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Above is an unpublished letter in response to: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....

Being bossy without being a leader

Is protein evolution as duplication + divergence + recombination ?

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

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]

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"

Cycling Through Fairfield [BikeFairfield]

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

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

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

Some random quick thoughts on wines

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

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

mpage

to print multiple page on linux

The addition of small epsilons to give a big delta

attachments in outlook express

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

Quick thoughts on Reading Supercrunchers

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

<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

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

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

"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

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

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)

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" .