking and analysis of The Game.

Professional and Olympic athletes are of course already familiar with managing their very public personal information, body measurements, performance statistics, and effectively real-time video surveillance for large fractions of their career, both on and off season. With the growth in understanding the linkages between athletic ability and genetics, public disclosure of personal genomic information of athletes may be just a logical extension of what is already in place. Analyzing how athletes deal with this new form of personal information will be of particular interest to the rest of society in learning how to manage and deal with the eventual disclosure of personal physical and genetic information.

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

Animal Symbolism

2009-10-31T11:11:00.001-04:00

Supposedly....

Turtle is symbol of:
Patience longevity connection

Rabbit is symbol of:
Patience quick thinking timidity ingenuity fertility

Salmon is symbol of:
Determination fertility wisdom prophecy

Frog is symbol of:
Transformation creativity fertility water

let. to ed. re. "Driven to Distraction: Drivers and Legislators Dismiss Cellphone Risks" -- NY Times

2009-08-30T14:03:00.001-04:00

I would like to respond to the recent article on the relationship between cellphone and other portable device usage and driver safety. I full agree with the premise of this article that this is a dangerous new phenomenon. However there are a number of connections that could have been probed a bit further. In particular, are there any instances when one is using a cell phone when driving that are actually safer than driving without one? That is, one could imagine that a drowsy driver on a dark street might have a easier time keeping alert and concentrating if he was carrying on a conversation over a cellphone rather than driving alone? Also, the implication of the article was that talking to someone on the cellphone is more dangerous than talking to a fellow passenger in the car. I do not know if this is always the case -- as anyone who has experienced a bunch of rambunctious young children in the car might attest to.

Above text is an unpublished letter in response to:
http://www.nytimes.com/2009/07/19/technology/19distracted.html
July 19, 2009
Driven to Distraction: Drivers and Legislators Dismiss Cellphone Risks
By MATT RICHTEL

let. to ed. re. "Baseball’s Use of DNA Raises Questions" -- NY Times

2009-08-30T13:59:00.001-04:00

Schmidt & Schwarz’s article raises serious concerns regarding the use of DNA testing in baseball. It is likely, however, that these concerns represent only the tip of the iceberg. Teams invest millions in their players; given this, would an owner pass up the opportunity to learn more about a player’s long-term potential through a relatively cheap genome analysis? Further, baseball, like many professional sports, sustains a strong statistics subculture that will likely see genetic testing as an integral component of a player’s dossier (along with height, weight and say ERA). In a worst case scenario, this testing would ignore the significant privacy concerns -- both to the individual and their family that share’s much of the same genes -- resulting from the disclosure of a person’s genetic predispositions. It could be even done surreptitiously by a fan or rival based on trace DNA remains lifted off of personal items.

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

Above text is an unpublished letter in response to:
Baseball’s Use of DNA Raises Questions
By MICHAEL S. SCHMIDT and ALAN SCHWARZ
Published: July 21, 2009
http://www.nytimes.com/2009/07/22/sports/baseball/22dna.html

let. to ed. re. recent article in NY Times -- "Why We Need Health Care Reform"

2009-08-30T13:53:00.001-04:00

I read with great interest the recent editorial advocating health care reform by the government. It is certainly impressive to see is the President writing in the Times. One thing in that was especially notable was that in one paragraph the President calls for insurance companies to pay for mammography and colonoscopy and the following sentence points how this will reduce the incidence of breast and prostate cancer. I wonder exactly how these two things are connected and to what degree these sentences show about the type of health and medical advice that the President is getting.

Above is an unpublished letter in response to:
http://www.nytimes.com/2009/08/16/opinion/16obama.html
Why We Need Health Care Reform
By BARACK OBAMA
Published: August 15, 2009

let. to ed. re. recent article in NY Times -- "Senator Moves to Block Medical Ghostwriting"

2009-08-30T13:48:00.001-04:00

I read with great interest the recent article describing the issue where medical school professors have articles ghost written for them by writers commissioned by drug companies. The article pointed to the obvious conflict of interest -- and the way that drug companies were using this to unfairly market their products. It also pointed a finger at granting agencies and universities to somehow crack down on this behavior. While I agree that this is certainly a problem, I wonder whether it might make more sense to focus on journalists and publishers. Should it not be the case that an article can only be accepted into a reputable scientific journal if all the authors have been declared (i.e. no ghostwriters) and that the roles of each of these individuals and their conflicts are described somewhere in the text? I think this simple step would do a lot to clean up this problem and many other problems in scientific publishing.

Above is an unpublished letter in response to:
http://www.nytimes.com/2009/08/19/health/research/19ethics.htm
Senator Moves to Block Medical Ghostwriting
Minh Uong/The New York Times
By NATASHA SINGER
Published: August 18, 2009

Biking in Fairfield County

2009-08-23T14:30:00.006-04:00

Routes (Overview image)

BikeNFairfield [28-Jun-08]
BikeWestport [12-Jul-08]
BikeNWestport [14-Jun-09] (27 miles)
BikeGreensFarms [31-Jul-09] (~20 miles, cut short by rain) (Route is Google-Map KML ; also, route directly in Google Map)
BikeDarien [8-Aug-09] (~20 miles)
BikeNewCanaan [16-Aug-09] (21 miles)

Photos
General Flickr and Picasa collections (with map). Closeup on New Canaan .

Links
http://delicious.com/mbgmbg/FunBikeNFairfield
http://delicious.com/mbgmbg/FunBikeNWestport
http://delicious.com/mbgmbg/FunBikeWestport

See also earlier post on this subject.

A Question that I had on using Picasa

2009-08-23T13:01:00.002-04:00

Just posted this in
Google Help > Picasa > Discussions > Picasa for Mac (Labs) > PC / Mac Compatibility
(http://www.google.com/support/forum/p/Picasa/thread?tid=0e2e942a3e7212d6&hl=en ):

I'm using a mac with OS X and running vmware fusion with windows XP. Despite what's being said above, I want, recklessly, to try and go back and forth between both windows and mac picasa. Each has some advantages -- i.e. the mac version is faster but the windows one handles geotagging. I find if I go back and forth with the current versions of the program (as of Aug. 2009), things actually kind of work. (This wasn't true with earlier versions.) However, after a bit of edits on the mac, the OS X version of picasa often will create two copies of each picture in a folder, one where my edits are not properly applied. This does not seem to happen to the PC copy. Refreshing the folder doesn't fix things. Moreover, checking the "hidden" picasa files (.picasa.ini file and .picasaoriginals on the mac) reveals that these are not duplicated in any way and don't seem corrupted. What's happening? One workaround that I discovered is that if I carefully do "Folder Menu: Remove from Picasa..." on the whole folder and then "File Menu: Add Folder to Picasa..." things are usually fixed. But I'd like a cleaner solution.

Trips to the West Coast in Spring '09 [TripSF + SeattleTrip]

2009-08-22T22:55:00.011-04:00

Visiting Bay Area (+ Tucson)

Photos: Picasa, Flickr (including some shots of rows of grapes)
Google Maps: Running, Cycling
Lectures: 1, 2, 3, 4
Links

Visiting Seattle

Photos: Picasa, Flickr (including some shots of famous artworks juxtaposed on a map with analogous ones from the East Coast)
Google Maps: Cycling
Links

My current list of iphone applications

2009-07-11T16:34:00.006-04:00

I got an iphone recently and predictably I've been very interested in acquiring all sorts of applications. Here's my (ranked) list at the moment:

Most Useful
Google, Mobile Fotos, Night Stand, Yummy, FullScreen

Somewhat Useful
Google Earth, RK Free, NYTimes, Skype, Zillow

Not that Useful
RedDelicious, Trulia, iNapkin, RedLaser

(Suggestions to add to this list would be welcome.)

The above list was current as of the time of this post.

My continuously updated list is here.

let. to ed. re. "Personal Genomics: Access Denied?" -- Technology Review

2008-12-29T00:12:00.002-05:00

Dear Sir:

Misha Angrist's recent article astutely notes the states' misguided attempts to regulate personal genomics by treating the personal genomics product as more medical relevant than the data currently warrants. While Ms. Angrist sees these regulatory intrusions as somewhat benign, we see significant concerns: The state actions will effectively sanction those personal genomics companies that do meet the states' relatively low bar- sending a signal to consumers that it's ok to proceed impetuously; the State has your back! Similarly, Federal attempts assuage popular apprehension with genetic testing through the recently passed Genetic Information Nondiscrimination Act (GINA) will provide false security to those consumers concerned with their genomic privacy. Personal genomics raises many non-trivial privacy concerns that are as of yet unaddressed by either state or federal actions. Recreationally minded consumer oriented personal genomics companies that imprudently suggest that their customers share their genomic results often without concern for either their or their close relatives' (that share a large percentage of their genetic complement) medical privacy will expose their consumers current and potentially future genetic diseases and dispositions long before we even understand what the data means or how it can be used.

Dov Greenbaum JD MPhil PhD and Mark Gerstein, PhD

Above is an unpublished letter in response to:
http://www.technologyreview.com/biomedicine/21250
Misha Angrist's Personal Genomics: Access Denied? Technology Review (Sept/Oct 2008)

let. to ed. re. "Lawyers Fight DNA Samples Gained on Sly" -- NY Times

2008-12-29T00:05:00.002-05:00

Ms. Harmon’s recent article surveying the expansion of warrantless collections of DNA is particularly thought provoking; Whereas, a simple fingerprint merely identifies the individual, unrestrained collecting of DNA can disclose personal and private information, irrespective of the relevance to the case or the guilt of the suspect.

With rapidly evolving DNA technology, it is now possible to extract vast amounts of genomic data from the biological miscellany that is continuously shed over our daily lives. Science can discern details of a person's appearance, latent diseases, and even personality traits from this genomic data, exposing not only the suspect’s personal information but their relatives’ as well.

As law enforcement collects and archives DNA, this link to personal information will be perpetuated and privacy never completely restored.

Any legal or ethical discussion ought to be cognizant of these very real concerns, especially with regard to data security and sharing protocols.

Dov Greenbaum JD, PhD and Mark Gerstein PhD

Above is an unpublished letter in response to:
http://www.nytimes.com/2008/04/03/science/03dna.html
Amy Harmon's article: Lawyers Fight DNA Samples Gained on Sly
NY Times, April 3 2008

let. to ed. re. "When in Doubt, Spit It Out" -- NY Times

2008-12-28T23:58:00.004-05:00

Dear Sir:

Allen Salkin's recent article skillfully captures the consumer laissez-faire response to personal genomics. While personal genomics companies may bill themselves as recreational and non-medical to circumvent FDA oversight, there remain numerous unappreciated privacy concerns on par with sharing personal medical records.

Your genome describes--in exquisite detail --your propensity toward character traits and disease. And even if we can't decipher much of it now, scientific advances will eventually decode enough to substantially affect your children's privacy –with whom you share a large chunk of your genome.

Further, recent studies suggest that the genomic anonymity relied upon by many companies to share your data may be quickly eroding, further exposing the consumer and their family's genomic data. Like the erosion of online privacy, personal genomics will eventually push society to reevaluate our notions of privacy. Until then, personal genomics companies need to be especially vigilant in protecting our privacy.

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

Above is an unpublished letter in response to:
http://www.nytimes.com/2008/09/14/fashion/14spit.html
Allen Salkin's "When in Doubt, Spit It Out" (September 14, 2008, page ST1 of the New York edition), NY Times

let. to ed. re. "Double Helix Dept. Ptooey!" -- New Yorker

2008-12-28T23:54:00.003-05:00

Dear Sir:

The recent article in the New Yorker about the much publicized "spit
parties" organized by personal genomics companies skillfully captures
the consumer laissez-faire response to personal genomics. While
personal genomics companies may bill themselves as recreational and
non-medical to circumvent FDA oversight, there remain numerous
unappreciated privacy concerns on par with sharing personal medical
records.

Your genome describes -- in exquisite detail -- your tendency
propensity toward character traits and disease. And even if we can't
decipher much of it now, scientific advances will eventually decode
enough to substantially affect your children's privacy -- with whom
you share a large chunk of your genome.

Further, recent studies suggest that the genomic anonymity relied upon
by many companies to share your data may be quickly eroding, further
exposing consumers and their families' genomic data. Like the erosion
of online privacy, personal genomics will eventually push our society
to reevaluate notions of privacy. Until then, personal genomics
companies need to be especially vigilant in protecting our privacy.

We wonder if all the celebrities having their "DNA scanned" would be
as relaxed about other (more conventional) invasions of their privacy
(e.g. having their photo taken on the street) as they are with their
genome, if all these implications were transparent.

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

Above is an unpublished letter to the editor in response to:
http://www.newyorker.com/talk/2008/09/22/080922ta_talk_schulman
Double Helix Dept.
Ptooey!
by Michael Schulman September 22, 2008

Certain innovations—cell phones, the umbrella—started out as symbols of wealth
before trickling down to the masses. Getting to know your genotype may be next
on the list. In 2006, Linda Avey and Anne Wojcicki founded a company called
23andMe (that’s chromosome pairs), which gives its customers the chance to
decode their genes....

let. to ed. re. "Dawn of Low-Price Mapping Could Broaden DNA Uses" -- NY Times

2008-12-28T23:47:00.001-05:00

Mr. Pollack's recent article discussing Complete Genomics entrance into the DNA sequencing market raises numerous concerns, particularly with the opportunity for companies to now outsource their sequencing at Complete Genomics' cut-rate prices.

Plummeting costs will further lower the barriers-to-entry into the personal genomics market, inundating this nascent industry with a myriad of consumer opportunities.

Like the erosion of online privacy, personal genomics will push society to reevaluate its notions of privacy: Your genome describes -- in exquisite detail -- your propensity toward character traits and disease. Even though we can't decipher all of it now, science will eventually decode enough to substantially affect your children's privacy -- with whom you share much of your genome.

We wonder if everyone interested in having their DNA scanned would be as relaxed about other (more conventional) invasions of their privacy as they are with their genome if the privacy implications were as transparent.

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

The above is an unpublished letter in response to:
Andrew Pollack's article: "Dawn of Low-Price Mapping Could Broaden DNA Uses"
NY Times, October 6, 2008
http://www.nytimes.com/2008/10/06/business/06gene.html

let. to ed. re. "You’re Leaving a Digital Trail. What About Privacy?" -- NY Times

2008-12-28T23:40:00.003-05:00

John Markoff's article on the arrays of sensors digitally recording our trails was very informative. The piece's upbeat assessment of collective intelligence refreshingly focuses more on the wisdom of crowds than the tyranny of the mob. And while the piece acknowledges some personal privacy concerns along with collective intelligence's many benefits, it fails to address a very real complication: how one person's digital acquisition of their environment through these sensor arrays impacts another's privacy, particularly those who have not yet acquiesced to the emerging privacy attitudes of the MySpace generation. Although I may be content to memorialize and broadcast my surroundings, what of all the other people inadvertently caught in my digital dragnet of sensors? Are they comfortable with having this information recorded and shared? Shouldn't we be equally if not more concerned for their privacy as we seem to be for those who have actively submitted to these technologies?

Dov Greenbaum JD MPhil PhD
Mark Gerstein, PhD

The above is an unpublished letter in response to:
http://www.nytimes.com/2008/11/30/business/30privacy.html
John Markoff's "You’re Leaving a Digital Trail. What About Privacy?"
Nov. 29, 2008, NY Times
See also:
http://delicious.com/mbgmbg/clust_digitaltrail

Random Info. about Yale Club in NYC

2008-12-25T13:42:00.002-05:00

* Dress code (2000,07.23)

M-Th, F, Sa-Su
C = casual
F = formal
N = no service

roof din. rm breakfast - C, C, C
roof din. rm lunch/dinner - F, F, N
Tap rm lunch - C,C, N
Grill rm dinner - C,C,N
main lounge and bar - F,C,C
(casual in main dining rm on Fri betw mem. and labor)

* Breakfast

Business casual (no jeans, collared shirt, no tee-shirt) necessary for breakfast.
Quiet use of wi-fi is briefly available in the library but there really is no place in the club for an extensive business meeting with open laptops, so if this is necessary it probably best to walk to Starbucks

* Yale Club
http://maps.google.com/maps?f=l&hl=en&geocode=&q=yale+club&near=44th+st.+and+vanderbilt+ave.,+ny,+ny&ie=UTF8&ll=40.754064,-73.977208&spn=0.00139,0.002883&z=19&iwloc=A&om=1
http://www.yaleclubnyc.com/

* Nearby locations one could probably sit with a computer

Cucina & Co At Metlife Building
200 Park Ave, New York, NY
(212) 682-2700 - Rated 3.8 out of 5.0 - 0.1 mi NE
+ Sit down place where one could probably bring laptops

Cosi
38 E 45th St, New York, NY
(212) 883-6814

Blake & Todd
52 Vanderbilt Ave, New York, NY
(212) 883-0010

Starbucks
400 Madison Ave, New York, NY
(212) 319-1676

http://www.starbucks.com/retail/locator/PrxResults.aspx?a=1&LOC=40.7516440790587%3a-73.9759210889539&CT=40.7516440790587%3a-73.97592108895391.78126408441369%3a1.33594806331027&countryID=244&FC=RETAIL&dataSource=MapPoint.NA&Radius=5&GAD2=Lexington+Ave&GAD3=New+York%2c+NY+10017&GAD4=United+States&IC=40.7516440790587%3a-73.9759210889539%3a32%3aLexington+Ave

* Nearby Kinkos

New York NY Vanderbilt
230 Park Ave
New York, NY 10169
USA
Phone: (212) 949-2534
Fax: (212) 949-2540
+ has full service computers and printers

* Nearby Restaurants

mike jordans (gct), Metrazur (gct), cafe centro, cafe naples, grand hyatt hotel

Trip to Greece

2008-11-28T04:02:00.008-05:00

Pictures
* Overall ~100 pictures of things in Greece, organized on Flickr and Picasa
http://www.flickr.com/photos/mbgmbg/sets/72157610294361788
http://picasaweb.google.com/bluehat/GreeceThings02 (map of this)

* Some nice subsets of the images

- Just of Santorini: http://www.flickr.com/photos/mbgmbg/tags/santorini
(Map of the above: http://www.flickr.com/photos/mbgmbg/tags/santorini/map)

- Visiting and looking at Parthenon
Some of the ruins in Greece were a bit beaten up (tag "ruinedruins")

- A particular specialization of the above is a focus on rather dynamic graffiti interposed with iconic architecture and well known sites. See tag "graffiti" and map of it. (This includes images in other locations than just Greece.)

- Some other fun tags to look at are "abstract" and "landscape"
(These include images in other locations.)

Collection of links
relevant to the trip (includes some useful guidebooks)
http://delicious.com/mbgmbg/fungreece
http://delicious.com/mbgmbg/funathens

Rough track
of walk up to Parthenon

let. to ed. re. "Many Holes in Disclosure of Nominees’ Health" -- NY Times

2008-10-25T07:00:00.000-04:00

The 19 October front-page in the air Times has an interesting juxtaposition
of articles about health information and privacy. On one hand we heard about
Dr. Church's genome project and how will reveal all the information about
himself and 10 individual volunteers. On the other hand, we heard about the
presidential candidates strongly restricting access to their personal health
information in this year's campaign. While the volunteers for Dr. Church's
project are to be commended for revealing literally all about themselves, could one imagine the presidential candidates in an election consenting to have their genome
sequenced and mined for all to see.

Above is an unpublished letter in response to:

http://www.nytimes.com/2008/10/20/us/20gene.html
October 20, 2008
The DNA Age
Taking a Peek at the Experts’ Genetic Secrets
By AMY HARMON

http://www.nytimes.com/2008/10/20/us/politics/20health.html
The Doctor’s World
Many Holes in Disclosure of Nominees’ Health
LAWRENCE K. ALTMAN
Published: October 19, 2008

Trip to Toronto (TripToronto + TripISMB08 + Fall08)

2008-10-06T05:23:00.010-04:00

* Public shots of buildings and other stuff

http://picasaweb.google.com/bluehat/TripTorontoThings#
http://www.flickr.com/photos/mbgmbg/sets/72157607038288351/

* Some relevant links to fun stuff and things at the conference

http://delicious.com/mbgmbg/FunTripISMB08
http://delicious.com/mbgmbg/link_ismb08
http://delicious.com/mbgmbg/bioinfoconfmg

* Some Lectures that I gave:

http://lectures.gersteinlab.org/summary/ismb08pub-20080723-textmining
http://lectures.gersteinlab.org/summary/ISMB08-SS-20080721-Nets
http://lectures.gersteinlab.org/summary/ISMB08-SIG-20080721-GenomeTechAnnotate
http://lectures.gersteinlab.org/summary/ISCB-SC-20080718-motions

* Interesting quote

we should == I will

* Rough GPS track of a long Sunday Walk

http://maps.google.com/maps?q=http://gerstein.info/gps/TripISMB08-SunEdit.kmz

(Addendum)
Some more pictures from another visit in the fall
http://picasaweb.google.com/bluehat/AP20081109TorontoFallThings#
http://flickr.com/photos/mbgmbg/sets/72157610352978523

let. to ed. re. "It’s Still a Big City, Just Not Quite So Big" -- NY Times

2008-08-05T03:46:00.004-04:00

Here's a letter to the Times that wasn't published:
I was very struck by the recent article, which explained that the figure for New York City's land mass had decreased by about 5%. We are accustomed to thinking that the size of the city is a fixed, unchanging number. But the fact that this number has changed so dramatically -- without any apparent cause -- underscores how many other numbers that we have come to regard as fixed and unchangeable can so easily be altered through better measurement and careful statistics. There are many other numbers that we regularly deal with in the commercial or natural world that we have come to regard as unchanging facts, but when probed in detail, actually are mere estimates. It seems that, with greater study, very large error bounds and systematic biases can have dramatic effect. This all goes to show that there's a somewhat shaky underpinning to the numerical foundations of our common sense.

Letter in response to:
http://www.nytimes.com/2008/05/22/nyregion/22shrink.html
It’s Still a Big City, Just Not Quite So Big
By SAM ROBERTS
Published: May 22, 2008
Somehow, Michael S. Miller resisted the temptation when he got home not long ago. “Honey,” he would have been completely justified in proclaiming to his wife, “I shrank the city.” Mr. Miller, a geographer for the Department of City Planning, has calculated that New York City is 17 square miles smaller than it was long thought to be. For two decades, the city’s official directory, the Green Book, has stated definitively that the five boroughs encompass nearly 322 square miles of land....

Being bossy without being a leader

2008-08-03T13:53:00.001-04:00

Is protein evolution as duplication + divergence + recombination ?

2008-08-03T13:45:00.000-04:00

Some interesting points in "Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution" by Sean B. Carroll

2008-08-03T13:27:00.007-04:00

Enjoyed Making of the Fittest. Some things that caught my attention:

1 * Vision

- Old world monkeys trichromatic vision vs. new world ones . Duplication of opsin on X. Birds have 4 and can see UV! Only 2 for nocturnal vision.

- Whales and eels at similar depth converged on blue sensing of rhodopsin - an ex. of convergent evol.!

- Whales lost color vision

- Only 2 color receptors in primates & many other mammals since they're nocturnal .

- However, howler monkey (NW) has 3 color receptors & fewer olfactory receptors. Same dupl. of gene but smaller size and diff. AA. Represents convergence since only one in lineage.

2 * Smell

- Humans lost VR1 (vomeronasal) genes

3 * Related to other stuff

- MyH16 is pgene in humans but gene in other primates associated w. a big jaw !

- Glivec as tyr kinase inhib. against CML but evo. fights against this

- Incidence of malaria vs mosquito occurrence in Africa

- "Unique among primates, the colobine monkeys have adapted to a predominantly leaf-eating diet by evolving a foregut that utilizes bacterial fermentation to breakdown and absorb nutrients from such a food source." This monkey has a duplicated ribonuclease which works in more acid conditions as it is ruminant .

More of my notes on this book are at :
http://delicious.com/mbgmbg/clust_makingfittest0mg+Tag_Cluster_Overview_Link

(Some even rawer ones are tagged with makingfittest0mg in my email.)

Memorial Day Sightseeing and Cycling in Brooklyn [MemDayBklyn]

2008-07-05T10:49:00.005-04:00

Cycle route on Google maps:
http://maps.google.com/maps?q=http://gerstein.info/gps/MemDayBklyn-May08.kmz

21 miles without linker between West Side and Williamsburg bridge, which is about 7 miles.

Related links:
http://del.icio.us/mbgmbg/FunBikeBklyn

Photos from the weekend:
http://www.flickr.com/photos/mbgmbg/tags/kwmemdaybrooklyn
http://picasaweb.google.com/bluehat/MemDayBklyn

Photo Maps:
http://picasaweb.google.com/bluehat/MemDayBklyn/photo#map
http://www.flickr.com/photos/mbgmbg/sets/72157605990175832/map

Collection of Brooklyn Bridge Photos:
http://www.flickr.com/photos/mbgmbg/tags/brooklynbridge

(Keywords for the day include: kwmemdaybrooklyn, kwmemdaybklyn, MemDayBklyn.)

The FDR "balloon"

2008-06-25T02:25:00.002-04:00

Cycling Through Fairfield [BikeFairfield]

2008-06-24T06:15:00.004-04:00

25 miles in total. Gentle roads near beach plus a trail near Pine Creek Road. Lots of interesting houses.

Route taken on Google Maps:
http://maps.google.com/maps?q=http://gerstein.info/gps/BikeFairfield-Jun08.kmz

Useful additional routes and points of interest:
http://del.icio.us/mbgmbg/FunBikeFairfield

Some photos of the trip (many geotagged):
http://www.flickr.com/photos/mbgmbg/tags/bikefairfield

Snippet of "status" text to add at top of message in mbox format to tell Thunderbird it has not been deleted

2008-06-07T21:49:00.005-04:00

The below snippet shows what text to add to the head of a standard mbox formatted message to make sure Thunderbird think that it's not deleted. The key is the status lines in red.

From - Thu Apr 10 06:05:56 2008
X-Account-Key: account6
X-UIDL: ACJqv9EAAXDaR/0t8wsXrB8ZJMg
X-Mozilla-Status: 0011
X-Mozilla-Status2: 00000000
X-Mozilla-Keys:
X-Apparently-To: XXXX@yahoo.com via 209.191.106.39; Mon, 12 May 2008 06:52:53 -0700
X-Originating-IP: [207.106.133.17]
Authentication-Results: mta423.mail.re4.yahoo.com from=yale.edu; domainkeys=neutral (no sig)
....
Date: Mon, 12 May 2008 09:51:48 -0400
From:
Subject: Re: meeting
To: ....

\[\[*\]\] -- useful word expression for wildcards in MS word

2008-06-06T09:57:00.002-04:00

If you try hard enough, you can always find a way to be lazy.

2008-06-01T04:43:00.001-04:00

Some random quick thoughts on wines

2008-03-22T11:48:00.000-04:00

zinfandel & merlot - strong
chianti - fruity & goes with stripped bass
chateau du quint (merlot + cab mixture) - goes with fish
pinot noir - goes with fish

Yale Reverse Phone Number Lookup

2008-03-03T15:35:00.008-05:00

http://scripts.its.yale.edu/cgi-bin/ph/directory.yale.edu?Query=office_phone%3D432-6105

mpage

2008-03-03T15:35:00.006-05:00

to print multiple page on linux

The addition of small epsilons to give a big delta

2008-03-03T15:35:00.005-05:00

attachments in outlook express

2008-03-03T15:35:00.002-05:00

tools --> options --> security tab --> checkbox

Quick thoughts on Reading Supercrunchers

2008-03-02T21:14:00.003-05:00

Liked this book. Some things that I remembered:

* Nice ending with a motivation of Bayesian stats with a test for breast cancer afflicting 1% wtih a high FP rate.
* Useful stat that SD on pregnancy 9 months +/- 15 days.
* Suggestion of "mining free" products.
* Privacy concerns as the "darkside of digitization".
* Potential of a face recognition company to ID photos on flickr.
* Mentions that AOL search was comprimised by one keystroke (correct?).
* Discusses centralizing shift of power implicit in move to supercrunchers
* Some characters Donaghue (?), Levitt vs....
* Mentions Ec. miner who find evidence of cheating in wide point spreads
* Some dubious stuff: Is regression really exponential complexity (???) and NN the main new mining technique ?
* Buying and selling race

http://del.icio.us/mbgmbg/link_supercrunchers

Simple Ex of HTML to create a forwarding webpage

2008-03-02T07:43:00.006-05:00

<html>
  <head>
    <title>Redirecting...</title>
    <meta http-equiv="Refresh" content="0; URL=http://outbox.gerstein.info/"
>
  </head>
  <body>
    Click <a href="http://outbox.gerstein.info/">here</a> if you are not for
warded immediately.
  </body>
</html>

Where one's stuff is splattered over windows

2008-03-02T04:53:00.010-05:00

I find it frustrating that my "personal data" is often splattered all over different locations on Windows XP. Here's a list of some places that I've uncovered below. (My windows userid is "mbg".)

* List of recent files used in Office
C:/Documents and Settings/mbg/Application Data/Microsoft/Office/Recent

* List of temp files
C:/Documents and Settings/mbg/Local Settings/Temp

* Contains list of profile directories
c:/Documents and Settings/mbg/Application Data/Thunderbird/profiles.ini

* contains X1 index files
C:/Documents and Settings/mbg/Local Settings/Application Data/X1 Desktop Search

* contains outlook data file
C:\Documents and Settings\mbg\Local Settings\Application Data\Microsoft\Outlook

* contains all of firefox's data, which is cleared by the clear private data command
C:\Documents and Settings\mbg\Application Data\Mozilla\Firefox\Profiles\ingyn1a7.default
C:\Documents and Settings\mbg\Application Data\Mozilla\Firefox\Profiles\s2ocgep1.default

* contains all the pictures and videos from a palm sync, which don't seem to get deleted properly by the palm application.
C:\Documents and Settings\mbg\My Documents\My Pictures\Palm Photos\mbgtre\Expansion card 1319\Palm
C:\Documents and Settings\mbg\My Documents\My Pictures\Palm Photos\mbgtre\Internal\Palm
C:\Documents and Settings\mbg\My Documents\My Pictures
C:\Documents and Settings\mbg\My Documents\my videos\Palm Videos

* contains a listing of recent files opened
C:\Documents and Settings\mbg\recent

* cygwin home (could be reset to a different directory, useful to clear history)
C:\cygwin\home\mbg

* Windows Temp -- doesn't seem to have much personal data beyond what is cleared directly through clearing the IE cache
C:\WINDOWS\Temp

* Additional things include:
- removing all one's palm files (C:\...\palm)
- Disabling calendar sync stuff (e.g. change passwd on google calendar sync. & disable "syncmycal" agent)
- Start Picasa and remove all folders. Then it will compact its DB.
- Start firefox and delete all private data. Start IE and do the same .

Driving Directions to Claire's in New Haven

2008-02-16T12:23:00.007-05:00

Here's how to get from GW bridge to Merritt.

Here's how to get from Merritt to Claire's.

Entrace to parking garage is between Chapel and Crown on College St.

Thunderbird issues

2008-02-10T08:40:00.004-05:00

"Thunderbird can't use the profile because it is in use to continue close the running instance of thunderbird"
In relation to the above error message found the only thing to cure this is to restart windows and re-run thunderbird.

The lock file that often gums up a thunderbird session is:
D:\vmshared\PERS\mailstuff\mbg\parent.lock

My other thunderbird hints are at: http://del.icio.us/mbgmbg/Link_ThunderbirdFixes

Some Ipod Notes

2008-02-09T02:51:00.001-05:00

Notes on water proofing an iPod
http://www.waterproofcases.net/headphones.html
http://ilounge.com/index.php/reviews/comments/otterbox-for-ipod-4g-photo-ipod/
http://www.ilounge.com/index.php/reviews/comments/h2o-audio-sv-imini-underwater-housing-ipod/
B0009I2M7C
B0009IZSAK
http://www.slicsound.com/ss001.asp

To reset an iPod with a Click Wheel
(below extracted from a page on the web)
Including the following:
* iPod mini
* iPod mini (Second Generation)
* iPod with color display (iPod photo)
* iPod (Click Wheel)
* iPod nano
* Fifth Generation iPod (also known as iPod with video)

1. Toggle the Hold switch on and off. (Slide it to Hold, then turn it off again.)

2. Press and hold the Menu and Select buttons until the Apple logo appears, about 6 to 10 seconds. You may need to repeat this step.

Tip: If you are having difficulty resetting your iPod, set it on a flat surface. Make sure the finger pressing the Select button is not touching any part of the click wheel. Also make sure that you are pressing the Menu button toward the outside of the click wheel, and not near the center.

If the above steps did not work, try connecting iPod to a power adapter and plug the power adapter into an electrical outlet, or connect iPod to your computer. Make sure the computer is turned on and isn't set to go to sleep
http://docs.info.apple.com/article.html?artnum=61705

let. to ed. ("23andMashup") re. "23AndMe Will Decode Your DNA for $1,000" -- Wired

2008-02-01T06:42:00.001-05:00

Here's a letter to the Wired that was published:
23andMashup
I enjoyed the article about personal genomics company 23andMe ("Your DNA Decoded," issue 15.12). I was especially interested in the visionary and somewhat whimsical idea of connecting social networking with understanding one's genome. We can take this idea a step further and combine it with another phenomenon — the rise of easy-to-make consumer mashups. People could use Web services to share their genomic information in meaningful ways. For instance, friends on a social networking site might look beyond external characteristics like hair and eye color and instead search for sequence variants they have in common. Alternatively, you could mash up genomic profiles with marathon times and highlight common characteristics of fast runners. However, people will only share genomic information if it's done in a way that doesn't reveal too much about themselves: To be viable, genomic mashups should be interesting, but not too specific about future health implications.

Citation of the Letter:
http://www.wired.com/culture/culturereviews/magazine/16-02/rants
Wired Magainze, Issue 16.02, Pg. 17 (Feb.)
Mark Gerstein, New Haven, Connecticut
Rants Section

Article letter is in response to:
Wired Magainze, Issue 15.12
23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics
By Thomas Goetz
http://www.wired.com/medtech/genetics/magazine/15-12/ff_genomics
At the age of 65, my grandfather the manager of a leather tannery in Fond Du Lac, Wisconsin, suffered a severe heart attack. He had chest pains and was rushed to the hospital. But that was in 1945, before open heart surgery, and he died a few hours later. By the time my father reached 65, he was watching his diet and exercising regularly. That regimen seemed fine until a couple of years later, when he developed chest pains during exercise, a symptom of severe arteriolosclerosis. A checkup revealed that his blood vessels were clogged with arterial plaque. Within two days he had a triple bypass. Fifteen years later (15 years that he considers a gift), he's had no heart trouble to speak of.....

Text that was submitted to the magazine (before editing):
I enjoyed the recent article about the new personal genomics company, 23andMe, and was especially interested in their visionary and somewhat whimsical idea of connecting social networking with understanding one's genome. We can take this idea a step further and combine it with another emerging phenomenon of the past year -- the creation of easy-to-make consumer mash-ups (such as Yahoo Pipes). Then, we can begin to imagine people using web services to interrelate and give personal meaning to their genomic information, just as we currently see discrete bits of apparently meaningless data related to location come together into an emergent whole when they are mashed up with a map service such as Google's -- think of collecting all the photos taken near Times Square on Flickr to get an overview of the neighborhood. However, unlike the case of vacation photos, people will only be willing to share genomic information if they are not worried that it reveals too much about themselves. That is, to be viable mash-ups of genomic information should be interesting, but not too specific about future health implications.

WinXP within WinXP with VMware (BlogEntry_VMconfigT60b_Xmg)

2008-01-29T04:24:00.001-05:00

This document contains some public notes I've made on the arduous process of getting VMware to run with a Win XP guest on a Win XP host. (One might wonder why I'm trying to do this, but this will take too much text here. I'll let any reader just speculate.) In general see below and some of my relevant del.icio.us links .

## Del.icio.us Links

My central collection of bookmarks around this endeavor is:
http://del.icio.us/mbgmbg/Useful_VMconfigT60b_Xmg

In addition, some extensions that I found useful for Firefox and Thunderbird
http://del.icio.us/mbgmbg/UsefulExtension

## Outlook

Getting Outlook to work with the Palm Treo and VMware

* Have to keep main outlook DB in
C:/Documents and Settings/mbg/Local Settings/Application Data/Microsoft/Outlook

Doesn't seem to work when moving it another location.

* archive stuff to archive.pst and then compacted

* When synching with the VMware and treo, host application often seizes the "context." This happens particularly on the second sync attempt. Have to tell it to "take no action" on a sync on the host application dialog box.

* See treo hints under http://del.icio.us/mbgmbg/useful_vminstalls to work with Verizon wireless sync.

## Blackberry
Works fine in VM

7750M_PBr4.0.0_rel201_PL1.5.0.30_A4.0.0.171.exe
BlackBerry_400_33_desktop_ml.exe
user "mbg"
Select "Blackberry Internet Email" Option

Run desktop mgr
set it to use USB
use default folder
C:/Documents and Settings/mbg/Application Data/Research In Motion/BlackBerry

## Thunderbird
Getting it to run in VM and then have it's mail directory outside.

* Install normally
but then edit c:/Documents and Settings/mbg/Application Data/Thunderbird/profiles.ini
to be thus:

[General]
StartWithLastProfile=1
[Profile0]
Name=default
IsRelative=1
Path=Profiles/knnjxcfu.default
[Profile1]
Name=mbg
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg
Default=1
[Profile2]
Name=mbg2-yahoo
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg2
[Profile2]
Name=mbg-old-rec
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg-old-rec
[Profile3]
Name=mbg-old-sent
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg-old-sent

* To access profiles,
"C:/Program Files/Mozilla Thunderbird/thunderbird.exe" -ProfileManager

* Profile0 was there, now adding profile1
Thunderbird should then come up with full mail setup

* One has to install quicktext manually.
Then all the stuff should be there.

Make sure you check the auto download of messages.

## Google Earth
It runs under VMware but not in directX mode

## Itunes
Key point here is putting iTunes DB in another location and then configuring VMware to access this location with another.

## MS Office

* Installs fine on the VM
* Transferred settings from "office-saved-settings-for-MG-29Dec07.OPS"

However, then ran to documents to go problem -- interface with word was messed by copying over the prefs (see above). Found fix at http://support.dataviz.com/support.srch?docid=12792 , viz:

How to manually uninstall Word Add-In:
1. Open Word
2. Go into Tools menu
3. Click on Templates and Add-Ins
4. Uncheck DVZWDAddin.dot - this menu should then be removed
5. Close Word, then press CTRL-ALT-DELETE to bring up the Task Manager, and check to make sure all instances of WINWORD.EXE are closed
6. Go into the following directory: C:/Documents and Settings/<user name>/Application Data/Microsoft/Word/STARTUP
(NOTE: The Application Data folder is a hidden folder. If you can't see hidden folders, go to Tools > Folder Options, select the View tab, select the option to "Show hidden files and folders" and click OK.)
7. Delete the file "DVZWDAddin.dot" and all of its temp files (i.e. ~$ZWDAddin.dot)

## This doc

Tips in formatting include using ^l (in word) instead of ^p before import into Google Docs. Within GoogleDocs one can just do "shift-return" .

Your fingers are the best comb.... -G Ray

2007-12-25T15:17:00.001-05:00

let. to ed. re. "For a Tunnel to Go 16 Miles, No Light Yet" -- NY Times

2007-12-24T11:52:00.000-05:00

Here's a letter to the Times that wasn't published:
I was very intrigued by your recent column about a proposed tunnel
connecting Long Island to Westchester. As the piece noted, this
tunnel follows a route long ago advocated by Robert Moses. If such a
tunnel were ever to be built, it would validate one of Moses' original
designs for the road network encircling New York City; thus, in a way,
this proposal revitalizes his original dream. However, it is worth
pointing out that Moses' original plan was for a bridge, not a tunnel.
Moses, in fact, strongly disliked and actively opposed tunnels,
whereas he felt bridges made a stronger and grander statement. Thus,
the interesting twist in the column is how it simultaneously revives
Moses' original dream just as it implicitly criticizes his
stubbornness.

Letter in response to:
http://www.nytimes.com/2007/11/29/nyregion/29towns.html
November 29, 2007
Our Towns
For a Tunnel to Go 16 Miles, No Light Yet
By PETER APPLEBOME
GARDEN CITY, N.Y.
A reasonably sane person contemplating the modest proposal of the
developer Vincent Polimeni to build a $10 billion, privately financed,
16-mile tunnel linking Long Island and Westchester the longest
autos-only tunnel in the world and the first to be privately built in
the United States might start with two thoughts.
The first: This might be a brilliant idea or a nutty one, but in an
era of shrunken ambitions, give the guy credit for a big idea that
goes back to Robert Moses, who in the 1960s championed a bridge over
pretty much the same route.....

Cycling in DC (TripBethesda)

2007-12-03T04:37:00.000-05:00

Cycling from Bethesda into DC and back

Route taken on Google Maps
Summary: ~40 miles cycling
Geotagged images, served from [P]icassa or [F]lickr (also look at overall flickr map)

Potential alternate terms RFBRs for chIP-chip "hits"

2007-12-02T22:21:00.001-05:00

The ENCODE paper coined the term RFBR for "hits" in chIP-chip experiments, viz: "We refer to regions with enriched binding of regulatory factors as RFBRs. RFBRs were identified on the basis of ChIP-chip data in two ways..." Some other terms were considered instead of RFBR. Here's a list of some of them:

CHIRP -- chip hit of regulatory potential
EIGR -- experimentally identified genomic region (like mountain)
GRAF -- Genomic region associated with function
GRAB -- Genomic region associated with binding
MONOD
RELIC -- Regulatory element in living cells
GELC -- Genomic element in living cells
FELC -- Functional event in living cells
MOJO
EDGE -- Experimentally determined genomic element
GEMMS -- Genomic element defined by multple methods
LORE
REIVE -- Regulatory element in vivo
GERP -- Genomic element of regulatory potential
TRE -- transcriptional regulatory element
GIVE -- Genomic in-vivo element
LRE -- long-range element
RFBS -- regulatory factor binding site

Bad MILK. How does milk know when to expire? - Bad Astronomy and Universe Today Forum

2007-11-11T05:27:00.000-05:00

Some useful quotes on what makes milk go bad:
"Generally, if kept constantly cold, bacteria in milk will grow at a constant slow rate. The bacteria generally feeds on the lactose, turning it into lactic acid. As it accumulates, it makes the milk taste more and more sour. But our taste buds will generally ignore the small bit of sourness. The milk is considered bad when the sourness becomes noticeable. The proteins in the milk will start to stick to each other in an acid environment. However, for this to happen on a large scale requires the milk to be fairly acid (pH around to 5.5). Our taste buds register sour at a much higher pH (~6)."

Some Durable Indoor Plants (from visiting a nursery)

2007-11-01T01:36:00.000-04:00

Pictures of them at http://www.flickr.com/photos/mbgmbg/tags/kw30sep07nurseryvisit

Listing of plants

Snake Plant - http://en.wikipedia.org/wiki/Sansevieria_trifasciata
(verabella?) palm plant
Jade Plant - http://en.wikipedia.org/wiki/Jade_plant
ZZ plant (durable) - http://en.wikipedia.org/wiki/Zamioculcas
Rubber Plant (not as durable) - http://en.wikipedia.org/wiki/Ficus_elastica
Bamboo plants (need to be immersed in water) - http://www.bamboogarden.com/care.htm

Cycling and Walking around Vienna, with Pictures (TripVienna)

2007-10-30T17:51:00.001-04:00

Attempted to carefully integrated image and geo data on last summer's vacation to Vienna

Photos
(Geotagged images, served from [P]icassa or [F]lickr)

All of the photos [P][F] (also look at overall flickr map)
Various Subsets (sublime to ridiculous):

Interesting Architecture [P][F]
Street Art [P][F]
Generic, non-geotagged shots [P][F]
Graffiti [P][F] (alternate picassa with subset map)

Shots of People [P] (need auth. key)

Cycling and Walking Routes

Cycling along Danube near Vienna, ~58 km (13 July 2007);
Route taken on Google Maps (Garmin HST file)
Walking through city center (11 July 2007);
Route taken on Google Maps (Garmin HST file)
Walking through city outskirts, including Naschmarkt, Palace and Freud museum (12 July 2007);
Route taken on Google Maps (Garmin HST file)

Useful Links

Overall, FunVienna1, FunVienna2, FunVienna3, FunVienna4

Cycling near New Haven (BikeCT + BikeOrchard)

2007-10-28T08:18:00.000-04:00

BikeCT
Cycling along CT coast near Guilford and Branford, with a lunch in Branford.
Route taken on Google Maps
(kmz colored by course heading)
Associated useful links.
Summary: ~52 miles cycling (7 hrs. of biking time)

BikeOrchard
Cycling to Lyman Orchard, with a lunch there.
Route taken on Google Maps
(kml colored by elevation -- note hills.)
Associated useful links.
Summary: ~41 miles cycling (7.5 hrs. of total time)

Some examples of Cockney rhyming slang

2007-09-28T19:50:00.000-04:00

Cockney rhyming slang - Wikipedia, the free encyclopedia:
'plates' means 'feet' ('plates of meat')
'brown' means dead ('brown bread')
'titfer' means hat ('tit for tat')

Some Useful Tidbits on Asthma

2007-09-23T05:54:00.000-04:00

The Harvard Medical School Guide To Taking Control Of Asthma

by Christopher H. Fanta (Author), Lynda M. Cristiano (Author), Kenan Haver (Author)
http://www.amazon.com/Harvard-Medical-School-Taking-Control/dp/0743224787/ref=ed_oe_p/104-6142984-5779139?ie=UTF8&qid=1190536146&sr=1-6
http://books.google.com/books?id=ohIbOrVcRBwC

Leukotriene Inhibitors

[From link above:]
"Molecular biology promises to provide drugs that will control our immunologic and biochemical reactions. Several pharmaceutical companies are now producing leukotriene receptor blockers - the first of the new line of agents being developed to control the inflammatory response in asthma. The first agents coming to market in Canada are zafirlukast (Accolate) and montelukast (Singulair). Both act by blocking the most potent of the leukotrienes, L4. Asthma is felt to be due to allergens triggering an inflammatory response. .... Leukotrienes were found to be the active factor in the old SRSA (slow releasing substance of anaphylaxis) first described in 1938. They are 1000x more potent in inducing bronchospasm than histamine. They are part of the lipoxygenase pathway that is also involved in prostoglandin production. These pathways are also used in allergic rhinitis. At the moment, leukotrienes are hoped to be the appendix of the immune system - of no good use, but known to cause problems....."

Beta Blockers & Asthma

[From link above:]
"What is a beta-blocker? A beta-blocker is a medicine used to treat high blood pressure and heart problems. Some beta-blockers are atenolol (brand name: Tenormin), metoprolol (brand names: Lopressor, Toprol XL) and propranolol (brand name: Inderal). A beta-blocker blocks the harmful effects of stress hormones on your heart. This medicine also slows your heart rate. Beta-blockers can also be used to prevent migraine headaches in people who get them frequently. Can I take a beta-blocker if I have asthma or chronic lung disease? Beta-blockers are generally not used in people with asthma. A beta-blocker can cause asthma attacks.... "

Beta-agonists

[From link above:]
"Beta-agonists are bronchodilator medicines that open airways by relaxing the muscles around the airways that tighten during an asthma attack....
Beta-agonists come in many different forms. Some common beta-agonist medicines are: albuterol, Alupent, Brethine, metaproteronol, Metaprel, Proventil, Salbutamol, terbutaline, Ventolin. "

The concept of "Pre-treatment" with beta-agonist

Preventing Respiratory Viruses

[From Harvard Med. Guide above:]
"Most viruses are spread from oral or nasal secretions onto surfaces, are picked up by hand contact, and are then spread from your hands to your nose and mouth. So wash your hands frequently..."

http://en.wikipedia.org/wiki/Purell

Eosinophils: mischief-makers in asthma

[From link above:]
"Whatever are eosinophils?

Eosinophils are a type of white blood cell (corpuscle) and take up the red dye eosin when blood is examined under a microscope by the commonest method.

They accumulate wherever allergic reactions like those in asthma take place. Their natural role is to defend us against parasites. In fact allergies such as asthma are probably a malfunction of our protective mechanism against parasites...."

AOI

2007-09-21T07:00:00.000-04:00

Interesting acronym: AOI = achievements, objectives, issues

Triathlons I've done

2007-09-10T14:19:00.000-04:00

2007 MADISON SPRINT TRIATHLON
Swim .5 miles/Bike 13 miles/Run 3 miles
Saturday Sept 8, 2007 | Surf Club - Madison, CT
Part of running route
http://www.madisonjc.com/trimaps.shtml
http://www.madisonjc.com/triathlon.shtml
Cache: C:\...\pers\misc\exercise\Sept07-triathlon\madtri07.txt + related

JONES BEACH TRIATHLON
SEPTEMBER 26, 2004
FINSIH LINE ROAD RACE TECHNICIANS - www.FLRRT.com
1/2 Mile Swim, 14 Mile Bike, 3.1 Mile Run
http://metrotri.com/document/45330
Cache: D:\...\y10.unzip\pers-pics\pers\clip\jones-beach-triathalon

VYTRA TOBAY TRIATHLON
TOWN OF OYSTER BAY, OYSTER BAY, NEW YORK
AUGUST 19, 2001
FINSIH LINE ROAD RACE TECHNICIANS, www.FLRRT.com
1K Swim - 15K Bike - 5K Run
http://bioinfo.mbb.yale.edu/~mbg/dom/fun3/tobay-triathalon
Cache: file:///D:/.../y6-021014-closed/y6/bikemaps/tobay-times/tri01m.txt

TRIATHLON IN MODESTO
Modesto, CA ; 13 October 1996
Pool swim, Bike, Run
Can't find any more details

let. to ed. re. "Mom's Genes or Dad's? Map Can Tell" -- Washington Post

2007-09-07T13:01:00.000-04:00

Here's a letter to the Washington Post that was published:
Regarding the Sept. 4 front-page article "Mom's Genes or Dad's? Map Can Tell," about the unraveling of the Venter "diploid" genome: The article noted that sequencing an individual's DNA provides a wealth of information not only about that person but also about his or her relations. But it did not mention that sequencing also provides information about all of an individual's unborn descendants. Thus, when an individual's genome sequence is publicly released, consent implicitly is being given for these unborn descendants without their approval.
Fifty years from now, our understanding of genomic information will undoubtedly be more sophisticated than it is today. In the future, from a bit of sequence, it might be possible to glean a tremendous amount about such things as the diseases or behavioral anomalies that might befall someone. What might these unborn descendants have to say about the release of such highly personal information?
It is worth underscoring that when information is publicly released, it gets widely distributed (via the Internet and other means); any such decision made today will have far-reaching and irreversible consequences.

Citation of the Letter
http://www.washingtonpost.com/wp-dyn/content/article/2007/09/06/AR2007090602362.html
DNA Rights and Wrongs
Friday, September 7, 2007; A20
MARK GERSTEIN
New Haven, Conn.

Citation of Article Letter Responds to
http://www.washingtonpost.com/wp-dyn/content/article/2007/09/03/AR2007090301106.html
Mom's Genes or Dad's? Map Can Tell.
One Man's DNA Shows We're Less Alike Than We Thought
By Rick Weiss
Tuesday, September 4, 2007; Page A01
Scientists have for the first time determined the order of virtually every letter of DNA code in an individual, offering an unprecedented readout of the separate genetic contributions made by that person's mother and father....

Other Articles that this Letter Potentially Responds to
http://www.nytimes.com/2007/06/12/opinion/12tue4.html
June 12, 2007
Editorial
The Discoverer's DNA
When scientists talk about sequencing the human genome, they have been talking
so far about creating a composite picture drawn from the gene sequences of many
people. That has now changed for good. Recently, the director of the Human
Genome Sequencing Center at the Baylor College of Medicine gave James D. Watson
— who with Francis Crick discovered the structure of the DNA molecule — two DVDs
that contained the complete sequence of Mr. Watson's DNA.....

http://www.nytimes.com/2007/06/03/weekinreview/03harm.htm
June 3, 2007
6 Billion Bits of Data About Me, Me, Me!
By AMY HARMON
JAMES D. WATSON, who helped crack the DNA code half a century ago, last week
became the first person handed the full text of his own DNA on a small computer
disk. But he won't be the last.
Soon enough, scientists say, we will all be able to decipher our own genomes —
the six billion letters of genetic code containing the complete inventory of the
traits we inherited from our parents — for as little as $1,000.
Just what we will do with the essence of who we are once we bottle it, however,
is likely to be as much a social experiment as a scientific one....

http://www.nytimes.com/2007/06/01/science/01gene.html
June 1, 2007
Genome of DNA Discoverer Is Deciphered
By NICHOLAS WADE
The full genome of James D. Watson, who jointly discovered the structure of DNA
in 1953, has been deciphered, marking what some scientists believe is the
gateway to an impending era of personalized genomic medicine.
A copy of his genome, recorded on two DVDs, was presented to Dr. Watson
yesterday in a ceremony in Houston by Richard A. Gibbs, director of the Human
Genome Sequencing Center at the Baylor College of Medicine, and by Jonathan M.
Rothberg, founder of the company 454 Life Sciences.
"I am thrilled to see my genome," Dr. Watson said....

let. to ed. re. "Logged In and Sharing Gossip, er, Intelligence" -- NY Times

2007-09-05T00:21:00.000-04:00

To the Editor:

I was very impressed by the recent article in the week in review about
how the intelligence community could use collective knowledge in the
form of wikis and blogs to help combat potential threats. While I
think this idea is great, I was surprised that the article did not
mention the public episode a few years ago where it was suggested that
the Defense Advanced Research Projects Agency (DARPA) establish a
Policy Analysis Market to help predict terrorist threats. In the
framework of the article, the DARPA 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, which led to the resignation of DARPA head John Poindexter.

Mark Gerstein

Above is an unpublished letter in response to:
September 2, 2007
Logged In and Sharing Gossip, er, Intelligence
By SCOTT SHANE
http://www.nytimes.com/2007/09/02/weekinreview/02shane.html
Week in Review

AMERICA’S spies, like America’s teenagers, are secretive, talk in code and get
in trouble if they’re not watched closely. It’s hard to imagine spies logging on
and exchanging “whuddups” with strangers, though. They’re just not wired that
way. If networking is lifeblood to the teenager, it’s viewed with deep suspicion
by the spy.....

Cycling along the Hudson

2007-09-04T05:57:00.000-04:00

BikeNyack
Cycling through Palisades Park to Nyack, with a long lunch at famous Runcible Spoon.
Route taken on Google Maps
(kmz colored by elevation, note tough climb at end of park when one joins highway)
Associated useful links.
Summary: ~51.2 miles cycling (7.3 beyond that shown in KML)

BikeStormKing
Walking in StormKing sculpture park then cycling from there through Newburgh, over Hudson on I84 bridge, and into Beacon and then back.
Route taken on Google Maps
(kmz colored by speed)
Associated useful links.
Summary: ~23.1 miles cycling and 3 miles walking

BikeCroton
Cycling along Old Croton Aqueduct Trail, which is dirt. Trip aborted by rain in northern portion.
Route taken on Google Maps
Associated useful links.
Summary: ~18.5 miles

Cycling in the Bronx (BikeBx)

2007-08-14T03:27:00.000-04:00

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)

2007-07-29T05:51:00.000-04:00

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)

2007-07-24T07:42:00.000-04:00

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

2007-07-22T02:32:00.001-04:00

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

2007-07-22T00:01:00.000-04:00

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

2007-07-21T15:04:00.001-04:00

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)

2007-07-20T06:08:00.000-04:00

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)

2007-07-17T06:31:00.000-04:00

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?”

2007-07-16T13:01:00.000-04:00

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

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

2007-07-01T00:21:00.000-04:00

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)

2007-06-27T15:31:00.000-04:00

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)

2007-06-25T13:45:00.000-04:00

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)

2007-06-24T13:02:00.000-04:00

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

2007-06-09T23:12:00.000-04:00

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

2007-06-02T09:14:00.000-04:00

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

2007-05-28T02:59:00.000-04:00

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.

2007-05-16T00:10:00.000-04:00

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

2007-05-16T00:05:00.000-04:00

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!

2007-05-08T06:00:00.000-04:00

[quote]

Capsaicin - Wikipedia, the free encyclopedia

2007-05-05T19:43:00.000-04:00

The molecule that makes Chili peppers hot.

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

Hiking in Sleeping Giant Park

2007-03-30T14:08:00.000-04:00

Route on Google Maps
Extra Data on the route: Just Climbing Down [kml], ERockClimbing-HighPoints.jpg, DipInMiddle-After1stHighPt.jpg, Overview.jpg

Stats on the Hike
Spreadsheet
HeartRate-Elev-Profile.jpg

	Absolute-from-start			delta-vs-previous-step
	Time	Dist (mi)	Elev (ft)	Time	Dist (mi)	Elev (ft)	Lat. (dd)	Long. (dd)
Start	0:00:00	0	89				41.4216	-72.89847
1st-top	0:33:59	1.44	713	0:33:59	1.44	624	41.42608	-72.89899
Middle-dip	0:57:21	2.05	467	0:23:22	0.61	-246	41.42832	-72.89726
2nd-top	1:21:16	3.03	814	0:23:55	0.98	347	41.43053	-72.89052
Leave-top	1:23:55	3.13	707				41.43044	-72.89068
End	1:48:57	4.62	182	0:25:02	1.49	-525	41.42137	-72.89822

External Links
http://www.sgpa.org [http://www.sgpa.org/colormap.pdf , Map Detail ]
http://www.ct.gov/dep/cwp/view.asp?A=2716&Q=325264

American Artist Rankings

2007-03-28T05:51:00.000-04:00

Type	Name	RS	MG	Link Wiki	Link Y!	??
artist	Edward Hopper	5	1	=	948000
artist	Fredrick Church	9	2	=	820000
artist	Frank Stella	-	3	=	829000
artist	Sargent	4	4	=	597000
artist	Bierstadt	-	5	=	111000
artist	Pollack	-	6	=	383000
artist	Jasper Johns	6	7	=	567000
artist	Rauschenberg	14	8	=	247000
artist	Inness	-	9	=	54800
artist	Thomas Cole	8	10	=	2890000
artist	Eakins	6	11	=	134000
artist	Homer	10	12	=	1460000
artist	Wyeth	-	13	=	323000
artist	Rothko	7	14	=	364000
artist	O'Keefe	15	15	=	371000
artist	Copley	16	16	=	314000
artist	James Whistler	-	17	=	279000
artist	Cassatt	2	-	=	294000
artist	Hassam	3	-	=	101000
artist	T Robinson	11	-	=	1780000	?
artist	Milton Avery	12	-	=	265000
artist	C Durand	13	-	=	164000	?

architect	Frank Lloyd Wright	6	1	=	605000
architect	P Johnson		2	=	1170000
architect	Gehry		3	=	429000
sculptor	Calder	1	4	=	70500
architect	Venturi		5	=	89500
photographer	Walker Evans		6	=	293000
photographer	Dorothea Lange		7	=	167000
sculptor	Noguchi		8	=	47400
architect	Saarinen		9	=	110000
architect	Gordon Bunshaft		10	=	27800
photographer	Leibowitz	2	-	=	36200
photographer	Richard Avedon	3	-	=	701000
photographer	Stieglitz	4	-	=	97500
other	Louis Tiffany	5	-	=	3060000
photographer	Gordon Parks	7	-	=	438000

http://gerstein.info/gps/artist-rankings.xls

More on Cameras

2007-03-27T02:54:00.000-04:00

Panasonic SV AS10 is a very Small Camera
http://reviews.cnet.com/Panasonic_SV_AS10/4505-6501_7-30556974.html
My old stuff : http://textstream.blogspot.com/2007/01/subcompact-camera-comparison.html

Letter responding to "One Number For All Your Phones" -- NY Times

2007-03-27T00:30:00.000-04:00

Here's a letter I sent in which wasn't published:
I read with great interest the recent article about
GrandCentral.com. I just want to point out that this service closely
resembles SimulRing -- a simultaneous ring service that went out of
business several years ago. (See
http://www.thedigest.com/more/146/146-230.html ). My use of SimulRing
attempted to overcome the problem of changing your phone number that
was alluded to. I had one of my (multiple) phone numbers redirect to
the (hidden) SimulRing number and then had this call all the others. I
really liked SimulRing but was disappointed when I lost my phone
number (in addition to the service) when the company went bankrupt. It
might have been good to point out the bankruptcy risk to people
reading the article and contemplating enlisting.

Article Commented on:
http://query.nytimes.com/gst/fullpage.html?res=9C01EFDC1E31F936A25750C0A9619C8B63
STATE OF THE ART; One Number For All Your Phones
By DAVID POGUE
Published: March 15, 2007
If you have only one telephone with one phone number, this column won't be of
any interest to you. Skip to another article, you eccentric you.
But first, count your blessings. Millions of people have more than one phone
number these days -- home, work, cellular, hotel room, vacation home, yacht --
and with great complexity comes great hassle. You have to check multiple
answering machines. You miss calls when people try to reach you on your cell
when you're at home (or the other way around). You send around e-mail messages
at work that say, ''On Thursday from 5 to 8:30, I'll be on my cell; for the rest
of the weekend, call me at home.''....
[L2E]

Slow Down, Multitaskers; Don’t Read in Traffic - New York Times

2007-03-26T12:51:00.001-04:00

This is definitely a factor in my productivity: 8 * 15' block < 90' straight!

http://del.icio.us/mbgmbg/Link_Multitasking

History, Digitized (and Abridged) -- NY Times

2007-03-22T10:39:00.000-04:00

Particularly relevant to image collection -- digitize or disappear !

History, Digitized (and Abridged)
Article Tools Sponsored By
By KATIE HAFNER
Published: March 11, 2007
THE National Steinbeck Center, at the top of Main Street in this farming community, exhibits an array of artifacts from John Steinbeck's life and works: family memorabilia, a passport from the 1960s and movie stills from ''The Grapes of Wrath.'' Downstairs, in a climate-controlled vault, is the original manuscript of ''The Pearl,'' his novella published in 1947. There is also an exuberant letter that Steinbeck wrote to a distant relative when he was a teenager, as well as rare footage of him on 16-millimeter film, introducing a 1961 movie, ''Flight.'' .....
http://select.nytimes.com/search/restricted/article?res=FA0A14FD38550C728DDDAA0894DF404482#
[clipcache]

Letter in response to "Say Everything" -- NY Magazine

2007-03-20T08:15:00.000-04:00

Below is a letter I wrote in response to the article at bottom (which was never published). Sort of the ultimate in blogging. It's a bit of the extreme in the on-line world, but maybe a hint of the future. Viz:
I enjoyed the article about the seeming irreverence for privacy displayed by young people using the Internet. The article frequently alludes to what will happen in the future when we can mine and search for all the information young people are now posting. One can imagine historians of the future combing through the vast trove of past postings on the web, looking for subtle patterns and connections between individuals that weren't at all apparent in the present. However, it is one thing for historical analysis to turn up interesting facts someone left behind about himself; it is another for it to turn up facts about someone else. In particular, what will happen with young kids posting pictures on the web of their friends in all sorts of compromising situations? Beyond the extreme case alluded to in the article of salacious images posted without consent, what are we to make of the seemingly innocent practice of party pictures, snapped in instant but posted on the web for eternity. The kids posting this information are of course unaware of the potential long-term harm they are doing to others. New rules need to be developed governing what can and can't be posted about others without their consent.

http://nymag.com/news/features/27341/
Say Everything
By Emily Nussbaum
February 12, 2007 issue of New York Magazine
As younger people reveal their private lives on the Internet, the older generation looks on with alarm and misapprehension not seen since the early days of rock and roll. The future belongs to the uninhibited.
Yeah, I am naked on the Internet," says Kitty Ostapowicz, laughing. "But I've always said I wouldn't ever put up anything I wouldn't want my mother to see."
She hands me a Bud Lite. Kitty, 26, is a bartender at Kabin in the East Village, and she is frankly adorable, with bright-red hair, a button nose, and pretty features. She knows it, too: Kitty tells me that she used to participate in "ratings communities," like "nonuglies," where people would post photos to be judged by strangers. She has a MySpace page and a Livejournal. And she tells me that the Internet brought her to New York, when a friend she met in a chat room introduced her to his Website, which linked to his friends, one of whom was a photographer. Kitty posed for that photographer in Buffalo, where she grew up, then followed him to New York. "Pretty much just wanted a change," she says. "A drastic, drastic change."...
[L2E]

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

2007-03-18T05:08:00.000-04:00

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

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

Climbing Ratings - Climbing With Mike

2007-03-16T00:01:00.000-04:00

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

For me:

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

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

2007-03-15T14:39:00.001-04:00

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

2007-03-13T06:46:00.000-04:00

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

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

Brain Man -- 60 minutes

2007-03-12T11:02:00.000-04:00

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

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

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

2007-03-11T08:02:00.000-04:00

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

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

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

2007-03-10T07:42:00.000-05:00

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

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

2007-03-02T05:02:00.000-05:00

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

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

Letter in response to "Commercial Break" -- Wired

2007-02-27T06:32:00.000-05:00

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

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

New Weapon in Web War Over Piracy -- NY Times

2007-02-20T08:12:00.000-05:00

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

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