A secular analysis of news, culture and kitsch. Following the slide into theocracy and fascism and encouraging signs of resistance.
Saturday, July 29, 2006
Friday, July 28, 2006
The Neanderthal Genome Project
The Neanderthal Genome Project
A study with a lot of balls
From The Economist print edition
A brave attempt to sequence the Neanderthal genome
THE Human Genome Project is sooo yesterday. So what is a firm with a clever, new gene-sequencing technology to do in order to make a splash? Look yesterday squarely in the face, of course. And that is exactly what Jonathan Rothberg and Michael Egholm, of 454 Life Sciences, plan to do.
The particular yesterday they have in mind was about 40,000 years ago. It was the day when a man died in a cave in the Neander valley in what is now Germany. His skeleton is the type specimen of Homo neanderthalensis—Neanderthal man—and Dr Rothberg and Dr Egholm obtained permission to remove a few grams of the skeleton's right arm in order to extract the DNA therein. From it, they hope to work out a complete sequence of the chemical base pairs that constitute its genetic letters; in other words a Neanderthal genome.
Neanderthal man is a controversial creature. He inhabited Europe from 300,000 to 35,000 years ago, his disappearance coinciding with the arrival of Homo sapiens. Once, it was thought the one might be ancestral to the other. That is no longer believed. But the question of whether Neanderthals were deliberately exterminated by their more modern rivals, or merely outcompeted, is unresolved, as is that of whether the two species ever interbred. The Neanderthal Genome Project that Dr Rothberg and Dr Egholm have embarked on in collaboration with Svante Paabo, of the Max Planck Institute in Leipzig, may answer the second of those questions. It may also, by providing a genome that can be compared with both modern humans and chimpanzees, shed light on what it means, genetically, to be human.
The gene-sequencing technology used by 454 relies on specially designed chips with 1m or more tiny wells in them. The DNA to be analysed is broken up into fragments about 100 base pairs long (one of the advantages, from 454's point of view, is that time has already performed the task of breaking the DNA up into fragments of the right length). It is then shaken up in a mixture of water, a special silicone-based oil, a large quantity of tiny plastic balls, and the reagents of the polymerase chain reaction (a way of duplicating DNA to make small samples bigger).
The aim is to get the smallest sample possible—a single type of DNA molecule—into each well on the chip. That is done by shaking the mixture to create an emulsion of tiny, watery droplets in the oil. Get the conditions right, and many of the droplets will have a single DNA molecule in them, while most of the rest have none. The droplets will also contain the PCR reagents, which are soluble in water but not oil, and the plastic balls.
The next stage is to let the polymerase chain reaction do its work of multiplying the DNA strands in the droplets. The nature of the plastic means that the strands tend to stick to it, and the upshot is hundreds of thousands of balls each covered with a single sort of DNA. These can, with a little persuasion, be encouraged to drop into the wells on the chip. The DNA molecules on the balls can then be analysed by a technique that uses fluorescence to read the sequences of the bases of which they are composed.
Once the sequences of the DNA fragments have been obtained, the overlaps between them can be used to stitch them together into a complete message, as has been done for many other species. Those species, though, have still been alive. This will be the first time the genome of an extinct animal has been read.
Most of the Neanderthal genome is expected to resemble that of modern humans and (slightly less closely) modern chimpanzees, which are Neanderthals' two closest living relatives. The places of particular interest are those that the genome shares with neither species. Not only will these define what is uniquely Neanderthal, but they will also help to define what is unique to Homo sapiens, by showing which of its differences from chimpanzees are the result of common hominid heritage, and which the result of species-specific evolution.
Drs Rothberg, Egholm and Paabo hope to have their answer within two years. For Dr Paabo, the genome itself is the thing. It will be the culmination of a decade and a half of studying ancient DNA (and, along the way, providing the inspiration for “Jurassic Park”). Dr Rothberg and Dr Egholm, meanwhile, hope that this demonstration of their technology's power will lead to medical applications.
They aim to be able to sequence a human genome from scratch for $500,000. That is a lot of money, but peanuts compared with the billions spent on the Human Genome Project itself. And it is a small enough sum for it to be worthwhile looking at the entire genomes of people with diseases that have complex genetic causes, in order to see how they differ from healthy individuals.
Of course, technology gets cheaper all the time. One day, the firm hopes, its chip-and-ball technology will be cheap enough for clinical use. But if its collaboration with Dr Paabo bears fruit, it will surely be the cave-man connection that keeps it in the public eye.
Tuesday, July 25, 2006
Keeping up with the war
Some good recent stuff:
Stephen Frug does a good round up of response to Dershowitz & company who want to introduce gradations of humanity to justify war crimes.
The Angry Arab has a nice biting response to NYT pontificator Nicholas Kristof: "I have always believed that people who can finish a whole column by Kristof should receive a blender as a gift ... I really believe that American liberals are the true inheritors white supremacist colonialism."
In a lethal non sequiter, Paul Woodward of War in Context argues that the meme "Israel has the right to defend itself" is really a kind of Trojan horse; a truth that deftly transports a lie. The lie is that by killing hundreds of Lebanese civilians and destroying the country's infrastructure, Israel is engaged in nothing more than an act of self-defense.
Birthday Parties & the Ground War: Lebanon might be small but in two weeks, the Israelis have only -- at best, and by their accounts-- managed to take control of a border village or two. If they want to invade further into the country, with tanks and the whole shebang, they're going to be sorry for having taken out all the roads and bridges. Which reminds me of the clever fellows who set fire to the Danish Embassy in Beirut last February-- from the bottom up-- and then had to jump to their deaths from the fourth floor.
Sunday, July 23, 2006
I have never liked Bill Maher. The fact that he passes for a representative of the left in the U.S. is in itself an indictment of the shallowness of our political culture--of our culture. After this puff piece on the Huffington Post though, I refuse to believe that anyone serious can take him seriously.
I Love Being on the Side of My PresidentWhere to begin? With the overt racism? With the casual dismissal of the the blood being spilt? With the failure to even pretend to confront the specifics of the situation? With the depth of ignorance? With the trivializing of massacre? No Lebanon...just Arabs? No Palestine...just Palestinians. The same argument was used to justify the genocide against Native Americans. With the mindless repetition of propaganda? With the confusion of is and ought? Surely he can't be arguing that the deportation of the Jews is a good precedent. But that's what he says.
[Obligatory sexual innuendo deleted] ... I love it that a U.S. president doesn't pretend Arab-Israeli conflict is an even-steven proposition. Lots of ethnic peoples, probably most, have at one time or another lost some territory; nobody's ever completely happy with their borders; people move and get moved, which is why the 20th century saw the movement of tens if not hundreds of millions of refugees in countries around the world. There was no entity of Arabs called "Palestine" before Israel made the desert bloom. If those 600,000 original Palestinian refugees had been handled with maturity by their Arab brethren, who had nothing but space to put them, they could have moved on -- the way Germans, Czechs, Poles, Chinese and everybody else has, including, of course, the Jews.
How about with the advocacy of a war crime? "Deportation or forcible transfer of population" is a crime against humanity under the Rome Statute of the International Criminal Court Article 7 Sec. d.
He is in this sense "a good American" in good company with torture aficionado Alan Dershowitz, who in the LA Times this weekend argues that all civilians deaths may seem equal but some are more equal than others, dutifully echoing the earlier statement of official U.S. policy by U.N. Ambassador John Bolton and the celebration of the bombing as the "birth pangs" of a new Middle East by Secretary of State Condoleezza Rice, a celebration for which Billmon has found the perfect illustration.
Saturday, July 22, 2006
Dance like a monkey
The New York Dolls come back from the grave to teach creationists how to "dance like a monkey."
Oh oh oh no god no...
Thursday, July 20, 2006
Send Pizza to the IDF
Wednesday, July 19, 2006
Praying for you
Nothing fails like prayer, so it's no surprise that that is what the U.S. is offering Lebanon, as we affect patience and disinterest while our client state goes on a mad and bloody rampage with the weapons we bought for them.
Rice tells Sfeir U.S. is 'Praying' for Lebanese CiviliansAnd oh yes, the Democrats are rushing up to prove that they have an even bigger hard on for mass murder than the current bunch of psychopaths in charge of the government. Thus spake Hillary:
U.S. Secretary of State Condoleezza Rice told Patriarch Nasrallah Sfeir on Tuesday that Americans were praying for Lebanese civilians amid the conflict with Israel.
"We are, of course, working very hard to minimize the impact of the current conflict on the Lebanese people," the State Department quoted Rice as saying in the telephone conversation.
"And I want you to know that we're not only working very hard, but we're also praying for the people of Lebanon," she was quoted as saying.
Sfeir replied that Israel was placing Lebanon under attack and that his country did not have the means to respond.
"When some are having arms and the others have not there is no equality," the State Department quoted Sfeir as saying.
"We will stand with Israel because Israel is standing for American values as well as Israeli ones" ....She may be right about this, but not in the way she thinks.
The hollow rhetoric of freedom and justice convinces so few now, you have to wonder why they bother any more. Perhaps to try to convince themselves that they are not in fact the callous sociopaths that the news and images from all corners of the empire insist that they are. "Out out, damn spot." But the spot just deepens and grows.
Wednesday, July 12, 2006
Rumsfeldian quote of the day
Asked about the various atrocities, including the rape and murder of a 14 year old woman, "allegedly" commited by U.S. troops that have been center of controversy in Iraq recently, Donald opined:
"Ninety-nine percent of the American troops and the coalition forces are performing in a highly professional, courageous and skillful way," he said, and allegations of murder "obviously hurts the 99.9 percent of the troops as much as anybody."Of course it is the allegations that hurt the most. They surely are the kindest, bravest, warmest, most wonderful troops anyone has ever been massacred by in their whole life.
Tuesday, July 11, 2006
Tuesday, July 04, 2006
Negativland's Christianity is Stupid with video from the Passion of the Christ and other holy epics = The Mashin' of the Christ
News for patriots
The Reality Beneath the Flag-Waving
by Paul Craig Roberts
Americans who get their propaganda from Fox "News" or are told what to think by right-wing talk radio hosts are outraged at news reports that U.S. troops planned and carried out the rape and murder of a young Iraqi woman. They are not outraged that the troops committed the deed; they are outraged that the media reported it. These "conservatives," who proudly wear their patriotism on their sleeves, dismiss the reports of the incident as a Big Lie floated by "the anti-American liberal media" in order to demoralize Americans and reduce public support for the war....
Britons see US as vulgar empire builderand that's "New Europe"
By Ben Fenton
Most Britons see America as a cruel, vulgar, arrogant society, riven by class and racism, crime-ridden, obsessed with money and led by an incompetent hypocrite....
Burning love of country
The Pledge of Allegiance
by Jello Biafra
I pledge defiance to the flag of the United Snakes of Captivity
And to the Republic for which it stands, I dip it in kerosene,
and stick it up the ass of you know who--and light it
One nation, under God--or else
One nation, under psychopath Pentagon gangsters,
whose idea of democracy is concentration camps
for the people who go and use the drugs
that the government supplies themselves
One nation, under Wall Street:
If the cops and the President are all criminals,
I might as well be one too, ha ha!
One Nation of tabloid robots
who actually believe what they see on tv, even MTV
but when asked about it say “I don’t care.”
One nation, drowning in its own garbage
Indivisible from the from the fall of Rome
With liberty and justice for all--who can afford it
Burn, Baby, Burn Old Glory
The Yankee Swastika
Burn, Baby, Burn Burn, Baby, Burn
Whenever I see you I see red
Whenever I see you I see red
If the Communists can do it, why can’t we
Throw the bastards out and try some real Democracy
Not by rich people
Not by Army people
Not by sons of senators sons of senators sons of senators sons
After all, have you noticed
The more they dole out Democracy over there
The more they take it away over here
Now, before it’s too late
Be a good boyscout
Take the Swastika
The Yankee Swastika and let it
Burn Burn Burn, baby Burn