Thursday, April 29, 2004

A sad note: I noticed that the robin's nest in the hanging flower plant in front of my house that a couple days ago had two eggs in it is now empty. I saw a squirrel in the area recently and suspect the worst.

I'm also sad to not that I still haven't been offered a Gmail account.

Wednesday, April 28, 2004

Just figured out how to change the New Post interface. For future reference: hit the Edit Profile link on the Blogger home page.
Still no offer for gmail. How long must I wait?

Strange weather today -- not the type of weather that I usually identify as a type with Southern California. But I wonder if it is not as uncommon as I think it is. Gray and breezy, but not breezy from the NW, but breezy from the south/southeast. Gives the landscape a kind of desolate, cul-de-sac of the world feel to it. Sort of as if all the rubble, leaves, and detritus that had been blowing into their designated nooks and crevices by the prevailing winds had been unsettled and blown back out into the open. Wildflowers in garden, as taken off-guard by it as me, as tousled as my hair.

Passed three Asian-American guys this afternoon kneeling in the middle of library walk praying. I overheard the prayer leader saying, "Prepare to sharpen our swords for the next battle, Lord." Not sure if they were on their way to a midterm, or a holy war.

Sunday, April 25, 2004

Just came across this.

Where are you now?
Your life isn't just on your personal computer. Your personal info is not all over the Internet, too.

By Hiawatha Bray, Globe Staff | April 26, 2004

Even the smartest people have a knack for overlooking the obvious. That's how Sergey Brin, cofounder of the Internet search service Google, has lately earned the wrath of the same computer users who once idolized him.

Brin takes the credit, or the blame, for Google's plan to offer Gmail, a new, free Web-based e-mail service that can hold up to a gigabyte of personal e-mail messages--a lifetime's worth for most people.

''It was originally designed for me, basically," said Brin, who wanted a more convenient way to deal with the roughly five gigabytes of e-mail in his own inbox.

But the idea has infuriated Internet privacy groups like London-based Privacy International, which has filed complaints with the European Union and 16 European nations in an effort to force major changes in the service. Gmail's critics say that in its present form, Gmail will lead to a vast concentration of personal information onto a single Internet service.

Brin said he was caught by surprise by the flood of criticism. ''In retrospect, obviously I shouldn't have been," he said.

Indeed, the outcry over Gmail has alerted many Internet users to a truth that should have been obvious all along: Little by little, people are moving more and more of their lives onto the network. Data that people once kept on paper or on their desktop hard drives are now housed thousands of miles away on remote servers.

It's not just e-mail. We swap instant messages or post comments on Web-based bulletin boards and blogs. Millions of us join global entertainment networks to play games against challengers on the other side of the world. Millions of us use Web-based software to invest our savings, pay our bills, and file our tax returns.

In each case, some far-off computer collects a significant chunk of information about us, information that could be abused by criminals, profit-hungry businesses, or overzealous cops.

''If you kept that information in your desk drawer, the cops would have to come and knock on your door," said Ari Schwartz, associate director of the Center for Democracy and Technology, a privacy think tank in Washington, D.C. ''Now that you're keeping it online with a third party, the cops can go to them."

Schwartz and other privacy advocates have been talking about this issue for years, but more people are listening, thanks to the Gmail announcement.

The sheer size of the Gmail service is one reason. Other free Web-based e-mail systems, like those run by Microsoft Corp. or Yahoo Inc., offer just a few megabytes of storage space, only enough to store a few weeks or months of messages. Many people use their Web mail accounts as handy supplements to their main e-mail service.

But with a whole gigabyte on offer, many people could choose to route all of their messages through the Gmail service. That means giving Google control over a vast concentration of personal data.

If that wasn't scary enough, Google then announced its plan to analyze every word of these e-mails. Actually, that's less shocking than it sounds. All free e-mail systems scan for viruses and unwanted spam messages. But Gmail goes further. First, it uses Google's renowned search technology to create an index of all of your mail messages. It's a valuable service that allows the user to search his entire e-mail collection in a split second.

But Google uses the same index to select advertisements and display them on your computer screen. If you swap e-mails with a friend about a story on last night's ABC News broadcast, you might get an ad for the ABC News website.

''The ads are going to be related to whatever is in the message," said Brin.

The whole system is automated; humans don't read the user's mail, and no information is extracted that could be used to create a personal profile of the Gmail user. But the very idea of analyzing private messages caused an explosion of outrage. For instance, Privacy International's complaint asserts that the Gmail system is a clear violation of European Union privacy law.

Critics fret over other issues. For instance, suppose someone chooses not to use Gmail, for fear of having his e-mails stored on Google's computers. That won't help him if he has to send a message to somebody else who does use Gmail.

Big Internet companies like Google must regularly back up their stored data to guard against equipment breakdowns. How long will the backup copies be kept? Even if an Gmail user deletes all of his messages, the backup copies could be kept for weeks or months.

''We're going to make all reasonable efforts to delete it as quickly as possible," Brin said.

What if the government wants to investigate your e-mail messages? Under a 1986 law, police would need a search warrant to get any e-mails composed in the past 180 days. That means convincing a judge that a crime has probably been committed. To get a subpoena, you only need to assert that a crime may have been committed.

And a subpoena is all the cops need to read messages more than 180 days old. So if you keep years' worth of messages on Gmail, you've made life simpler for investigators.

''You've completely lost your Fourth Amendment protection by storing it on Google," said Ari Schwartz of the Center for Democracy and Technology.

Apart from privacy, there's the matter of reliability. Most e-mail users download their messages onto a local machine. But if they switch to Gmail and keep all of their messages with Google, they'll be totally dependent on the reliability of the Google network. The average user of Yahoo Mail or Microsoft Hotmail can live without it for an hour or two. If Gmail catches on, it'll become as vital as the telephone network, so reliability will have to be absolute.

But it's important to look past the Gmail controversy. Apart from Google's plan to analyze its user's messages, every criticism of Gmail applies to other Web-based services as well. Larry Grothaus, lead product manager for Microsoft's MSN online service, notes that Hotmail serves up ads to its users too, based on their age, sex, language and nationality -- all information that Microsoft requests from Hotmail users.

''We try to do advertising based on demographic information," Grothaus said. ''You're a younger person, maybe you'll get information on a hip new car."

For $60 a year, Hotmail will sell you up to 100 megabytes of mail storage, room enough for many months of messages. Even deleted files will be preserved on backup tapes for up to 37 days. And of course, the cops can always get a warrant or, after 180 days, a subpoena.

Internet security consultant Richard Smith of Braintree points to other Web-based services crammed with private data. Smith makes his travel arrangements through the Expedia website partly because it remembers all of his previous travel data.

''It saves like the last year's worth of trips," Smith said.

Then there's book shopping at Amazon.com, which remembers customers' favorite authors and literary genres.

Even if you create an anonymous e-mail address and send messages from a public library or cyber cafe, the messages will carry a numerical address that can be linked back to the computer that originated it.

''If you're going to commit a crime on the Internet through e-mail, you're going to go to jail," said Smith. ''It's very, very hard to hide your traces."

Schwartz said that Gmail isn't really the issue.

''Gmail just highlights the problem," he said. ''As storage gets cheaper and cheaper, services were bound to offer to store more and more data for you."

And when people get broadband connections, data stored half a world away is just as accessible as the data on their desktops. Besides, if it's on the Internet, you can get your information at any computer terminal on earth.

To Google's Sergey Brin, the benefits of such a centralized data storehouse seem obvious. Now, thanks to the Gmail furor, so do the drawbacks.

Boston Globe
What would I doing if I lived according to my preferences? Gardening, surfing, teaching a composition class now and then, playing croquet afternoons and poker evenings, tidying things up. I don't really want to live in a world in which I can't live like this. Unfortunately, this is the world in which I live.
Laying in bed this morning, prior to getting up, I worked out a few things I need to write today. But now that I sit down to actually write them out, they are lost. Which is worst than having not sketched them out in the first place. Instead of just writing from scratch, now I have to try to retrieve what was already satisfactorily formed.

Still no offer for Gmail, by the way.

Saturday, April 24, 2004

Still trying to get a GMAIL account. Also, can't figure out how to get out of safe mode with the post interface.

Weather continues beautiful.

Friday, April 23, 2004

Just started this blog really to set up a GMAIL account. I noticed an option on the blogspot home page my other blogger blog. But there is no option here. What's that about? The post interface is also different.

Wednesday, April 07, 2004

Book Notes : The Century of the Gene, Evelyn Fox Keller

FOX KELLER, CENTURY OF THE GENE

**1**
5 A convert -> transformed expectations
6 "Sequence gazing" -- new era of "genomic analysis"

=> Fall of Celera: with all Venter's promise, why is he out? Why is Sequenom selling equipment? Market & state out of balance? Good/bad?

6 Walter Gilbert - "vision of the Grail"
7 call for FUNCTIONAL GENOMICS; the sequence not end, but tool
8 gap "genetic info" : "biological meaning"
9 no more extreme reductionism
10 defying classification between animate and inanimate || "gene talk"

**2**
13 Darwin - mechs of transformation, not conservation
14 problem of "trait stability" presupposed the gene *
15 developmental stability - metazoan orgs *
15-6 WEISMANN'S QUESTION
17 GERM PLASM (Weissman's term)
18 Two Articles of Faith
1. Genes the fundamental unit of bio
2. fixity of material element
20 "spontaneous transmutation" of atoms, chems
23 famous "blender experiment" -- Hershey and Chase
25 1968 - a restriction enzyme
27 50s & 60s ORNL - radiation damages expers
28 "communicative" - a network, not an individual (gene) DNA REPAIR MECHS
29 radiation biology - suspect (under AEC)
31 stability of genes - "biochem dynamics rather than mob. status"
32 balance between mutability and stability a product of evolution => repair mechs that sacrifice fidelity -> genetic

variations
33 error-prone mech of repair -> EVELYN WITKIN ('67)
34 stab/mut at mercy of enymatic processes; balance varies in response to cellular reg (not trad. DNA neo-Darwin

view)
35 MUTATOR GENES - defective genes supp to reg stab.
36 RECOMBINATION -> all somatic cells, diff in sex (?)
=> diff for bact. & human sex cells?
37 mechs for evolvability
=> Radman: "positively selected" mutagenesis (?)
a challenge to neo-Darwinism? (38)
39 GERHART & KIRSCHNER - evolvability
41 mechs of stab not a prod of n.s. (but isn't all?)
42 DYSON's answer to LIFE - dual origins of Ilahita Arapesh

**3**
48 Problem: self-reproduction to a particle
49 Two tasks for Muller: find gene's structure & function (animism, monster by tail [48])
53 BEADLE-TATUM : one gene-one enzyme
54 Central Dogma (simplicity itself)
55 JACOB & MONOD - structureal, regulator genes
57 OPERON MODEL (split genes)
59 Late 70s : Exons and Introns (junk DNA)

63 ONE GENE - MANY PROTEINS

63 Who chooses the protein? "reg dynamics of the cell"
63 true Gene - mRNA transcript (itself not fixed?)
65 FIGURE?
64 ALLOSTERY: changes in structure of protein
67 concept of gene in blatant disarry
GELBART - gene concept with bit of baggage
69 the word GENE
70 VALUE OF HGP - exposed naivite of hopes
71 gene no longer unit of intergenerational memory (?)
71 DNA - indispensable raw material, but no more than that
72 need new words
73 instructions in every cell (EV NEC)
76 Mayr: bean-bag genetics
77 WADDINGTON : development perspective
78 epigenetic theory
85 theoretical analysis of BONNER "genetic program"
88 cloning - enucleated ooplast - NOT cytoplasm of ord. cell -> epigenetic factors req. epigenetic inheritance
90 obstacle to reprogramming - relationship betwe. nucleus & cytoplasm
95 "something that is historically defined"
97 "master control gene" quibble
100 interactions as important as structure
program irreducible?

**4**
104 development: Gould's videotape countless plot variations - same ending
108 Kant on the question of self-org
111 GENE-KNOCKOUTS, redundancy - sometimes improve function
112 extensive polymorphism
113 NULL MUTANTS
113 "Redundancy strikes fear into the hearts of geneticists" Sydney Brenner
115 unit of selection - the whole organism
118 CANALIZATION - many variations, one end
124 behavior-based robotics - situatededness and embodiment
128 HGP - bioinformatics
128 "single genes do not affect phenotype" James Bailey
130 the major shift
131 Jacob - "bricolage"

**CONCLUSION**
136 popular image of gene dislodged
138 EFK on words
140 the marker

Don't scientists require great precision in the language they use? Well, yes and no--that is, in some ways they do, but in other wasys, just as in ordinary communication, too much precision would in fact be paralyzing. Where precision is necessary (and absolutely so) is in particular laboratory practices. Moreover, it is from the specificity of the experimental context in which they are invoked that technical terms acquire the precision they need. Terms like gene may be subject to a variety of different meanings; but locally, misunderstanding is avoided by the availability of distinct markers directly and unambiguously tied to specific experimental practices. Within that practice, the marker has a clear and unambiguous reference. Change the practice, and different markers will need to be employed. And inevitably, these different markers will pick out somewhat different physical entities.* Nevertheless, as long as one stays within the context of a given and clearly understood set of experimental conventions, the term gene can still safely serve as an operational shorthand indicating (or pointing to) the marker of immediate experimental significance. (139-140)

*For example, in one context, the term may refer only to regions of DNA characterized as an "ORF of length x," while in another, it might include noncoding regions of DNA that are used as templates for RNA molecules. In yet a third context, it might refer to the mature (postsplicing) RNA molecule used in the actual translation process.


[And in a fourth, an outlandish promise of return on investment.]

143 biotech marketing

COMMENTS
DNA as necessary vs. sufficient [EFK 99]
DNA (HGP) ----> phenotype (medicine) -- filling in the middle parts the hard part
single gene (ie discrete) mutations - only viable targets?

3 big changes
HGP - race
Maezenich - special ed
EFK - gene

New Heresy
one gene - many proteins
one protein - many functions

single mutation -- sickle cell

Two things marketed
1. HG Sequence
single mutation -> disease -> drug
2. Personalized medicine
80% of people don't respond to drug therapies
Drs not needing to see patient

Affymetrix patent estate for sale

Prions - proteins that cause disease

ORF - Open Reading Frames
encode for a protein (start-end signals) but don't know which protein