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

---

Above is an unpublished letter in response to: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

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

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

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

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....

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

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.....

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

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.....

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

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

---

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

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

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

---

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

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

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

---

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

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

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

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

---

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

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

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

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

---

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