Animal Symbolism

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

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Above text is an unpublished letter in response to: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

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"

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"

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

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

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]

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

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

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

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

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

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

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

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

* 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

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

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)

* 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

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....