HAR1: The Uplift gene?

David Brin wrote a series of science fiction novels about "uplift" -- genetic manipulation applied to create human-like cognition in nonhuman animas. Carl Zimmer, a man who defines the true power of the blog, gives us an excellent interview of a gene Brin can reference in his next book ...

The Loom : And the award for the fastest-evolving piece of human DNA goes to...

... The scientists found 49 candidate segments. These segments have evolved a lot in our lineage. The most drastically altered of all is a segment the scientists dubbed HAR1 (for human accelerated region). It is 118 base pairs long. Chimpanzees and chickens, separated by over 300 million years, carry versions of HAR1 that are identical except for two base pairs. In humans, on the other hand, 18 base pairs have changed since we split from chimps.

What's HAR1 for? This is the sort of question that seems like it should be easy to answer unless you're the scientist doing the answering. The scientists found that human cells make RNA molecules out of the HAR1 segment. Specifically, they found that brain cells do. Specifically, brain cells in the cortex, the hippocampus, and certain other regions. We do love our brains, and so it is reasonable to consider that HAR1 took on some new role in the brains of human ancestors. The sequence of HAR1 suggests that an RNA molecule produced from it would be stable enough to carry out some important job, such as regulating the activity of protein-coding genes. HAR1 probably plays several roles. It is not just active in the adult brain, but in development-guiding cells in the fetus.

In a commentary that also appears in Nature, two Oxford scientists point out that HAR1 is also active in the ovary and testis of adult humans. And it is true that genes associated with sex are fast-evolving. So they don't want to rule out the possibility that selection has acted on HAR1 in connection with reproduction, rather than with thought. It's a fair point, but I was struck by the fact that the expression of HAR1 is far smaller in the sex cells than in the brain.

Still, it's a strange point that may be worth raising at your next party: we have genes that are only active in our brains and sex cells.

Elsewhere I read this gene is most active in humans from 7-19 weeks of gestation. How long before we tweak it in chimps? Just a bit ...

It would be interesting to study the effect of ultrasound on the operation of RNA that doesn't code for proteins.

CastingWords: Distributed transcription using Amazon's Amazing Turk services

CastingWords Podcast Transcription Store FAQ markets itself as a podcast transcription service. It uses the human bot network assembled by Amazon -- the 'Amazing Turk' service.

Cost is per minute of transcription. Best suited to public material rather than, say, medical or legal transcription. Jon Udell describes his experience.

Why don't they appreciate all we've done for them?

I want a counter on my desktop that will tell me how long Bush has left to rule:

Brad DeLong's Semi-Daily Journal: Why Oh Why Are We Ruled by This Clown?

Joshua Marshall: ...president expressed frustration that Iraqis had not come to appreciate the sacrifices the United States had made in Iraq, and was puzzled as to how a recent anti-American rally in support of Hezbollah in Baghdad could draw such a large crowd. "I do think he was frustrated about why 10,000 Shiites would go into the streets and demonstrate against the United States," said another person who attended...

Atheists, Jews, Professionals, Internationalists, Nihilists and Cosmopolitans: Michael Barone channels F. Chernov

Michael Barone writes for the WSJ editorial pages. Mao would understand Michael Barone. Here a brilliant blogger (billmon) provides a set of quotes contrasting the writings of Barone with those of another like-minded fellow …

Whiskey Bar: Rootless Cosmopolitans

... The Connecticut primary reveals that the center of gravity in the Democratic Party has moved . . . to the secular transnational professional class that was the dominant constituency in the 2004 presidential cycle.

Michael Barone
Wall Street Journal Op-Ed
August 10, 2006

Consisting in part of cringing before foreign things and servility before bourgeois culture, rootless cosmopolitanism produces special dangers, because cosmopolitanism is the ideological banner of militant international reaction, the ideal weapon in its hands for the struggle against socialism and democracy.

F. Chernov
Bolshevik Magazine Op-Ed
March 1949 …

It goes on. Brilliant, really. I’d worry they’re coming for me, but I’m working to be classified in the ‘harmless whacko’ group. They’ll do us last. Credit to TMW.

Google will date and file your images shortly ...

You have 5,000 prints you've just scanned in the Acme PrintScanner 2008. How do they get dated and named? What print has Aunt Madge in 1940 vs. Benjamin Francis in 2001? Google wants to help ...

Official Google Blog: A better way to organize photos?

Neven Vision comes to Google with deep technology and expertise around automatically extracting information from a photo. It could be as simple as detecting whether or not a photo contains a person, or, one day, as complex as recognizing people, places, and objects. This technology just may make it a lot easier for you to organize and find the photos you care about. We don't have any specific features to show off today, but we're looking forward to having more to share with you soon.

Upload all to Picasa. Provide the core data set: dated images of Madge and Benjamin at ages 1, 3, 5, 9, 11, 13, ... 25 ... 70 ... 90 etc. Let Picasa do the work, churning through thousands of images, attaching metadata to them ...

If your head isn't spinning, you're not paying attention ...

Don't let your children grow up to be atheletes

Schneier analyzes lessons from the Tour de France …

Crypto-Gram: August 15, 2006

... In the end, doping is all about economics. Athletes will continue to dope because the Prisoner's Dilemma forces them to do so. Sports authorities will either improve their detection capabilities or continue to pretend to do so -- depending on their fans and their revenues. And as technology continues to improve, professional athletes will become more like deliberately designed racing cars. ...

Don’t let your children grow up to be athletes. Just don’t.

Interesting observation on the effect of time-shifting — a test that’s negative with current technology will be positive in the future. The same thing applies to encryption. Interested persons are sure to collect all the strongly encrypted data they have, knowing that in 10 years they’ll be able to break the encryption …

Schneier speaks: The limited value of airplane security measures

Schneier is the wise man of security — both cyber and wetworld. In a few terse paragraphs he outlines the issues and dismisses much of the conventional reasoning about the liquid bomb attack. Emphases mine.

Crypto-Gram: August 15, 2006

... Last Week's Terrorism Arrests

Hours-long waits in the security line. Ridiculous prohibitions on what you can carry on board. Last week's foiling of a major terrorist plot and the subsequent airport security changes graphically illustrates the difference between effective security and security theater.

None of the airplane security measures implemented because of 9/11 -- no-fly lists, secondary screening, prohibitions against pocket knives and corkscrews -- had anything to do with last week's arrests. And they wouldn't have prevented the planned attacks, had the terrorists not been arrested. A national ID card wouldn't have made a difference, either.

Instead, the arrests are a victory for old-fashioned intelligence and investigation. Details are still secret, but police in at least two countries were watching the terrorists for a long time. They followed leads, figured out who was talking to whom, and slowly pieced together both the network and the plot.

The new airplane security measures focus on that plot, because authorities believe they have not captured everyone involved. It's reasonable to assume that a few lone plotters, knowing their compatriots are in jail and fearing their own arrest, would try to finish the job on their own. The authorities are not being public with the details -- much of the "explosive liquid" story doesn't hang together -- but the excessive security measures seem prudent.

But only temporarily. Banning box cutters since 9/11, or taking off our shoes since Richard Reid, has not made us any safer. And a long-term prohibition against liquid carry-on items won't make us safer, either. It's not just that there are ways around the rules, it's that focusing on tactics is a losing proposition.

It's easy to defend against what terrorists planned last time, but it's shortsighted. If we spend billions fielding liquid-analysis machines in airports and the terrorists use solid explosives, we've wasted our money. If they target shopping malls, we've wasted our money. Focusing on tactics simply forces the terrorists to make a minor modification in their plans. There are too many targets -- stadiums, schools, theaters, churches, the long line of densely packed people in front of airport security -- and too many ways to kill people.

Security measures that attempt to guess correctly don't work, because invariably we will guess wrong. It's not security, it's security theater: measures designed to make us feel safer but not actually safer.

Airport security is the last line of defense, and not a very good one at that. Sure, it'll catch the sloppy and the stupid -- and that's a good enough reason not to do away with it entirely -- but it won't catch a well-planned plot. We can't keep weapons out of prisons; we can't possibly keep them off airplanes ...

As you can guess by the excessive bolding, I am under Schneier’s sway. I particularly liked the comment about “we can’t keep weapons out of prisons”. Individual prisoners may not be terribly creative, but they share the human power of the evolving gestalt.

Schneier makes a point here that I think is new for him. He mentions “the sloppy and the stupid”. I think most of us have worried about the threat from smart terrorists (that’s a human flaw — we imagine everyone is like us …). I think what we missed is that, until now, the talent pool of al Qaeda has been shallow. A passion for the Dark Ages, an inclination to suicide, and the emnity of a lot of wealthy nations has probably discouraged smarter killers. We do need to maintain a core set of “security theater” for the sloppy and the stupid — of which there are many.

I fear that Bush’s incompetence is recruiting a smarter set of terrorists — at least Hezbollah class. My 9/01 scenarios were really wrong, so chances are I’m still wrong …

Fortune cookie quote

This showed up in my fortune cookie:

Young men think old men are fools; but old men know young men are fools.

Allegedly by Truman Capote? I suspect an earlier source, but I couldn't turn up a good reference. I think they're both right.

Infectious obesity: fattening the calf

The one thing missing from modern descriptions of obesity is "free will". That's good. Free will is an important deception, but it has little explanatory power.

Lately we've moved beyond the obvious environmental influences (600 calorie vending machine snacks that are claimed to hold "4 servings", neighborhoods without sidewalks, mega-schools) and genetics to focus on more obscure environmental influences, such as sleep practices and infection ...

Fat Factors - New York Times

... Gordon [jf: no relation] says he is still far from understanding the relationship between gut microflora and weight gain. “I wish you were writing this article a year from now, even two years from now,” he told me. “We’re just beginning to explore this wilderness, finding out who’s there, how does that population change, which are the key players.” He says it will be a while before anyone figures out what the gut microbes do, how they interact with one another and how, or even whether, they play a role in obesity. And it will be even longer before anyone learns how to change the microflora in a deliberate way.

A few months ago I posted that several human adenvorisuses are believed to induce adiposity in some animals. Now bacteria, our worldly overlords, are in the spotlight. It's a tangled web indeed.

What's in it for the bacteria? Well, they do eat us when we die. The fatter the host, the finer the feeding ...

This is bad. Using inmates in drug trials.

This is reallly bad.

Panel Suggests Using Inmates in Drug Trials - New York Times

An influential federal panel of medical advisers has recommended that the government loosen regulations that severely limit the testing of pharmaceuticals on prison inmates, a practice that was all but stopped three decades ago after revelations of abuse...

Who the hell was on this panel? The article is unclear. I think it was an IOM panel, and allegedly their primary criteria was benefit to the prisoners. This will go down as one of the IOM's biggest blunders; they're usually better than this. Professor Kligman, in particular, suffers from a utilitarian fallacy -- please take him off the Penn medical ethics committee.

Recruiting for phase I trials (safety trials) is a really hot potato. One of these trials just killed (they're walking deadmen) five UK citizens, all of whom shared rather poor judgment. Doing these trials ethically is going to greatly increase the cost of drug development -- we'll have to do more primate studies (getting the ethics right there as well - it can be done), more simulations, and we'll have to forget about "volunteers" and start paying professional testers boatloads of money to take significant risks for significant payoffs.

This will come to tears.

Another reader suspects the Economist might be in decline

Tim Bray suspects something's amiss with the Economist. He's a bit late to the party -- the decline began in the mid-90s and it's been in the mud for years. I'm giving it a rest for a year or so.

He'll figure it out eventually ....

MySpace: So what's there?

Myspace seemed to have enough zeitgeist to it that I decided to sign up. Lest anyone get the wrong idea, my profile has my DOB in 1910, my build as "extra pounds", and my wife and daughter in my 'to meet' list.

I can now reveal the shocking, astounding and unexpected news that MySpace is all about recreational encounters. The more information you provide, the more "friends" appear in your network. I thought there'd be some interesting web 2.0 technology, but it's very much web 1.0.

Other than the lack of Ajaxity, the other surprise was that you can't readily display your real name. First and last names are private.

My kids are too young for this stuff, but I can see I need to catch up on my Gibson security podcasts. In a few years I'll be wanting some fairly sophisticated traffic analysis software ... (Cell phones, what cell phones?)

john

Cataclysmic change: Faughnan.com dog picture changes

A change of this magnitude should not go unremarked.

In addition to the Gordon's Notes and Gordon's Tech blogs, I have ten + year old personal web site: http://faughnan.com. It changes little these days, I maintain a few of the more popular pages every few monhts. One item that's been slow to update is the main page picture, which for 10 years was my dog Molly. Molly went wherever we all go about two years ago, but only now has her heir appeared. Kateva is now the iconic representative of my ancient site. Happily she's relatively young.

Why do (some) humans hate democracy?

Conversely, why do some love tyrants rather than futile blogging about authoritarian trends?

Ocrinus reviews the literature.. Alas, there's not that much science to the review, but it is illustrative. Evolutionary anthropology is probably a better explanatory source.

Ten cosmologies and Theory 10

I agree with FMH. Theory 10 is oddly persuasive; there's something to be said for explaining the bizarre features of our universe as computational artifacts.

Theory 10 is, of course, fundamentally indistinguishable from the 'omnipotent deity' explanation, that should warm the hearts of the Creationists.

Incidentally, one must give due credit to the last 15 years of science fiction writing, which has explored many aspects of 'life in a simulation'. One of my favorites featured a simulation-within-a-simulation-within-etc. The very alien inhhabitants of the ultimate simulation went to immense lengths to explain their fundamentally illogical universe, much to the amusement of those who'd created the simulation. Incredibly they finally produced an internally consistent explanation of their odd cosmology; their solution propagated outside the simulation and destroyed the host universe ...