Sequencing dinosaur DNA -- the jungle fowl

BBC NEWS | Science/Nature | Chicken gives up genetic secrets

Scientists have published a detailed analysis of the chicken genome, the biochemical "code" in the bird's cells that makes the animal what it is.

... The primary subject for the study was the red jungle fowl (Gallus gallus), the wild species from which domestic poultry was bred several thousand years ago.

... There are about 1.1 billion base-pairs in the chicken genome wound into 40 distinct bundles, or chromosomes. Written in the DNA are roughly 20-23,000 genes ... In the human genome, there are 3 billion base-pairs and 20-25,000 genes ...

... The analysis reveals that just 2.5% of the human code can be matched to chicken DNA.

It is an important finding. This small portion contains genes that have been largely preserved over the 310 million years since humans and birds shared a common ancestor.

... On a pure research level, though, there are some real gems in the chicken genome.

These include the realisation that the birds have a keen sense of smell. Scientists can also see genes related specifically to feathers, claws and scales - code sequences that are absent in humans.

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Yes, scales. As in dinosaur scales. Keen sense of smell -- like dinosaurs. It will be interesting to compare these sequences to other legacies of the dinosaur era. Although humans have more base-pairs, the number of genes between bird and man are remarkably similar. Does this mean we are of roughly equal complexity? I wonder how much of the DNAis apparently non-coding? There's going to be a heck of a lot of fascinating science coming from this ...

How to talk usefully about the funding of public education

A call to action for Twin Cities schools

The time has come for the state of Minnesota to put up the money needed to fund public education adequately or let school districts raise the money they need themselves, a group of Twin Cities-area school district officials said Tuesday.

The Association of Metropolitan School Districts estimates that its 26 member districts face more than $88 million in cuts in 2005-06, unless state funding formulas dramatically increase. That gloomy picture is just part of a trend, the group's leaders said at a St. Paul news conference. Over the past three years, member districts -- which educate about one-third of the state's schoolchildren -- have eliminated the jobs of more than 2,800 employees, including about 2,000 teachers.

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Of all the sterile discussions I have to endure, among the least valuable are discussions about educational funding. In my experience, no-one presents any useful data.

I'd like each presentation to begin with 4 charts, with an optional 5th chart for discussions of local funding (all inflation adjusted of course):

1. A 15 yr chart of per student funding.
2. A 15 yr chart of spend on infrastructure (buildings, etc).
3. A 15 yr chart of the average salary of a state legislator.
4. A 15 yr chart of the % of students enrolled in public education (vs. private education).
5. Optional: A 15 yr chart of local tax revenue.

Once those charts are up front, one can talk intelligently. I would expect student per student costs to rise faster than inflation because:

1. Knowledge workers are becoming more costly, so there's increasing competition for teachers.
2. We're working harder to educate chidlren with language, cognitive and income disadvantages.
3. Regulations and computerization are impacting infrastructure spend.
4. Migration to private schools or to wealthier districts increases public school educational costs (private schools "cherry pick" children who are less costly to educate).

If one finds that educational spend is barely tracking inflation, then we likely have a serious underspend.

Ahh, but what if tax revenues are declining? Our population is aging and may consider education to be a lower priority. That is the crux of the matter. It is fundamentally the same issue we face with social security "reform". What is the duty owed by society to citizens, and citizens to society?

The Harrow Group: Futurist newsletters

The Harrow Group

Nanotech, singularity, politics, biology. Sounds like my kind of guy.

Soviet america. Four years ago, I wouldn't have given this much credence ...

Salon.com News | Whitewashing torture?

Col. C. Tsai, a military doctor who examined Ford in Germany and found nothing wrong with him, told a film crew for Spiegel Television that he was 'not surprised' at Ford's diagnosis. Tsai told Spiegel that he had treated 'three or four' other U.S. soldiers from Iraq that were also sent to Landstuhl for psychological evaluations or 'combat stress counseling' after they reported incidents of detainee abuse or other wrongdoing by American soldiers.

Artiga and other higher-ups in the 223rd M.I. Battalion deny Ford's charges. But in the aftermath of the Abu Ghraib scandal, federal agencies including the Department of Defense, the Army's Criminal Investigation Command (CID), and the FBI are finally looking into them. The Department of the Army's Office of the Inspector General has launched an investigation, according to Ford and his attorney, Kevin Healy, who have been contacted by investigators. If Ford's allegations are proven, the Army would be faced with evidence that its prisoner abuse problem is even more widespread than previously acknowledged -- and that some of its own officers not only turned a blind eye to abuses but actively participated in covering them up...

...The propellers of the huge turboprop engines on the C-130 sent scorching blasts of superheated air back toward the group, almost hot enough to singe the skin on a face. (When I left Iraq from the same tarmac a few months later, I did get burned from the blasts.) As Ford's gurney sank into the steaming tarmac, Madera and the other medical officer wheeled him up the long ramp and into the aircraft's cavernous interior. Once they were airborne, Madera unstrapped Ford and motioned for him to sit next to her on one of the hard benches that run along the sides of the plane. "She told me that she was forced to get me out of Iraq ASAP by Ryan and Artiga, who she claimed were scared to death by what I might say. She also told me that she wanted me to get out of Iraq as soon as possible because she feared for my safety." Ford said Madera also told him, "These people are serious and very scary." She apologized for having orchestrated such an exit, but said there was no other way. "I told her that I understood, but felt as though I had just been kidnapped." According to Ford, Madera replied, "You were."

Madera did not respond to several requests to be interviewed for this story.

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Four years ago I'd not have given this much credence. Now I'd give it a 50% chance of being at least partially true. Indeed, one wonders if straightforward murder isn't more often used to silence critics. It would be much tougher to track down.

I wonder if any mainstream media will pick this up. There are enough names provided in this article that if there's any truth to the allegations we should learn more fairly easily.

Fake psychiatric "diagnoses" and psychiatric "sentencing" were mainstays of the Soviet union. Some days I think GWB is a deep soviet plant.

Bush/Rumsfeld is making us all crazy.

The self-service economy - your home as a warehouse

Economist.com | The self-service economy

SO YOU want to withdraw cash from your bank account? Do it yourself. Want to install a broadband internet connection? Do it yourself. Need a boarding card issued for your flight? Do it yourself. Thanks to the proliferation of websites, kiosks and automated phone systems, you can also track packages, manage your finances, switch phone tariffs, organise your own holiday (juggling offers from different websites), and select your own theatre seats while buying tickets. These are all tasks that used to involve human interaction. But now they have been subsumed into the self-service economy...

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This September 2004 article described the number of ways that service roles have become self-service. Today, as we struggled to find mittens for our kids, I realized something else had been outsourced to us -- inventory management. The modern home is a warehouse.

I see this mostly with clothing. Children's clothes are dirt cheap now, but supply is as unpredictable as quality. One day there's a deluge of small mittens. Another day it's socks. Another day hats. Then large mittens. One cannot go to the store FOR an item. One must conduct store surveillance, purchasing items of interest.

The clothing supply chain behaves as though it has no inventory.

So where's the inventory? In the home. Suburban homes of middle class Americans are pretty large, with lots of storage space. When Walmart has size M mittens, the avid shopper can buy twenty or thirty pairs. That would last us ... a week. Ok, so it's a season for most people.

It makes sense. No-one wants to hold inventory any more. It's expensive and risky. Far better to slash prices, and transfer the inventory burden to the consumer.

Global warming summary and recommendations

eBulletin - Global Warming: A Perspective from Earth History

An interesting summary. It looks like we'll see sea level rise sharply over the next 30-90 years. Maybe 10 meters higher. The solutions given current technology seem unlikely to be implemented and are not necessarily feasible.

Looks like options are:

1. Immense research into alternative energy sources. Unfortunately these don't look promising.
2. Immense investment into energy conservation -- this could decrease emissions significantly. Best funded by a serious tax on energy. Sigh.
3. Teach humans to live underwater. Hmm.

Ok, so we don't have any great options. I'd say humanity is pathetic at solving these kind of problems, but we did manage the freon transition. This is only a hundred to a thousand times harder. We must hope China will be smarter than the US.

More in the solar system than thought possible?

The New York Times > Science > Sun Might Have Exchanged Hangers-On With Rival Star

...Either encounter would also leave alien planetoids in our solar system (and some of ours in the alien system) orbiting at a steep angle to the plane in which the planets go around. And so the next step is to search for such objects.

Sedna itself has only a moderately inclined orbit, the astronomers say. A more likely candidate for an extra-solar origin is another icy wanderer, known as 2000 CR105, about half the size of Sedna, discovered out beyond Neptune in 2000. Its orbit is inclined 20 degrees to the planets.

The detection of objects with inclinations of 40 degrees or more, the authors write in Nature, 'would clinch the case for extrasolar objects in the solar system.'

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Great. Planetary bodies whipping around in unexpected orbits. The article doesn't say how far out these objects are supposed to be.

Cruise ship nursing homes?

The New York Times > Health > At Sea, Care for Aged (and All You Can Eat)

For only slightly more than the average cost of a year in an assisted living residence, older people can live aboard a luxury liner with many of the same services, including meals, housekeeping and medical care at all hours - not to mention entertainment.

While it may not be a serious option for people with chronic or severe medical disorders, life at sea may have its benefits for those who can take it, according to a study in the November issue of The Journal of the American Geriatrics Society.

'A lot of people in assisted living facilities are dissatisfied with what they're paying and the services that they get,' said Dr. Lee Lindquist, an instructor of medicine at the Feinberg School of Medicine at Northwestern and the lead author of the study. 'A nice facility can be extremely expensive, and a lot of seniors have to go into their own savings because Medicare doesn't cover it. When you think about all the amenities you get, living on a cruise ship is more desirable for certain people.'

Dr. Lindquist, a geriatrician, came up with the idea for the study on a recent cruise. At dinner one night, she was chatting with some people who reminded her of her patients. Then the idea hit.

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Hey! I thought of this one years ago. Except I was thinking it would make a great nursing home. Just wheel me off at one spot or another ...

On the external representation of information in string theory

The New York Times > Science > String Theory, at 20, Explains It All (or Not)

....For years physicists have looked for the origins of string theory in some sort of deep and esoteric symmetry, but string theory has turned out to be weirder than that.

Recently it has painted a picture of nature as a kind of hologram. In the holographic images often seen on bank cards, the illusion of three dimensions is created on a two-dimensional surface. Likewise string theory suggests that in nature all the information about what is happening inside some volume of space is somehow encoded on its outer boundary, according to work by several theorists, including Dr. Juan Maldacena of the Institute for Advanced Study and Dr. Raphael Bousso of the University of California, Berkeley.

Just how and why a three-dimensional reality can spring from just two dimensions, or four dimensions can unfold from three, is as baffling to people like Dr. Witten as it probably is to someone reading about it in a newspaper.

In effect, as Dr. Witten put it, an extra dimension of space can mysteriously appear out of "nothing."

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Hmm. Of course if one assumes that the "universe" being described by string theory is itself a sort of simulation running on god's own computer ...

I can see why Caltech's Dabney House was so popular with physicists in the 1970s.

The NYT publishes an extensive review of string theory

The New York Times > Science > String Theory, at 20, Explains It All (or Not)

The string revolution had its roots in a quixotic effort in the 1970's to understand the so-called 'strong' force that binds quarks into particles like protons and neutrons. Why were individual quarks never seen in nature? Perhaps because they were on the ends of strings, said physicists, following up on work by Dr. Gabriele Veneziano of CERN, the European research consortium.

That would explain why you cannot have a single quark - you cannot have a string with only one end. Strings seduced many physicists with their mathematical elegance, but they had some problems, like requiring 26 dimensions and a plethora of mysterious particles that did not seem to have anything to do with quarks or the strong force.

When accelerator experiments supported an alternative theory of quark behavior known as quantum chromodynamics, most physicists consigned strings to the dustbin of history.

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A very thorough summary! Despite reading some popular books on the topic, I'd not known that string theory's first iteration was back in the 1970s, nor that Feynman had done it in with QCD.

The social security crisis: it's political, not fiscal

The New York Times > Opinion > Op-Ed Columnist: Inventing a Crisis

... But since the politics of privatization depend on convincing the public that there is a Social Security crisis, the privatizers have done their best to invent one.

My favorite example of their three-card-monte logic goes like this: first, they insist that the Social Security system's current surplus and the trust fund it has been accumulating with that surplus are meaningless. Social Security, they say, isn't really an independent entity - it's just part of the federal government.

If the trust fund is meaningless, by the way, that Greenspan-sponsored tax increase in the 1980's was nothing but an exercise in class warfare: taxes on working-class Americans went up, taxes on the affluent went down, and the workers have nothing to show for their sacrifice.

But never mind: the same people who claim that Social Security isn't an independent entity when it runs surpluses also insist that late next decade, when the benefit payments start to exceed the payroll tax receipts, this will represent a crisis - you see, Social Security has its own dedicated financing, and therefore must stand on its own.

There's no honest way anyone can hold both these positions, but very little about the privatizers' position is honest. They come to bury Social Security, not to save it. They aren't sincerely concerned about the possibility that the system will someday fail; they're disturbed by the system's historic success.

For Social Security is a government program that works, a demonstration that a modest amount of taxing and spending can make people's lives better and more secure. And that's why the right wants to destroy it.

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Social security is ground zero in a debate about the role of government in american life. This is not a fight about financing social security, it's a fight about the role of government.

Since we Democrats lie bloodied and defeated on the field of battle, while our enemies wax triumphant about us, we might as well speak honestly. Krugman does a fine job here. All we can do is speak clearly and do our best to ensure that Americans know what's going to happen to them, and why it's going to happen. Unfortunately, this message will not be carried on Republican TV/radio/newspapers, etc.

Multiple sclerosis, birth month and sun exposure

BBC NEWS | Health | MS risk 'linked to birth month'

The team said other studies had suggested exposure to the sun or seasonal variations in a mother's vitamin D levels during pregnancy may have an impact on brain development.

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Children born in November & December in northern countries had a lower risk of developing MS as adults, May was a bad month. This suggests the disease may have a quite early onset, but only manifest later in life.

I like the sunlight theory myself. Twenty years ago I speculated about this as a medical student. It's the obvious explanation for the correlation between latitude and disease incidence; the theory must have occurred to thousands of students over the past forty years. I thought then that it might be related to cutanous immune cells. There is a lot of curious immunology that appears to go on in the skin and it makes sense that it could be affected by radiation exposure and by the adaptations to radiation exposure.

Research anyone, anywhere

Background Check, Phone Number Lookup, Trace email, Criminal record, Find People, cell phone number search, License Plate Search

Nothing surprising here -- only the expansion and integration of longstanding services for researching individuals. Yahoo's offered similar services for years. I wonder if they're offshore -- best place to avoid any pesky privacy laws.

Memory loss: middle-aged and more

The New York Times > Magazine > In Search of Lost Time

Every brain has an intrinsic aging rate. Based on data on human lifespan and inferred aging rates (natural lifespan: 60-120 years, mean 90*) the range is +/- 33%, with aging starting around age 20. So by age 40 some lucky people have a brain similar to that of the average 33 yo, others resemble the average 47 yo. That's a significant enough span that we begin to notice winners and losers in the aging lottery. I have not read anything, by the way, that tells me that this aging rate can be significantly improved upon (though severe dietary restriction might help if started at age 20 -- note, however, than anorexics have fairly severe acceleration of brain aging, possibly due to the direct toxic effects of stress hormones).

Now add disease. Even a relatively mild concussion ages the brain significantly. Vascular disorders, infections, neurologic disorders, persistent stress, substance abuse, even social standing all come into play. Some primary dementing disorders, such as Parkinson's, begin to manifest. (It's unclear to me if Alzheimer's is a primary disorder, or a disorders of accelerated aging of the brain. The distinction may be subtle.)

The result is that by our 40s many of us worry about our cognitive capacities. This is particularly true of "knowledge workers", and probably less true of managers, CEOs, or politicians (political skills seem to be far more resilient than mere IQ).

This NYT Magazine article provides a fascinating summary of recent thinking about these cognitive disorders, and about the consequences of an aging brain in a post-industrial world.

It has an important message for those who blithely assume that extended life expectancy means we can work longer. They confuse life expectancy with functional cognitive skills. They'd never assume that brick layer would be laying bricks at 60, but they imagine the brain is less vulnerable to age than the spine. (Ok, so the spine is a pretty crummy device, and is a strong argument against "intelligent design", but you get the idea.)

So, yes, we'll be working when we're 75. We won't, however, be devising new implementations of cutting edge nanotech. We'll be doing the 2030 equivalent of bagging groceries -- except for politicians and the lucky few who will have the brains of a 55 yo at age 70.

Ten years ago it was obvious that the best way to dodge the demographic bullet would be to throw great resources into identifying specific interventions that might slow the aging of the human brain. We didn't do that. Too bad.

* Update: being middle-aged myself, I naturally flubbed the trivial arithmetic here.

21st century propaganda: outsourced, distributed, malignant

Advocacy Groups Blur Media Lines (washingtonpost.com)

washingtonpost.com
Advocacy Groups Blur Media Lines
Some Push Agendas By Producing Movies, Owning Newspapers

By Jeffrey H. Birnbaum
Washington Post Staff Writer
Monday, December 6, 2004; Page A01

The Madison County Record, an Illinois weekly newspaper launched in September that bills itself as the county's legal journal, reports on one subject: the state courts in southern Illinois. A recent front page carried an assortment of stories about lawsuits against businesses. In one, a woman sought $15,000 in damages for breaking her nose at a haunted house. In another, a woman sued a restaurant for $50,000 after she hurt her teeth on a chicken breast.

Nowhere was it reported that the U.S. Chamber of Commerce created the Record as a weapon in its multimillion-dollar campaign against lawyers who file those kinds of suits....

... The National Rifle Association, which already has a national radio show, is thinking about buying its own radio stations...

... The National Rifle Association believes more lobbying groups will mimic traditional media formats or buy them outright to disseminate their viewpoints. If the NRA buys radio stations it won't bother to label them with its name. "We wouldn't need to any more than NBC needs a disclaimer that it's General Electric-produced or than ABC needs a disclaimer saying it's Disney-produced," said Wayne LaPierre Jr., the NRA's executive director.

"I hope everybody gets into the media business and, I think, many interest groups will," LaPierre said. "We have as much right to be at the table delivering news and information to the American public as anyone else does."

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Caveat emptor is the catchprase of the libertarian century.