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

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 !

Link to the Mathematics Genealogy Project

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

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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

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

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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

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

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

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

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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]

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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

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.

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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

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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.

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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.

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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

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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

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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

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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