Screening for berry aneurysms -- genomics

My PubMed RSS, embedded in Bloglines, continues to work beautifully.

Today's harvest from a month of fishing included 19 articles on Berry aneurysms. Much of the new activity is in identifying genes that predispose to forming berry aneurysms. As well as furthering the understanding of the disorder, it suggests that we may one day be able to identify persons at risk for subarachnoid hemorrhage and thus screen them by MRI. Whether this will add anything to our current screening criteria (two first degree relatives with SAH or BA) remains to be seen.

Biology of aging: telomeres predict your age

Fascinating: FuturePundit: Telomeres Wear Down Quicker In Men Than Women. It will be interesting to apply these techniques to different breeds of dog (age at different rates) and to identify slow aging humans. It will also be interesting to study middle-aged animals over a period of 1-2 years. I think we'll find that telomere erosion occurs in "bursts" rather than as a continuous process. The old saw about "he aged 10 years in a night" will turn out to be somewhat true. Then we'll study the mechanism of "aging bursts" and identify interventions.

Open source Java and a classic strategic blunder

Sun, a company with 3.98 extremities in the grave, finally makes an interesting move. They claim they'll open up Java, giving away one of their gems (Java is still important on servers).

Chief Says Sun Plans to Offer Open-Source Version of Java - New York Times

One of his first appearances since taking the helm of the struggling company three weeks ago, the executive, Jonathan Schwartz, told a gathering of software developers here that Sun viewed open-source software as a major part of its turnaround strategy...

It's unlikely to save Sun, but at least a part of their legacy might live on. Sun is following the path of the 1970s computer hardware companies that once ringed the twin cities -- shrinking and becoming a "services" company.

The story reminds me of one of the great strategic blunders of the 1990s. Netscape and Sun fought bitterly over who'd deliver "thicker client" capabilities to the browser. Netscape had an Ajax-like vision of JavaScript (no relation to Java) and enhanced markup with session management (not sure whether they had the asynchronous model though). Sun wanted everything, including the browser to run in a Java Runtime Engine. Actually, they wanted the browser to go away.

Meanwhile Microsoft, in one of Gates' most brilliant and ruthless moves, blew away all of its old software strategy and embraced, extended, and corrupted both the browser and Java. Gates is an evil force for computer geeks like me, but there's no denying his strategic brilliance. Nobody could shoot their own horse like Gates in his prime.

Sun destroyed Java on the Windows desktop with an unending series of tiny updates -- each of which destroyed a generation of installed software. Sometimes there were unmarked incompatible versions!

Sun delivered a second fatal shot when instead of building a cache solution for applets they persisted in a ridiculous vision of ubiquitous high speed computing. Applets should always be instantly available. Oh, and forget version control.

In the meantime, Microsoft sprinted while Netscape and Sun fought like psychotic wolverines.

Sun and Netscape destroyed one another. A classic lesson in strategic incompetence. Bottom line -- never forget that the 'enemy of my enemy is my friend'. It's better to take half of a trillion dollar market than nothing at all ...

100 years: likelihood of human survival

Pharyngula writes:

Pharyngula: The Seed Crystal Ball:

Our Seed Overlords have submitted yet another question to their blogulous oracle, i.e., us: Will the "human" race be around in 100 years?

I don't think it's a particularly good question, I'm afraid. The answer is simply "yes". If the question were about prairie chickens, cheetahs, or chimpanzees, it would be a more challenging question, but with a population of 6.5 billion of us, I don't think there's much doubt. We'll be here. The only question is what state we and the world will be in. I'll speculate a bit on possible outcomes.

To which someone responds (comments):

... 100 years is now a very LONG time. In terms of the accelerating rates of change in our de facto environment (which is technological and increasingly virtual) it's probably equivalent to 30,000 years of pre-10K BCE living.

I can't imagine any ecosystem catastrophe that would wipe out humans. So the options are:

1. Wild tech: Gray-Goo nano disaster, some weird vaccum energy thingie, etc. I'd put these all down as unlikely.

2. Engineered plague: A pimply 15 yo in southern China is upset by social rejection and engineers a virus using his home biotech kit that wipes out humanity. I'd put this at 20% when you consider all the folks that might try this.

3. AI: If we ever did produce a sentient AI, and if it turned out that 'intelligence' scaled to an IQ of, say, 100,000, then all bets are off on everything. I'd put that down as a 40% probability over a course of 100 years.

Since we have to survive both 2 and 3 to make the 100 year mark I'd say:

.8 * .6 = .48 or less than a 50% survival probability.

PS. The Fermi Paradox (aka the great silence) is not comforting here.

The surveillance society: Us and Them

The surveillanace society. It's about "us" and "them". Arkin says this well.

Early Warning by William M. Arkin - washingtonpost.com

... The government's position is that if you are "innocent," you have nothing to hide. It is a new version of 'you are either with us or against us.' Massive monitoring is of course meant to find terrorists; I completely believe that this is not some 1960's enemies list politically motivated effort. But these post 9/11 programs signal a new and different problem.

People of Middle Eastern and South Asian descent and Muslims are potential terrorists, machine selected as "of interest."

Throw in there callers and travelers to Pakistan and Saudi Arabia, recipients of wire transfers, purchasers of fertilizer, flight school attendees. These are the new guilty until proven innocent.

Innocent means of course mostly white, mostly Christian Americans who accept that the government knows best and that the national security state is only after the bad guys and would never apply its new found capacities in any illegitimate way.

The government and its new seamless surveillance culture are build ing a digital dividing line, even in our own society. The assumption is one of an enemy in our midst.

The government's failure to provide for domestic tranquility and basic security in our homes is rewarded by more power for the government; "innocent" Americans are increasingly primed and frightened to accept that greater government surveillance is required by the realities of infiltration, ceding even more power. It is as much a way of thinking as it is a way of life...

I wired cash to my sister in Canada a few months ago. I was electonically interrogated to match me and my transaction to an identify database entry. For all I know that alone added me to a watch list - at least added a few points to my Threat Score. This is how it goes now. Everything you do now, you can justifiably ask yourself -- will this put me on The List?

Just being Muslim may take you halfway to The List. Supporting Greenpeace might add some points too. Who you know, who your family knows ...

Being a white evangelical right wing Bush supporter will tend to keep you off The List.

Anyone remember the internment of the Japanese-Americans? That was about 63 years ago; I have a rather good book at home that was self-published by a child caught up in that despicable American mistake. I wonder if one of the forty remaining journalists in America might be troubled to interview a survivors of that time...

There's an election coming. How you vote will matter, again (sigh).

Gore 2008

Gore the bore. Ok, now that we've got that out of the way...

Talking Points Memo: by Joshua Micah Marshall: May 14, 2006 - May 20, 2006 Archives

Andrew Sullivan just published an email from a reader who says it'll be Al Gore in 2008 for the Democrats, not Hillary. I could see it. I could totally see it.

I don't think Hillary is anywhere near as strong as she looks or as people seem to think she is. And Gore would be formidable.

I believe him when I read that he doesn't feel compelled to run. I believe Tipper Gore is deadset against it.

However, I also recall that his daughter wants him to run again. Daughters can be very persuasive. He'd have my vote of course. If he runs, I'd expect a late entry.

Troops at the border? Humor is indicated

And now, for a much needed humor break.Shrill hysterical laughter is the only response to Bush's lastest brainstorm -- deploying the national guard along the Mexican border. Damn, what about all those snowbacks [1]?

[1] I saw this term first used in an early 20th century newspaper article. I wish I'd noted the reference. It may be an older term than "wetback"; illegal french canadian immigration was a big deal in the northeast back then. I wonder how my wife's Grandfather ended up there ...

Secondary outsourcing

I think it was Gary Trudeau (Doonesbury) who first popularized a programmer covertly outsourcing his work to India. A similar thing is happening in schools (DeLong).

These students, when they go to work, will use the same techniques. DeLong is annoyed with the reporter's gullibility, but it's neat to see a widely predicted future happening. There's a generational gap here -- I lack the outsourcing skills these college kids will have. I have, however, long had ideas about other uses for this sort of resource network ...

PS. I think Vernor Vinge's Fast Times at Fairmount High is our best current guide to the world ahead.

Are cars overbuilt?

I was chatting with a colleague about how long modern cars last, when it occurred to me that today's cars mostly die of trauma. It doesn't matter that a car will run for 15 years; given our aging drivers it'll be smacked within 10 years.

So are cars overbuilt? Should we be buying cars based on the costs of replacing body panels? A side blow to a van with motorized doors may be prohibitively expensive to repair, but a van with manual doors might survive the same accident.

Rove to resign?

Rove to resign post indictment?. I'd rate this one as high as 50%, based on a reading of the original source. There's a real journalist at the start of this blog thread.

The Descent of Dog

I'm fascinated by the evolution of the dog, a creature with a remarkably flexible genome and a survival strategy the cuckoo must envy. The BBC gives us an update:

BBC NEWS | Science/Nature | Exploring the wolves in dogs' clothing

.... According to DNA studies, domestic dogs owe their origins to a wolf cub that probably fell into the hands of humans some 40,000 years ago somewhere in Southeast Asia.

... "Originally, according to DNA samples, it would appear that the domestic dog is most closely related to the grey wolf.

"Point-two-percent is the difference between domestic dog DNA and grey wolf DNA, whereas the difference between coyote DNA and dog DNA is 4%.

... Experts are divided on how wolves first entered the lives of humans. Some believe that a band of hunter gatherers took wolf cubs back to their caves, perhaps to act as early guard dogs.

Others believe that wolves adopted people - creeping ever closer to human settlements to scavenge on discarded food.

By about 15,000 years ago, at the time of the last Ice Age, they were probably living alongside humans, perhaps retrieving wild animals felled with axes or bows and arrows.

The earliest archaeological evidence of dogs as true pets dates back to 12,000 to 14,000 years ago.

That is the estimated age of the remains of an old woman holding a puppy in her hand excavated in what is now Israel.

... Inside a glass case is the skeleton of an Early Bronze Age dog dug up in Tell el-Duweir near Jerusalem - the site of the ancient city of Lachish.

"Finds like these are really interesting for scientists because they give us clues as to how and when dogs became domesticated," says Dowswell.

"Although this is a relatively late example - examples have been found dating back as far as 15,000 years ago, the end of the last Ice Age - it seems that the dog skeletons they are finding are similar to wolf skeletons but much smaller.

"As a reduction in size is one of the first signs of domestication, and the fact that it's been found in a human settlement, this shows us pretty clearly that that's what's going on."

There's a very long interval between when "dogs" divide from wolves and when they become pets. Shortly after they're known to be pets humans begin building civilizations.

Total Information Awareness Lives

William Arkin (WaPo) lists Early 500 software tools used by the NSA in their vast data mining and intercept programs. There are no surprises here, through my work I come in contact with some of these companies. A lot of smart people work in small software companies that do contract work for the NSA.

It is an opportunity, however, to point out that Poindexter's 'Total Information Awareness' was not, of course, really terminated. The names were changed and the plans were executed. Only a naif would have bought the press stories a few years back that the program had been shuttered.

Christian nationalism and the scent of fascism

Salon, one of the last refuges of American journalism, has an excellent article by Michelle Goldberg on a group that's at the core of Bush's 30% base (emphases and links are mine):

Salon.com Books | "Kingdom Coming: The Rise of Christian Nationalism"

... On November 13, 2003, [Roy] Moore was removed from his position as chief justice of the Alabama Supreme Court after he defied a judge's order to remove the 2.6-ton Ten Commandments monument he'd installed in the Montgomery judicial building...

... Moore installed his massive Ten Commandments monument on August 1, 2001, and from the beginning, he and his allies used it to stir up the Christian nationalist faithful...

... As the controversy over the statue ignited, Moore's fame grew. At rallies across the country, he summoned the faithful to an ideal that sounded very much like theocracy. "For forty years we have wandered like the children of Israel," he told a crowd of three thousand supporters in Tennessee. "In homes and schools across our land, it's time for Christians to take a stand. This is not a nation established on the principles of Buddha or Hinduism. Our faith is not Islam. What we follow is not the Koran but the Bible.This is a Christian nation."

... After the Commandments were removed, a group of retired military men from Texas who called themselves American Veterans in Domestic Defense spent months taking the monument -- now affectionately called "Roy’s Rock" -- on tour all over the country, holding more than 150 viewings and rallies in churches, at state capitols, even in Wal-Mart parking lots...

... The group says it exists to "neutralize the destructiveness" of America's "domestic enemies," which include "biased liberal, socialist news media," "the ACLU," and "the conspiracy of an immoral film industry." To do this, it aims to recruit former military men...

According to Jim Cabaniss, the seventy-two-year-old Korean War veteran who founded AVIDD, the group now has thirty-three chapters across the country...

... "People who call themselves Jews represent maybe 2 or 3 percent of our people," Cabaniss told me after a January 2005 rally in Austin. "Christians represent a huge percent, and we don't believe that a small percentage should destroy the values of the larger percentage."

I asked Cabaniss, a thin, white-haired man who wore a suit with a red, white, and blue tie and a U.S. Army baseball cap, whether he was saying that American Jews have too much power. "It appears that way," he replied. "They're a driving force behind trying to take everything to do with Christianity out of our system. That's the part that makes us very upset."

Ed Hamilton, who'd come to the rally from San Antonio, interjected, "There are very wealthy Jews in high places, and they have significant control over a lot of financial matters and some political matters. They have disproportionate amount of influence in our financial structure."

Jews. Secular humanists. Intellectuals. Same old, same old. As Bush's support dwindles he needs this base more and more. There's more similarity than meets the eye. True, Bush has is no racist or anti-semite -- but he speaks of atheists and unbelievers in much the same fashion as Cabaniss (as did his father, for that matter). He shares an ideological heritage with this group; a heritage that Goldberg details for us. Note the remarkable connection to the immensely popular Left Behind theo-fantasy books:

Roy Moore and Rick Scarborough are Baptists, D. James Kennedy is a fundamentalist Presbyterian, and John Eidsmoe is a Lutheran. All of them, however, have been shaped by dominion theology, which asserts that, in preparation for the second coming of Christ, godly men have the responsibility to take over every aspect of society.

Dominion theology comes out of Christian Reconstructionism, a fundamentalist creed that was propagated by the late Rousas John (R. J.) Rushdoony and his son-in-law, Gary North....

Reconstructionism is a postmillennial theology, meaning its followers believe Jesus won't return until after Christians establish a thousand year reign on earth ... Most American evangelicals, on the other hand, are premillennialists. They believe (with some variations) that at the time of Christ's return, Christians will be gathered up to heaven, missing the tribulations endured by unbelievers.

... Since the 1970s, though, in tandem with the rise of the religious right, premillennialism has been politicized. A crucial figure in this process was the seminal evangelical writer Francis Schaeffer, an American who founded L'Abri, a Christian community in the Swiss Alps where religious intellectuals gathered to talk and study. As early as the 1960s, Schaeffer was reading Rushdoony and holding seminars on his work. Schaeffer went on to write a series of highly influential books elucidating the idea of the Christian worldview. A Christian Manifesto, published in 1981, described modern history as a contest between the Christian worldview and the materialist ...

... Schaeffer was one of the first evangelical leaders to get deeply involved in the fight against abortion, and he advocated civil disobedience and the possible use of force to stop it. "It is time we consciously realize that when any office commands what is contrary to God's Law it abrogates its authority," he wrote.

Tim LaHaye [Left Behind] ... was heavily influenced by Schaeffer, to whom he dedicated his book "The Battle for the Mind." That book married Schaeffer's theories to a conspiratorial view of history and politics, arguing, "Most people today do not realize what humanism really is and how it is destroying our culture, families, country -- and, one day, the entire world. Most of the evils in the world today can be traced to humanism, which has taken over our government, the UN, education, TV, and most of the other influential things of life.

"We must remove all humanists from public office and replace them with pro-moral political leaders," LaHaye wrote.

... In 1984, Jay Grimstead, a disciple of Francis Schaeffer, brought important pre- and post-millennialists together to form the Coalition on Revival (COR) in order to lay a blueprint for taking over American life. Tim LaHaye was an original member of COR's steering committee, along with Rushdoony, North, creationist Duane Gish, D. James Kennedy, and the Reverend Donald Wildmon of the influential American Family Association.

Between 1984 and 1986, COR developed seventeen "worldview" documents, which elucidate the "Christian" position on most aspects of life. Just as political Islam is often called Islamism to differentiate the fascist political doctrine from the faith, the ideology laid out in these papers could be called Christianism. The documents outline a complete political program, with a "biblically correct" position on issues like taxes (God favors a flat rate), public schools (generally frowned upon), and the media and the arts ("We deny that any pornography and other blasphemy are permissible as art or 'free speech'").

In a 1988 letter to supporters, Grimstead announced the completion of a high school curriculum "using the COR Worldview Documents as textbooks." Since then, there's been a proliferation of schools, books, and seminars devoted to inculcating the correct Christian worldview in students and activists. Charles Colson accepts one hundred people annually into his yearlong "worldview training" courses...

Those who don't have a year to spare can attend one of more than a dozen Worldview Weekend conferences held every year in churches nationwide. Popular speakers include the revisionist Christian nationalist historian David Barton, David Limbaugh (Rush's born-again brother), and evangelical former sitcom star Kirk Cameron. In 2003, Tom DeLay was a featured speaker at a Worldview Weekend at Rick Scarborough's former church in Pearland, Texas. He told the crowd, "Only Christianity offers a comprehensive worldview that covers all areas of life and thought, every aspect of creation. Only Christianity offers a way to live in response to the realities that we find in this world. Only Christianity."

I'm proud that when Salon was dying, I chipped in money to help keep them going.

Using father's dna to catch the son

This is not surprising. Criminality runs in families. Use a (former) crook to catch a crook..

Here's how it works. We take DNA samples from criminals when convicted. Later we find DNA samples at crime scenes. The proposal is that if past criminal's DNA resembles that found on a crime scene, we should test the criminal's relatives. One of them is likely the culprit. The implication is that the testing might not be voluntary.

FuturePundit likes this idea.

Of course, even if this were a good idea (I dislike it), it wouldn't end there. Inevitably, everyone's DNA would be on file.

Eventually we'd analyze the DNA to identify hi risk persons. They would need to be monitored. At first. Then they'd need to be sterilized....

They say the first kill is the hardest. The next steps are always easier. Before you know it ...

Public concern over the NSA: greater than expected

If you'd asked me what percentage of Americans cared about having the NSA listen in on their phone calls, I'd have guessed less that 20%. So 37% is good news:

Slashdot | Americans Not Bothered by NSA Spying

Snap E Tom writes "According to a Washington Post poll, a majority (63%) of Americans 'said they found the NSA program to be an acceptable way to investigate terrorism.' A slightly higher majority would not be bothered if the NSA collected personal calls that they made. Even though the program has received bi-partisan criticism from Congress, it appears that the public values security over privacy.

Whatever their rhetoric, Americans, like other humans, greatly value security over privacy. Alas, they don't realize that privacy is not the only thing they'll lose. They will also lose freedom, justice, and, ironically, security.

As long as the punishments for failing to stop an attack are high, and the punishments for false action are relatively low, humans will choose false action -- false accusation, false blacklists, false punishment.

It would be inhuman for a government, unrestrained by law, not to abuse its powers. Our government is manifestly human, and it will abuse this power as surely as night follows day. The most dangerous and terrible illusion we can have is to imagine we are "better" than those who've come before us. We are as they were, we need the safeguards that evolved to protect citizens from government as well as from each other.

Is there reason for optimism? Yes. The number that are concerned about the NSA's actions is higher than I'd have expected at this point in our history.