links for 2008-05-07

• Inventing illegal immigration. - The Edge of the American West
• Liquidity isn't apple pie - Interfluidity
• Spreads and paradoxical liquidity - Interfluidity
• K.C. Fed's Hoenig Worries About 'Inflation Psychology' - Real Time Economics
• Fannie Mae's Weird Rally - Felix Salmon
• Hunger hormone: Makes food more attractive - EurekAlert
• Bush Advisers Oppose Housing Measure, and Vow a Veto - New York Times
• Seeing Inflation Only in the Prices That Go Up - New York Times
• When Genes Go Retro - Olivia Judson
• Does conflict lead to cooperation – and corporate consolidation? - Vox EU

Comments

[anne]

http://judson.blogs.nytimes.com/2008/05/06/when-genes-go-retro/index.html

May 6, 2008

When Genes Go Retro
By Olivia Judson

Pssst! I'm going on a tour of the genome — want to come?

DNA. (Credit: Alfred Pasieka)I'm going to walk among the coiled spirals of DNA, and ponder the different histories of the different segments. For one of the most remarkable discoveries of recent decades is that genomes are not static, fixed entities that evolve as one; instead, they are highly dynamic. From one generation to the next, stretches of DNA may appear or disappear, or move from one location to another. From time to time, entire new genes appear and become established, thus expanding the organisms' genetic repertoire.

But where do new genes come from? It turns out that they can come from a wide variety of sources (I have written about some of them before). This week, I want to consider a particularly intriguing type of new gene: the retrogene. Retrogenes have been an important source of new genes in a number of species, including us humans.

The story of the retrogene is the story of three molecules: DNA, RNA and something called reverse transcriptase. If they were characters in a cartoon, they'd be the celebrity, the drudge and the joker. And, for reasons I shall reveal in a moment, if the cartoon had a title, it would be "X-odus."

The celebrity, naturally enough, is DNA. And what a celebrity it is! Its double helix structure is an icon of our times. I've seen double helix coins, stamps, necklaces, ear-rings and doorhandles; I've even spotted it in a modern stained glass window. Yet like many celebrities, DNA mostly sits about looking pretty. Much of the grunt work of running the cell is done by its less famous cousin, RNA.

RNA is chemically similar to DNA, but where DNA is usually double-stranded — hence, the double helix — RNA is usually single-stranded. As a result, its physical appearance is not generally considered so beautiful as DNA's, and it is far from being an icon. (It has, however, once appeared on a necktie. In the early days of molecular biology, a theoretical physicist called George Gamow, better known for his work on the Big Bang, founded a biology discussion club called the RNA Tie Club. Its members included Jim Watson and Francis Crick, co-discoverers of the structure of DNA.)

RNA has many roles in the cell, and more keep being discovered. But the one that's relevant to this story is its role as a messenger.

Messenger RNA is a genetic intermediary in the process of making proteins. To recap: a gene is a stretch of DNA that contains the instructions to make a protein. In order to make a given protein, the relevant stretch of DNA is first copied into RNA. The cell then makes the protein from this RNA template — the messenger.

In the early days of molecular biology, the assumption was that DNA could be copied into RNA, but not the reverse. But then, reverse transcriptase was discovered. This mischief-making molecule does what no one expected: it copies RNA into DNA.

Most of the time, this is for a nefarious purpose. Many viruses — among them, HIV — store their genes not as DNA, but as RNA, and use reverse transcriptase to copy themselves into DNA. They then insert themselves into the genomes of their hosts, where they may remain dormant for some period of time. Such viruses are known as retroviruses.

Reverse transcriptase makes trouble in other ways as well....

[anne]

http://krugman.blogs.nytimes.com/2008/05/07/against-the-grain/

May 7, 2008

Against the Grain
By Paul Krugman

From the annals of unusual political action (Felix Salmon): *

"The U.S. baking industry's trade association, representing firms such as Kellogg Co., Sara Lee Corp. and Interstate Bakeries Corp., plans a march on Washington by the firms' employees later this month to press for a reduction in U.S. wheat exports."

Here. **

* http://www.portfolio.com/views/blogs/market-movers/2008/05/06/the-wheat-exports-march-on-washington

** http://www.thestar.com/comment/columnists/article/308530

[Bruce Wilder]

From one of the links above, David Leonhardt tells me that I'm just imagining inflation: "Next week, the Bureau of Labor Statistics will release its monthly report on inflation, and it sure is going to sound strange. Wall Street is expecting the bureau to announce that the Consumer Price Index rose just three-tenths of a percentage point in April. Over the last year, the index has risen only about 4 percent."

strange indeed. The article tells me that the fact that rent, bread, gas, health care and education and everything related are skyrocketing means diddly, because the price of women's clothing has declined 1 percent over the last year.

Barry Ritholtz promises to explain all tomorrow.

Leonhardt is at pains to poo-poo an article in Harper's Magazine, May 2008 (available only with a subscription).

Given the economic condition of the country, the unemployment rate is beginning to seem pretty suspicious to me as well.

The often impenetrable Sterling Newberry takes up the gauntlet of proving that it is all a conspiracy of the plutocracy, to have a depression, which never shows up in the official statistics.

Price indices are never really accurate, any more than financial accounting can be accurate. Accuracy, in a realm with large subjective elements, is a less important virtue than integrity.

A price index is an arbitrary linear approximation of a fundamentally non-linear trend. It's very arbitrariness is a virtue, because such arbitrariness ensures integrity. It's why straight-line depreciation (or similarly arbitrary methods) tends to be preferred, in financial accounting. A depreciation method that made use of management's expectations could be more accurate, but at the cost of corruption -- management has an incentive to manipulate the accounting, and cannot be relied upon to be truthful in presenting its expectations.

We've been shaving inflation with hedonics and substitution for years, to keep from paying out too much for Social Security. Maybe, there's some subjective sense in which my $100 cellphone bill is less than my former $18 plain old telephone service bill of yore, adjusted for . . . adjusted for what? by whom? So, that Social Security payments are reduced by several billion dollars?

There have to be better ways to measure and track inflation than market-basket price indices. It seems to be that a vast enough sampling of actual transactions at intervals could supply the raw material for regression-based measures, which could parcel out the whole change in wages and income into increasing/decreasing productivity, rising/falling real costs, and monetary inflation.

[anne]

http://www.nytimes.com/2008/05/07/opinion/07wed4.html?ref=opinion

May 7, 2008

The Cost of Smarts
By VERLYN KLINKENBORG

Research on animal intelligence always makes me wonder just how smart humans are. Consider the fruit-fly experiments described in Carl Zimmer's piece in the Science Times on Tuesday. Fruit flies who were taught to be smarter than the average fruit fly tended to live shorter lives. This suggests that dimmer bulbs burn longer, that there is an advantage in not being too terrifically bright.

Intelligence, it turns out, is a high-priced option. It takes more upkeep, burns more fuel and is slow off the starting line because it depends on learning — a gradual process — instead of instinct. Plenty of other species are able to learn, and one of the things they've apparently learned is when to stop.

Is there an adaptive value to limited intelligence? That's the question behind this new research. I like it. Instead of casting a wistful glance backward at all the species we've left in the dust I.Q.-wise, it implicitly asks what the real costs of our own intelligence might be. This is on the mind of every animal I've ever met.

Every chicken that looks at you sideways — which is how they all look at you — is really saying what Thoreau said less succinctly: you are endeavoring to solve the problem of a livelihood by a formula more complicated than the problem itself. Thoreau himself would not dispute that he was hoping to recover the chicken's point of view. He went to Walden Pond "to remember well his ignorance."

Research on animal intelligence also makes me wonder what experiments animals would perform on humans if they had the chance. Every cat with an owner, for instance, is running a small-scale study in operant conditioning. I believe that if animals ran the labs, they would test us to determine the limits of our patience, our faithfulness, our memory for terrain. They would try to decide what intelligence in humans is really for, not merely how much of it there is. Above all, they would hope to study a fundamental question: Are humans actually aware of the world they live in? So far the results are inconclusive.

[anne]

http://www.nytimes.com/2008/05/06/science/06dumb.html?hp

May 6, 2008

Lots of Animals Learn, but Smarter Isn't Better
By CARL ZIMMER

"Why are humans so smart?" is a question that fascinates scientists. Tadeusz Kawecki, an evolutionary biologist at the University of Fribourg, likes to turn around the question.

"If it's so great to be smart," Dr. Kawecki asks, "why have most animals remained dumb?"

Dr. Kawecki and like-minded scientists are trying to figure out why animals learn and why some have evolved to be better at learning than others. One reason for the difference, their research finds, is that being smart can be bad for an animal's health.

Learning is remarkably widespread in the animal kingdom. Even the microscopic vinegar worm, Caenorhadits elegans, can learn, despite having just 302 neurons. It feeds on bacteria. But if it eats a disease-causing strain, it can become sick.

The worms are not born with an innate aversion to the dangerous bacteria. They need time to learn to tell the difference and avoid becoming sick.

Many insects are also good at learning. "People thought insects were little robots doing everything by instinct," said Reuven Dukas, a biologist at McMaster University.

Research by Dr. Dukas and others has shown that insects deserve more respect. Dr. Dukas has found that the larvae of one of the all-time favorite lab animals, the fruit fly, Drosophila melanogaster, could learn to associate certain odors with food and other odors with predators....

[anne]

Nelson Mandela is quite ill.

[anne]

http://www.anc.org.za/ancdocs/history/rivonia.html

April 20, 1964

"I am Prepared to Die"
By Nelson Mandela

Pretoria Supreme Court: Statement from the dock at the opening of the defence case in the Rivonia Trial.

I am the First Accused.

I hold a Bachelor's Degree in Arts and practised as an attorney in Johannesburg for a number of years in partnership with Oliver Tambo. I am a convicted prisoner serving five years for leaving the country without a permit and for inciting people to go on strike at the end of May 1961.

At the outset, I want to say that the suggestion made by the State in its opening that the struggle in South Africa is under the influence of foreigners or communists is wholly incorrect. I have done whatever I did, both as an individual and as a leader of my people, because of my experience in South Africa and my own proudly felt African background, and not because of what any outsider might have said.

In my youth in the Transkei I listened to the elders of my tribe telling stories of the old days. Amongst the tales they related to me were those of wars fought by our ancestors in defence of the fatherland. The names of Dingane and Bambata, Hintsa and Makana, Squngthi and Dalasile, Moshoeshoe and Sekhukhuni, were praised as the glory of the entire African nation. I hoped then that life might offer me the opportunity to serve my people and make my own humble contribution to their freedom struggle. This is what has motivated me in all that I have done in relation to the charges made against me in this case.

Having said this, I must deal immediately and at some length with the question of violence. Some of the things so far told to the Court are true and some are untrue. I do not, however, deny that I planned sabotage. I did not plan it in a spirit of recklessness, nor because I have any love of violence. I planned it as a result of a calm and sober assessment of the political situation that had arisen after many years of tyranny, exploitation, and oppression of my people by the Whites.

I admit immediately that I was one of the persons who helped to form Umkhonto we Sizwe, and that I played a prominent role in its affairs until I was arrested in August 1962.

In the statement which I am about to make I shall correct certain false impressions which have been created by State witnesses. Amongst other things, I will demonstrate that certain of the acts referred to in the evidence were not and could not have been committed by Umkhonto. I will also deal with the relationship between the African National Congress and Umkhonto, and with the part which I personally have played in the affairs of both organizations. I shall deal also with the part played by the Communist Party. In order to explain these matters properly, I will have to explain what Umkhonto set out to achieve; what methods it prescribed for the achievement of these objects, and why these methods were chosen. I will also have to explain how I became involved in the activities of these organizations.

I deny that Umkhonto was responsible for a number of acts which clearly fell outside the policy of the organisation, and which have been charged in the indictment against us. I do not know what justification there was for these acts, but to demonstrate that they could not have been authorized by Umkhonto, I want to refer briefly to the roots and policy of the organization.

I have already mentioned that I was one of the persons who helped to form Umkhonto. I, and the others who started the organization, did so for two reasons. Firstly, we believed that as a result of Government policy, violence by the African people had become inevitable, and that unless responsible leadership was given to canalize and control the feelings of our people, there would be outbreaks of terrorism which would produce an intensity of bitterness and hostility between the various races of this country which is not produced even by war. Secondly, we felt that without violence there would be no way open to the African people to succeed in their struggle against the principle of white supremacy. All lawful modes of expressing opposition to this principle had been closed by legislation, and we were placed in a position in which we had either to accept a permanent state of inferiority, or to defy the Government. We chose to defy the law. We first broke the law in a way which avoided any recourse to violence; when this form was legislated against, and then the Government resorted to a show of force to crush opposition to its policies, only then did we decide to answer violence with violence.

But the violence which we chose to adopt was not terrorism. We who formed Umkhonto were all members of the African National Congress, and had behind us the ANC tradition of non-violence and negotiation as a means of solving political disputes. We believe that South Africa belongs to all the people who live in it, and not to one group, be it black or white. We did not want an interracial war, and tried to avoid it to the last minute. If the Court is in doubt about this, it will be seen that the whole history of our organization bears out what I have said, and what I will subsequently say, when I describe the tactics which Umkhonto decided to adopt. I want, therefore, to say something about the African National Congress.

The African National Congress was formed in 1912 to defend the rights of the African people which had been seriously curtailed by the South Africa Act, and which were then being threatened by the Native Land Act. For thirty-seven years - that is until 1949 - it adhered strictly to a constitutional struggle. It put forward demands and resolutions; it sent delegations to the Government in the belief that African grievances could be settled through peaceful discussion and that Africans could advance gradually to full political rights. But White Governments remained unmoved, and the rights of Africans became less instead of becoming greater. In the words of my leader, Chief Lutuli, who became President of the ANC in 1952, and who was later awarded the Nobel Peace Prize:

"who will deny that thirty years of my life have been spent knocking in vain, patiently, moderately, and modestly at a closed and barred door? What have been the fruits of moderation? The past thirty years have seen the greatest number of laws restricting our rights and progress, until today we have reached a stage where we have almost no rights at all".

Even after 1949, the ANC remained determined to avoid violence. At this time, however, there was a change from the strictly constitutional means of protest which had been employed in the past. The change was embodied in a decision which was taken to protest against apartheid legislation by peaceful, but unlawful, demonstrations against certain laws. Pursuant to this policy the ANC launched the Defiance Campaign, in which I was placed in charge of volunteers. This campaign was based on the principles of passive resistance. More than 8,500 people defied apartheid laws and went to jail. Yet there was not a single instance of violence in the course of this campaign on the part of any defier. I and nineteen colleagues were convicted for the role which we played in organizing the campaign, but our sentences were suspended mainly because the Judge found that discipline and non-violence had been stressed throughout. This was the time when the volunteer section of the ANC was established, and when the word 'Amadelakufa' was first used: this was the time when the volunteers were asked to take a pledge to uphold certain principles. Evidence dealing with volunteers and their pledges has been introduced into this case, but completely out of context. The volunteers were not, and are not, the soldiers of a black army pledged to fight a civil war against the whites. They were, and are. dedicated workers who are prepared to lead campaigns initiated by the ANC to distribute leaflets, to organize strikes, or do whatever the particular campaign required. They are called volunteers because they volunteer to face the penalties of imprisonment and whipping which are now prescribed by the legislature for such acts.

During the Defiance Campaign, the Public Safety Act and the Criminal Law Amendment Act were passed....

[anne]

http://query.nytimes.com/gst/fullpage.html?res=9C0CE5DF1239F93BA25751C1A962958260

December 18, 1994

The Practical Mr. Mandela
By BILL KELLER

LONG WALK TO FREEDOM
The Autobiography of Nelson Mandela.
By Nelson Mandela.

ON my office bulletin board is a headline clipped from a Johannesburg tabloid last June, a month after Nelson Mandela's inauguration as the first freely elected President of South Africa. In huge, bold type, it says, "MANDELA: I'M NOT 'MESSIAH.' " ...

[anne]

http://query.nytimes.com/gst/fullpage.html?res=9405E2D61030F933A05752C1A962958260

November 30, 1994

How a Leader Emerged As if Called by History
By MARGO JEFFERSON

Nelson Mandela has already made history: now he has chosen to write it in the form of an autobiography.

"I am not and never have been a man who finds it easy to talk about his feelings in public," he acknowledges in "Long Walk to Freedom." When reporters asked how it felt to be free, he writes, "I did my best to describe the indescribable, and usually failed." His book is formal in tone: courtly, stern, ironic and, in its detailed accounts of political meetings and strategies, didactic. It is also fascinating because, like the hero in a Shakespearean history play, Mr. Mandela cannot help revealing himself: here are all the idiosyncracies and complications that turned a man into a leader and that have at last turned that leader back into a man....

[anne]

http://www.nytimes.com/2008/04/06/books/review/Morris-t.html

"[Pico] Iyer challenges us to see [the Dalai Lama] as one of a group of agents of transformation like Vaclav Havel, Desmond Tutu and Nelson Mandela, people who 'change the world by changing the way they looked at the world.' "

[anne]

http://afp.google.com/article/ALeqM5h4nSjgYgfpr8NWg1k2BcNdiWCKKQ

May 6, 2008

Queen, Razorlight to Headline Mandela AIDS Concert
By AFP

LONDON — Veteran rockers Queen along with Razorlight and Simple Minds will top the bill at an AIDS benefit concert in London next month to mark Nelson Mandela's 90th birthday, organisers announced Tuesday.

Precisely 46,664 tickets will go on sale for the three-hour gig in Hyde Park on June 27, which is in support of the former South African president's 46664 campaign against HIV/AIDS.

Nobel Peace Prize laureate Mandela, now retired from public life, is to make a rare appearance.

Other artists on the bill include Annie Lennox, Leona Lewis, the Sugababes, Shirley Bassey, Andrea and Sharon Corr, Eddy Grant, Jamelia, Zucchero, South African artists and the Sudanese "war child" rapper Emmanuel Jal.

Queen are now known as Queen plus Paul Rodgers, with their new frontman who has replaced the late Freddie Mercury.

"The concert will feature numerous unexpected appearances, with several major artists keeping silent about their involvement in order to take both Mr Mandela and the audience by surprise," organisers said.

Royalty, former US president Bill Clinton, British Prime Minister Gordon Brown, US actors Robert De Niro, Will Smith and Forest Whitaker, US television host Oprah Winfrey and Formula One driver Lewis Hamilton are to attend events spread over three days leading up to the concert.

The campaign, named after Mandela's prison number during his 27-year incarceration, aims to raise awareness of the HIV/AIDS epidemic which is rife in sub-Saharan Africa.

South Africa is one of the countries worst-hit by HIV, with 5.41 million people living with the illness....