Hairball science

At Nature, a report on the successful reconstruction by scientists at Penn State of most of the genome of the wooly mammoth.

Leading to discussions about whether a live mammoth could be brought to term inside the womb of an African elephant.

The NY Times report notes similar discussions about whether the now-reconstructed genome of Neanderthal man could be brought to life in a human embryo, or, if that's too ethically troubling, a chimp.

Yes, they are debating on the front page of the paper of record whether or not we should develop chimpanzee-Neanderthal hybrids.

Time to buy stock in the exotic pet distribution business?

Do you think they can keep a lid on this mad science for very long? Who knew Jurassic Park was going to end up being more like the Island of Dr. Moreau?

New York Times
November 20, 2008
Regenerating a Mammoth for $10 Million

By NICHOLAS WADE
Scientists are talking for the first time about the old idea of resurrecting extinct species as if this staple of science fiction is a realistic possibility, saying that a living mammoth could perhaps be regenerated for as little as $10 million.

The same technology could be applied to any other extinct species from which one can obtain hair, horn, hooves, fur or feathers, and which went extinct within the last 60,000 years, the effective age limit for DNA.

Though the stuffed animals in natural history museums are not likely to burst into life again, these old collections are full of items that may contain ancient DNA that can be decoded by the new generation of DNA sequencing machines.

If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant’s egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.

The same would be technically possible with Neanderthals, whose full genome is expected to be recovered shortly, but there would be several ethical issues in modifying modern human DNA to that of another human species.

A scientific team headed by Stephan C. Schuster and Webb Miller at Pennsylvania State University reports in Thursday’s issue of Nature that it has recovered a large fraction of the mammoth genome from clumps of mammoth hair. Mammoths, ice-age relatives of the elephant, were hunted by the modern humans who first learned to inhabit Siberia some 22,000 years ago. The mammoths fell extinct in both their Siberian and North American homelands toward the end of the last ice age, some 10,000 years ago.

Dr. Schuster and Dr. Miller said there was no technical obstacle to decoding the full mammoth genome, which they believe could be achieved for a further $2 million. They have already been able to calculate that the mammoth’s genes differ at some 400,000 sites on its genome from that of the African elephant.



There is no present way to synthesize a genome-size chunk of mammoth DNA, let alone to develop it into a whole animal. But Dr. Schuster said a shortcut would be to modify the genome of an elephant’s cell at the 400,000 or more sites necessary to make it resemble a mammoth’s genome. The cell could be converted into an embryo and brought to term by an elephant, a project he estimated would cost some $10 million. “This is something that could work, though it will be tedious and expensive,” he said.

There have been several Russian attempts to cultivate eggs from frozen mammoths that look so perfectly preserved in ice. But the perfection is deceiving since the DNA is always degraded and no viable cells remain. Even a genome-based approach would have been judged entirely impossible a few years ago and is far from reality even now.

Still, several technical barriers have fallen in surprising ways. One barrier was that ancient DNA is always shredded into tiny pieces, seemingly impossible to analyze. But a new generation of DNA decoding machines use tiny pieces as their starting point. Dr. Schuster’s laboratory has two, known as 454 machines, each of which costs $500,000.

Another problem has been that ancient DNA in bone, the usual source, is heavily contaminated with bacterial DNA. Dr. Schuster has found that hair is a much purer source of the host’s DNA, with the keratin serving to seal it in and largely exclude bacteria.

A third issue is that the DNA of living cells can be modified only very laboriously and usually at one site at a time. Dr. Schuster said he had been in discussion with George Church, a well-known genome technologist at Harvard Medical School, about a new method Dr. Church has invented for modifying some 50,000 genomic sites at a time.

The method has not yet been published, and until other scientists can assess it they are likely to view genome engineering on such a scale as being implausible. Rudolph Jaenisch, a biologist at the Whitehead Institute in Cambridge, said the proposal to resurrect a mammoth was “a wishful-thinking experiment with no realistic chance for success.”

Dr. Church, however, said that there had recently been enormous technical improvements in decoding genomes and that he expected similar improvements in genome engineering. In his new method, some 50,000 corrective DNA sequences are injected into a cell at one time. In the laboratory, the cell would then be grown and tested and its descendants subjected to further rounds of DNA modification until judged close enough to that of the ancient species. In the case of resurrecting the mammoth, Dr. Church said, the process would begin by taking a skin cell from an elephant and converting it to the embryonic state with a method developed last year by Dr. Shinya Yamanaka for reprogramming cells.

Asked if the mammoth project might indeed happen, Dr. Church said that “there is some enthusiasm for it,” although making zoos better did not outrank fixing the energy crisis on his priority list.

Dr. Schuster believes that museums could prove gold mines of ancient DNA because any animal remains containing keratin, from hooves to feathers, could hold enough DNA for the full genome to be recovered by the new sequencing machines.

The full genome of the Neanderthal, an ancient human species probably driven to extinction by the first modern humans that entered Europe some 45,000 years ago, is expected to be recovered shortly. If the mammoth can be resurrected, the same would be technically possible for Neanderthals.

But the process of genetically engineering a human genome into the Neanderthal version would probably raise many objections, as would several other aspects of such a project. “Catholic teaching opposes all human cloning, and all production of human beings in the laboratory, so I do not see how any of this could be ethically acceptable in humans,” said Richard Doerflinger, an official with the United States Conference of Catholic Bishops.

Dr. Church said there might be an alternative approach that would “alarm a minimal number of people.” The workaround would be to modify not a human genome but that of the chimpanzee, which is some 98 percent similar to that of people. The chimp’s genome would be progressively modified until close enough to that of Neanderthals, and the embryo brought to term in a chimpanzee.

“The big issue would be whether enough people felt that a chimp-Neanderthal hybrid would be acceptable, and that would be broadly discussed before anyone started to work on it,” Dr. Church said.



Supplemental material:

For a particularly crazed, unintentionally postmodern cinematic take on the breeding of chimeric manimals, rent yourself the DVD of John Frankenheimer's underrated 1996 version of The Island of Dr. Moreau, featuring the most over-the-top psycho-Brando ever (complete with his own mini-Brando homunculus), some extreme scenery chewing by Val Kilmer, David Thewlis somehow maintaining his composure throughout, and Ron Perlman as beast-man.

Honest Babe or Bape Star?

This morning's email brought the above from the folks at Adbusters. Pretty cool, I thought.

But then, maybe just because I am so much more cynical than them, I couldn't help but think in their effort to morph the Prez-elect with the Great Emancipator, they unintentionally managed to riff a very different (pop) cultural meme. Since they're Canadian, we'll give them one free pass for accidental racism.

The politics of apocalypse

The new issue of Reason has a very nice article, now online, about Tor Books and science fiction as a libertarian intellectual playground. With a compelling thread, I think, about the impact SF can have in introducing new ideas to the next generation:

Scratch a civil libertarian, and you’ll often find a 15-year-old who read a lot of Philip K. Dick. Ask a college guy protesting censorship at his student newspaper for his inspirations, and there’s a good chance Ray Bradbury’s Fahrenheit 451 will come up. Meet someone who thinks there might be an upside to anarchy, and you have probably found a girl who once read Ursula K. LeGuin’s The Dispossessed or a boy who loved Neal Stephenson’s Snow Crash.

“I suspect S.F. has an individualistic, antiauthoritarian trend to it not least because so many of the people who read and write it (not all by any means, but quite a few) are innerdirected introverts who make neither good leaders nor good followers,” emails Harry Turtledove, a best-selling author whose most famous novels pose questions about contingency in history and the importance of individual action. “Am I talking about myself? Well, now that you mention it, yes. But I ain’t the only one, not even close.”

Patrick Nielsen Hayden, the goateed and bespectacled Tor eminence who edited two of the house’s Prometheus finalists this year, draws a direct line between youthfulness and openness to libertarian ideas. “Young people read fiction to figure out how the world works,” he says, “and science fiction is an extremely effective, quick way of testing your views of how the world works.” Paraphrasing the late novelist and critic Thomas Disch, Hayden says, “Enormous quantities of science fiction and fantasy are about power, and who needs power fantasies more than teenagers, people who have a little bit of power for the first time in their lives and need to think about how power works?”

Topically, I had an interesting debate regarding the politics of mainstream post-apocalyptic scenarios with Matthew Bey Friday night (as we waited for the skronking horns of The Thing's "Viking Barbeque Jazz" at the 20th anniversary of the official lunch venue of the Turkey City Writer's Workshop, Ruby's BBQ (yes, they will mail it to you)). The discussion was queued by my wrestling with the issue in an essay-in-progress, with particular reference to my own adolescent immersion in a post-apocalyptic potpourri that even had me at one point mapping out the radioactive ruins of my hometown for a Gamma World scenario.

I postulated that the persistence of post-apocalyptic scenarios (as well as many disaster movies) expresses a latent yearning for the destruction of the state apparatus and the abolition of private property. At a deeper psychological level, I argued that the idea of roaming a depopulated earth rummaging for useful artifacts articulates the extent of our individual alienation in a thoroughly commodified society.

Matt had a different take on the private property aspect, contending that most-apocalyptic scenarios indulge libertarian fantasies. And that a credible Marxist reading would focus on the persistence in the stories of groups who obtain control over some scarce resource (think of the settlers in Mad Max 2/The Road Warrior) and use it as the base of their power over other survivors.

I suspect we are both right, and that post-apocalyptic scenarios, just like space operas and alternate histories and near-future dystopias, are perfect counterfactual playgrounds for experimental political theory.

Greed or Good

A while back I was sitting in the waiting area of the Veterans Administration Service office in Columbus, Georgia, and the conversation unfolding in that place was priceless. At the VA office, you arrive, sign in, and wait for a counselor to see you, with two or ten or twenty other people also waiting. I'm not a veteran; my mother is. She was a Master Sergeant in the Women's Army Corps and I was seeing the VA on her behalf. Others in the waiting room included widows, wives, and veterans of various vintages. They talked about Congress and other political figures; the economy that has ordinary people losing jobs and life savings while rich executives get golden parachutes; the length of wait in the VA office; Hurricanes Ike and Katrina (one of the waiting vets was a Mississippi native, his home community hard hit); the troubled state of the world; the length of the wait in the VA office; and the bankruptcy of Bill Heard Chevrolet, a company which originated in Columbus, had been headline news in Columbus for days, and was regarded in the VA waiting room as emblematic of larger issues.

There was a framed map of the world on the waiting room wall. One of the vets—a loquacious black man now employed as a barber—jumped up and ran his finger around the edge of the world map. "There's enough in this world," he said, "Enough for everyone, everywhere, except for greed!" His listeners nodded or said, "Mmmm—hmmm."

"Greed is good" is a famous line from the movie Wall Street. Greed regarded as good is how we got Wall Street's meltdown and worldwide casino capitalism in which everyone loses except the ultra rich. The greed-good equation created the perverted alchemy in which diamonds—marvels of the physical world—turn to blood because of the way they are mined and sold to fund wars. In another perverse alchemy, books—marvels of the imaginative world—become commodities, the commercially successful ones ground like wheat through the commercial mill, the unsuccessful ones thrown out like chaff. The same thing happens to music and visual arts.

Greed is one of the classical Seven Deadly Sins. (Lust, Gluttony, Greed, Sloth, Wrath, Envy, Pride.) In today's world greed may even be the worst of the lot. "The love of money is the root of all evil," said the Apostle Paul, without even having seen casino capitalism in action. Greed is not good. It's one pole of a perennial choice that faces most people and tribes, organizations and nations. The choice is greed OR good.

This nation had eight years of an administration that exemplified, enabled and exhorted greed. The restorative after 9-11 was go shopping, the stimulus to a faltering economy was a check for people to go buy stuff they don't need. The way to scratch a collective itch for war was to conquer an oil-rich country. Now the United States has to go in a new direction, staggering toward good instead of greed. The incoming administration has to attempt to steer the new course. Meanwhile we all have to choose between greed and good in our personal lives and cope with the fallout of bad choices that were outside of our control. And the ghosts of dead Iraqi civilians, drowned people in New Orleans, and extinct species, the ghosts of dead hopes and lost homes and defeated dreams, watch us during the day and whisper in our uneasily sleeping ears at night.

Kickoff time?

Technovelgy, an amazing site that tracks new ideas from science fiction, has picked up on a meme from my story "The Sun Also Explodes," included in Lou Anders' acclaimed new anthology Fast Forward 2. The new entry (including a short excerpt):

Ultimate Football League (UFL) — A football league without restrictions on human modification.

Crile scratched his silvery buzzcut, flexing a biceps that pulsed with the texture of manufactured tendons and polymerically enhanced blood vessels. He was one of the alpha generation of real celebrity cyborgs, a Texas star college quarterback who was among the first to go straight to the UFL.

The Ultimate Football League was the first to abandon professional athletics' anachronistic insistence on the prohibition of performance enhancements, be they pharmaceutical, biomechanical, or genetically engineered. It was a genius stroke by the founders. The audience was far more interested in superhuman performances than fidelity to nature, and the athletes were addicted to the potential of even greater power.

That's a wonderful memetic pickup for what was mainly included as backstory of a secondary character. Perhaps because it is so likely to actually happen, probably sooner than you think.

Yes we can (allow General Motors to die the death it deserves)

So, a week after the election, with the transition news settling into its Baby Boomer greatest hits groove, President-Elect Obama meets with President Bush. And uses the opportunity to ask Bush to bail out the big Detroit automakers. Is it okay to say, "WTF?"

To which the rejoinder might be, whaddaya want? The unions delivered big time for Obama all over the Rust Belt, as seen last Tuesday night, and probably made him prez. Which is okay, if we want to so quickly give the lie to the idea of a new politics. Because ideologically, it is hard to conceive anything more truly "conservative" one could do than preserve an ossified oligopoly of pre-World War II industrial conglomerates that have done more to damage the planet in the last 100 years than probably any other industry in the industrialized West. Along the way, killing basically all public transportation in America other than buses. You want me to pay my share of the losses of the people who bet their (and our) future on SUVs?

Granted, you are talking about 3 million jobs, $150 billion in personal income, and $60 billion in tax receipts in 2009. But there are plenty of other inefficient and outmoded businesses that won't survive the current credit crunch and consumer austerity. And don't deserve to.



The last American car I owned was a 1974 Chevrolet Caprice convertible that I sold in 1991. Since then, it's been an alternating mix of small cars from the leading Axis powers (that, and living walking distance to work or taking the bus). Driving to the coffee shop this morning, I was reminded why. I saw one of those new Chevy Malibus pulling into traffic. This is the car that is being widely touted as the hope for the future. Naturally, being a General Motors sedan produced after 1975, it is basically a mullet with wheels, as has been every American car I have rented in my adult life. The reason they are failing is because they so completely suck — as products, as businesses, as corporate citizens, as emblems of our American identity. (Unless you want a ranch-ready pickup, in which case they are right on the money.)



The only things the American automakers have really innovated in the past 30 years are (1) clever cupholders to holster the Big Gulps of saccharine and corn syrup that fuel the clotted vessels oxygenating our fat asses planted against the seat-heaters en route from our climate-controlled homes to our windowless cubes, and (2) televisions installed throughout the vehicle to anesthetize our mini-chubs with the latest sensory Soma from Disney. The Big Three are not our future.



The only hope for the American automotive industry is to allow Detroit to fail. Just as to bring back the healthy diversity within the soil you need to burn the ground cover clean, letting G.M., Chrysler and Ford and their earth-burning mega-cars collapse under their own weight will allow new transportation businesses to sprout, new businesses for a new era — people's versions of outfits like Tesla for those who want to drive, and news ways of moving us around that don't require navigating the on-ramp on insufficient stimulants. The pieces of Detroit that make sense will survive, sliced off through reorganizations that, like the hybrid lines and the utilitarian work vehicles (there will always be pickups and Town Cars).

And we will always have the ruins of Detroit, that American industrial Ozymandias monument whose own death has already been foretold in the urban shell of the city that once was.

Zeitgeist Level Cyber-Strategic Warfare

Prof. Nevin's upcoming paper on the deployment of post-Pentecostal Strategic Level Spiritual Warfare is well-timed, announced the same day as the Secret Service and the FBI revealed that they spent a large chunk of the summer fighting off foreign intelligence hacks of the internal computer systems of both major presidential campaigns. ArtVoice synthesizes:

Over the summer, the FBI had its hands full with simultaneous cyber crime investigations: the hacking of the Obama campaign computer system(s), and the hacking of the McCain campaign computer system(s). While the intrusions have been acknowledged, little else has been released or confirmed yet. At this point, it’s known for sure that the FBI was involved, that “a large number of files” were stolen from the Obama side, and that the attacks came from a “foreign entity” and definitely did not come from the opposing sides. The McCain campaign systems were intruded on in a similar fashion as the Obama systems, but the extent of the compromise on their side was unmentioned. The rest is speculation of course: security experts have suggested the attacks likely came from China or Russia, and anyone’s best guess is that the goal of such an intrusion was to gain an inside line on procedures and policies used by the campaigns for a leg up in future dealings with the to-be president.

This followed a report earlier in the week about successful hacks of the White House systems. From the Financial Times:

Chinese hackers have penetrated the White House computer network on multiple occasions, and obtained e-mails between government officials, a senior US official told the FT.

The cyber attackers managed to penetrate the White House system for brief periods that allowed them to steal information before US government experts each time patched the system.

US government cyber experts suspect the attacks were sponsored by the Chinese government, although they cannot say for definite.

“We are getting very targeted Chinese attacks so its stretches credulity that these are not directed by government-related organisations,” said the official.

The National Cyber Investigative Joint Task Force, a unit established in 2007 to tackle security, detected the attacks. The official stressed the hackers had accessed only the unclassified computer network, and not the more secure classified network.

“For a short period of time, they successfully breach a wall, and then you rebuild the wall . . . it is not as if they have continued access,” said the official. “It is constant cat and mouse on this stuff.”



Fortunately, it was also announced on election day that Jack Bauer will still be around to locate, detain and torture any Chinese hackers found infiltrating the White House of President Palmer, I mean Obama.

Not sure, though, what Jack and the rest of the California windbreaker warriors of CTU will do with the opportunistic wave of Obama-McCain spam. From NZ IT Brief:

Cyber crims have wasted no time in attempting to capitalise on world events with IT security and control firm Sophos warning about a new spam campaign that claims Barack Obama and John McCain have died.

Sophos says the email spam campaigns use sensational - if somewhat confused - subject lines masquerading as breaking news to promote an online Canadian pharmacy.

The ‘Breaking News:' subject lines include ‘Barak and McCane killed', ‘McCane died of heart stroke' and ‘McCane's wife private video'.



Dude, who wouldn't click on the Cindy McCain video link? No doubt like a cross between Ilsa She-Wolf of the SS and Chuck Norris' Missing in Action.

I anxiously await the arrival of her avatar in my in-box, dancing like some kind of warporn variation of the Leela virus from the opening of Hari Kunzru's brilliant Transmission:

SIGNAL

It was a simple message.

Hi. I saw this and thought of you.

Maybe you got a copy in your in-box, sent from an address you didn’t recognize; an innocuous two-line e-mail with an attachment.

leela.exe

Maybe you obeyed the instruction to

check it out!

and there she was; Leela Zahir, dancing in jerky QuickTime in a pop-up window on your screen. Even at that size you could see she was beautiful, this little pixelated dancer, smiling as the subject line promised, a radiant twenty-one-year-old smile

just for you.

That smile. The start of all your problems.

It was not as if you asked for Leela to come and break your heart. There you were, doing whatever you normally do online: filling in form fields, downloading porn, interacting, when suddenly up she flounced and everything went to pieces. For a moment, even in the midst of your panic, you probably felt special. Which was Leela’s talent. Making you believe it was all just for you.

But there were others. How many did she infect? Thousands? Tens, hundreds of thousands? Impossible to count. Experts have estimated her damage to global business at almost $50 billion, mostly in human and machine downtime, but financial calculation doesn’t capture the chaos of those days. During Leela’s brief period of misrule, normality was completely overturned. Lines of idle brokers chewed their nails in front of frozen screens. Network nodes winked out of existence like so many extinguished stars. For a few weeks she danced her way around the world, and disaster, like an overweight suburbanite in front of a workout video, followed every step.

Of course the whole thing made her famous, beyond even her mother’s wildest imaginings. Leela was already a rising star, India’s new dream girl, shinning up the greasy lingam of the Mumbai film world like the child in the conjurer’s rope trick. But while Leela’s mother had thought through most eventualities, she hadn’t factored the march of technology into her daughter’s career plan. Mrs. Zahir was decidedly not a technical person.

And so Leela found herself bewitched, the girl with the red shoes, cursed to dance on until her feet bled or the screen froze in messy blooms of ASCII text. Yet despite what her mother may have thought, she was a surface effect. The real action was taking place in the guts of the code: a cascade of operations, of iterations and deletions, an invisible contagion of ones and zeroes. Leela played holi, and her clinging sari diverted attention from the machinery at work under her skin.

A chain of cause and effect? Nothing so simple in Leela’s summer. It was a time of topological curiosities, loops and knots, never-ending strips of action and inside-out bottles of reaction so thoroughly confused that identifying a point of origin becomes almost impossible.

Morning through venetian blinds.

A cinema crowd watches a tear roll down a giant face.