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Above is an unpublished letter in response to: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 .