Friday, March 28, 2003

Pew has a new issue on GM Wheat.
Hot Shit from Science
Enterococci, such as E. faecalis, are also prominent members of the GI tract microbial consortium. However, enterococci have gained notoriety because they can cause infections, primarily among hospitalized patients, that are extremely difficult to treat owing to antibiotic resistance. Strains of enterococci from GI tracts of healthy humans rarely carry genetic elements conferring additional antibiotic resistance or overt virulence. The most problematic enterococcal isolates from infected patients, namely those harboring genes for resistance to multiple antibiotics, appear to constitute a rogue subgroup of the species that, in addition to antibiotic resistance, has also acquired a number of genes conferring infectivity and virulence. Paulsen et al. report the genome sequence of such an infection-derived isolate of E. faecalis, strain V583, which caused the first vancomycin-resistant enterococcal infection reported in the United States.

As a multiple antibiotic-resistant clinical isolate, this strain was found to be replete with mobile DNA elements, many of implied foreign origin. These mobile DNA elements include a pathogenicity island--a large mobile genetic element consisting of a number of virulence-associated genes--a transposon carrying the complex of genes that mediate vancomycin resistance, three plasmids conferring resistance to other antibiotics, and a host of insertion sequences. These mobile elements constitute over a quarter of the genome of this strain. The occurrence of the pathogenicity island on the side of the chromosome opposite that of the vancomycin resistance transposon, as well as its occurrence in strains that predate the acquisition of vancomycin resistance, strongly suggest independent selection for antibiotic resistance and virulence traits.

[ref.s removed for clarity; cites: perspective: "The Thin Line Between Gut Commensal and Pathogen," Michael S. Gilmore and Joseph J. Ferretti, Science Mar 28 2003; report: "Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis," I. T. Paulsen, et al., Science Mar 28 2003: 2071-2074.]

In other microbial news, SARS hits Canada and Connecticut as panic spreads in HK.

Thursday, March 27, 2003

ag miscelleny
The new Economist sports a biotech survey, including this article on Ag Biotech... FAO publishes 8-part focus on Ag Biotech, and a summary of their gene flow e-conference... Even as congress discovers it doesn't want to play the globalization game if it can't win, the House Ag comittee whines about restraint of trade. We used to call it "whistling dixie" [#2] back in New England. Meanwhile another unelected transnational conspiracy prepares to determine our future by releasing their biotech update which menacingly says absolutely nothing.
Home of the Brave
Thousands seek Canadian asylum -- from the US. FBI interrogating Iraqi-American citizens.

UPDATE There's more: those foolish enough to continue to seek asylum are being detained for "national security" reasons.

Having had the misfortune of being awoken two days in a row by our fearless leader (a.k.a. the steely-eyed rocket man) attempting to wrap his mind around the sisyphean task of producing monosyllables in an order capable of generating meaning, I wonder if there isn't something wrong with him -- like some kind of neurological disorder. Seriously. It's like watching the special olympics -- like language is an enemy that he is struggling to subdue. Either that or the neural implant connecting him to the Trilateral commission Carlyle Group puppetmasters is on the fritz. Could you ever have imagined a speaker who made this one's father sound coherent? Memo to White House: joint press conferences with Tony Blair (or, indeeed, anyone who knows how to form a complete sentence in their native language) are not doing you any favors.

But far more disturbing than his neurological afflictions is his, and his handlers', utter ineptitude. I can't bear to count the ways, but some of the more obvious examples are killing people in Iraq at this moment: I know they did not have much time to process the important lessons of French and Indian War, but surely they could have learned something about those "dirty trick" guerillas. Then there was the widely trumpeted assertion that ground troops would be superfluous in encouraging "patriotic Iraqis" to "liberate" themselves. Because, you know, that worked out so well for them last time. You can add your own favorites. But unless you take long breaks from your busy internet-trolling schedule to read print media, you did not see this chilling litany of stupidity from Elsa Walsh's 3/24 New Yorker profile of Bandar bin Sultan:

On April 16th, the White House announced that Crown Prince Abdullah planned to visit Bush at his ranch in Crawford. The circumstances were not promising. Abdullah's opinion of Bush was increasingly unfavorable, and by this time Bush had begun to declare that one of his goals was "regime change" in Iraq. Saudi support was essential, but unless something was done about the Israeli-Palestinian conflict, the Saudis could not oppose another Arab country, not even Iraq.

On April 24th, the eve of the visit, Bandar received a private briefing from one of the President's senior officials: Bush, he was told, was unaware of what was happening in the streets of the West Bank or Gaza. "This guy doesn't watch TV-he just doesn't know this stuff," the official said, adding that Bush's aides, many of whom were staunchly pro-Israel, shielded him. Bandar was in a hotel in Houston preparing Abdullah for his meeting with Bush the next morning. Bandar wanted Bush to see what Arabs saw daily on Al Jazeera, hoping that it would open his eyes, and so his aides were trying to get photographs. Eventually, they were able to find some, mostly pictures of dead Palestinian children-a five-year-old with a bullet wound to his head, a child cut in half. He did not want to show the most gruesome; the purpose was not to make Bush sick.

Bandar knew that if Bush was unaware of views within the Arab world, he couldn't understand the impact that the Palestinian-Israeli conflict was having in the region. Already the trip was becoming something of a fiasco. On Abdullah's first day in Houston, the White House had faxed Bandar a draft of a proposed communique, to be released by the two leaders following their meeting, which seemed to place all the blame for the increase in violence on Arafat and the Palestinians. "This is ridiculous-this is unacceptable," Bandar said to an aide, and he picked up the phone to call Powell. The Secretary of State claimed that he hadn't seen the latest version, and had rejected previous drafts. The draft had come from Vice-President Cheney's office, the rationale being that Abdullah is the Vice-President of Saudi Arabia. Bandar faxed back his rejection to the White House and warned that Cheney should not under any circumstances give a copy of it to the Crown Prince....

Later, back at the ranch:
The meeting was scheduled to last twenty minutes, but Bush and Abdullah talked for two hours. At one point, the Crown Prince handed Bush the photographs of the dead Palestinian children. Do you think it's right? he asked. Bush appeared surprised by the photographs and his eyes seemed to well up. One person familiar with the conversation summarized Bush's comments: "I want peace. I don't want to see any people killed on both sides. I think God loves me. I think God loves the Palestinians. I think God loves the Israelis. We cannot allow this to continue." At one point, Bush told Abdullah that he believed Muslims and Israelis were all God's children and that God didn't want to see children from either side die. The meeting ended with both leaders promising to deliver the other side: Abdullah pledged to rein in Arafat and Bush to rein in Sharon.

Someone suggested a break for lunch. Before beginning to eat, Bush bowed his head and reached for Saud's hand. "Let us pray," he said. A look of panic came over the Crown Prince, who was unfamiliar with the Christian custom of saying grace before meals. "What is he doing?" he whispered to an aide sitting nearby. "What should I do?" Powell also looked stricken, as if he couldn't believe what Bush was saying in front of his Muslim guests.

Update: Predictably, some people have been dismayed by my religious bigotry. Fine, pray to your little statuette or whatever it is to smite me down. But I don't want my hatred of cretinous zealots to get in the way of the larger point, thus:

The point of posting this wasn't the so-called cheap shot of mocking Bush's idol-worship, though I am happy to do that; it was the utter foreign-policy incompetence of the adminstration. That is the litany of stupidity to which I referred. The part that I quoted gives two other examples of this -- the retarded fax Cheney sent to Bandar and Bush's unawareness that Palestinians are dying. No wonder he sleeps so well. The article details many comical fuckups along the way to alienating our fanatical friends on the peninsula. People don't seem to understand that everybody wants to get rid of Saddam [partially because he is not sufficiently fanatical], but the administration's incompetence has prevented them from helping us even covertly.

Full disclosure: "Abdullah later told others that he had been impressed with the seriousness of Bush's religious convictions." You can interpret that however you want.

Oh, Enron, I almost forgot that you stole $45 billion dollars from California. Luckily, skimble is here to remind me. As a taxpayer of this great state I happened to notice that this amount of money greatly exceeds our current budget deficit.

Now, as to the Municipal Utilities that skimble notes helping out our Texan raiders:

Although Texas companies have gained the most notoriety for their role in California's energy crisis, more evidence is emerging that the Los Angeles Department of Water and Power may have violated state regulations by profiting unfairly from trading practices.

DWP officials have denied gaming the market.

But a summary of sealed evidence filed with federal regulators this week by California officials said the DWP and several smaller municipal utilities were willing partners in a congestion scheme known as "Death Star." The ploy allegedly involved scheduling nonexistent transmissions to create the appearance of congestion so that utilities and power generators could collect payments to relieve it.

The report also said state investigators had uncovered evidence that the DWP cooperated with private power providers to hinder the detection of "ricochet" transactions, in which energy companies moved electricity back and forth across the state border to increase its price.

Meanwhile, a state Senate investigator disclosed on Tuesday that California's power grid operator reported to the state attorney general last summer that the DWP's ricochet trades violated state regulations against manipulating the electricity transmission market.

The July 23 report by the California Independent System Operator, which has not been released publicly, found that the Los Angeles utility aggravated congestion during the fall of 2000 by moving power to the Oregon border to inflate its price, said Scott Chavez, the consultant for the state Senate select committee on the energy crisis.

The system operator took no action against the DWP over the alleged violation but turned its report over to federal regulators as well as to the state attorney general, Chavez said.

Transcripts obtained by the committee appear to show DWP traders discussing ricochet activities.

In one transcript, a DWP trader coaches another firm's trader on how to describe a Nov. 11, 2000, transaction that had been rejected by Cal-ISO as a prohibited ricochet.

According to the transcript, the DWP bought 50 megawatt-hours from the unregulated trading arm of Pacific Gas & Electric Co. for $70 each, moved it to the Oregon border, then sold it back for $95 a megawatt-hour. The PG&E trader, in turn, sold it for $250, which was then the state price cap.

In the tape-recorded conversation, the DWP trader scolded the PG&E trader for saying PG&E bought the power "back" from DWP.

"Don't say 'back,' because back is a bad thing," the DWP trader said. "Just say, 'Listen -- I'm buying this from you.' "

When the other trader repeated the phrase again, the DWP trader interjected, "No -- I'm telling you not to say the word 'back!' "

Later he expanded: "It's very important that you're buying from me, you know, not this back stuff or whatever... It kind of throws problems into the issue."

DWP officials said they already had refuted the charges of market gaming in an independent audit completed last month and that they were aware of nothing new in this week's filing. The audit, by law firm VanNess Feldman, said that the trade described in the transcript was not an illegal ricochet designed to defeat price caps.

DWP officials say the power never left California and that the agency simply was selling capacity on its transmission line.

The law firm's report also said that the DWP "would not necessarily be aware" that its transmission capacity was being used for such ploys.

The state attorney general's office, two other state agencies and the state's two largest electric utilities filed the allegations against 70 energy companies and municipal utilities Monday with the Federal Energy Regulatory Commission. The coalition is seeking $9 billion in refunds for alleged electricity overcharges during the energy crisis.

The companies and municipal utilities are disputing the allegations. Even so, the inclusion of the DWP -- as well as utilities for Glendale, Pasadena, Anaheim and other cities -- is rekindling a debate about how municipal utilities should balance their responsibility to the state in an emergency with their charge to reap returns for their ratepayers....

As energy prices soared in the state, DWP officials announced a policy in late 2000 of providing power at only 15% above cost. But an internal audit the next year showed DWP made profits exceeding 50%.

The VanNess external audit last month attributed the discrepancy to the use of computer models, instead of real-time information, to establish power bids.

Morrow, who handled the Senate committee's investigation of municipal utilities, led an 18-month campaign to extract documents from the DWP, whose resistance he described as "shameless." DWP executives in June produced transcripts of trader conversations but left out damaging comments. DWP officials later conceded that their transcriber inadvertently omitted the remarks.

[Doug Smith, "DWP May Have Profited Unfairly From Energy Crisis," LA Times 3/5/03, part 3, p. 1, which you would have to pay to read if you didn't have access to Lexis-Nexis]

I guess I can't complain, considering how much money my retirement plan made off JEDI...

Wednesday, March 26, 2003

Your tax dollars at work [Post]
The Agriculture Department's settlement with a Texas company that mishandled gene-altered corn, portrayed three months ago as a stringent crackdown designed to send a message to other potential violators, actually involved a no-interest $3.5 million government loan that means American taxpayers will effectively subsidize cleanup efforts.

The payment terms, worth as much as $500,000 in interest and other savings to the company over the next three years, are contained in a document newly uncovered in government files by a Washington advocacy group. The Agriculture Department did not release the information at the time it announced the settlement with ProdiGene Inc. of College Station, Tex.

Alisa Harrison, spokeswoman for the Agriculture Department, said there was no intent to deceive the public. "It wasn't that we made a conscious decision not to release it," she said. "It didn't occur to us."

So we don't seem to be shocking and aweing anyone except some auto mechanics and casual bystanders -- and cable news commentators, some of whom became visibly aroused last night at the mention of "e-bombs" (it was on Fox, but it could have been anywhere). A friend of Neal Pollack's explains the reality behind the abstraction:
A year ago this month, I was sitting on a ridge in Afghanistan hunting down Al-Qaeda stragglers in a valley near the Pakistani boarder. As I sat watching the sun set over the mountains to my east, I couldn't help but admire the sheer size and majesty of one particular snow-capped mountain. It was certainly bigger than any "mountain" I had seen back home in East Tennessee and it stood out from the rest of the mountains.

And then I watched the mountain disappear.

A huge red fireball of flames and sparks and smoke shot up thousands of feet into the air where a B-52 had just dropped a giant "Daisy Cutter." The twilight darkness covering the valley highlighted the incredible size of the explosion.

My best friend, one of my squad leaders, was sitting by my side while we shared an MRE. We watched the explosion, sat transfixed for a few moments, and then stared at each other in disbelief.

"Holy fuck," I remember one of us stuttering.

That is one of our "small" fuel-air bombs.

Tuesday, March 25, 2003

James Capozzola writes of the striking resemblance of the end of the Roman Republic to our own times, by which I assume he primarily means the evisceration of any function from the Senate except servility to the emerging executive power. While this is true, on some level, and interesting, it is important to bear in mind the difference between our own Senate and the Romans'. The latter was effectively a hereditary plutocracy which dealt with domestic policy by noblesse oblige and foreign conquest as a source of personal enrichment. (Ok, that last part sounds familiar). Not only was the Senate not representative, it was not supposed to be; in fact the Senate's whole purpose was to preserve its members' prosperity at the expense of everyone else. Actual slaves were often better off than the allegedly free masses who comprised the "clients" of the senators. Rome makes Brazil look like a workers paradise. The Senators who wrote Roman history (Cicero, Tacitus) were pissed off about the appropriation of their power by dictators, and therefore told the story in terms of tyranny vs. freedom. But they're talking about the freedom of a few hundred men.

That said, there are indeed obvious similarities in the current transformation of the Congress into a freedom-frying formality (Tom Paine, Kinsley, Kennan), which is why Sen. Byrd has been frothing at the mouth for months now -- a good example, because Byrd is primarily interested in preserving his august body's prerogatives. Something else worth considering is that the Roman Senate disintegrated not only because of tyrannical ambition, but because it didn't work any more -- it was incapable of administering an increasingly unwieldy empire.

Read: Syme, Roman Revolution, Gruen, Last Generation of the Roman Republic, Tacitus, Annals

More black humor foiled in advance: taking a pass on the "elite Polish forces," I was planning to make a joke about the Navy's trained dolphins, but Alternet reports that Morocco has in fact offered to send trained monkeys.

Monday, March 24, 2003

Outrage
I go away for a week and Adrian fucking Brody wins best actor? What the fuck were you thinking? No, the real outrage was Butler's shameful treatment of Rick Pitino yesterday.

It's hard to come up with something funny to say with people dying like this, so I'll just leave it. But lest I be misunderstood, the point is that most americans are not going to give a shit about this until it interferes with their constant stream of opiates, instead of merely augmenting it with war porn. Go get news at the agonist if you can stomach it.

Lesser landmarks on the road to apocalypse include: spreading mystery virus; more Halliburton profiteering details -- skimble has more; Chapela tenure review conflict of interest...

Friday, March 14, 2003

So long, stinktown
I'm leaving the country. Try to get off your knees before I get back.

Consider yourselves lucky to be spared my incisive commentary on Nature's proteomics "web focus" [free access].

On the other hand,
Why don't you stick to fries, you cretinous douchebags.
"I don't understand," said Senator Peter G. Fitzgerald, Republican of Illinois, "how those who can hear the howl of a wolf or the squeal of a dolphin can be deaf to the cry of an unborn child."
[Tom | Lisa | Kos]

Give all your money to NARAL before it's too late.

Wednesday, March 12, 2003

Chet Raymo writes intelligently about GM Food in yesterday's Globe.
We will win the war with Floridian fuel-air bombs and ham radio.

We will need our advanced technology to take out the menacing drone.

Food
The fact that the House cafeteria introduced "freedom fries" yesterday is too monumentally stupid to merit comment. How I long for the days when our duly elected douchebags bothered to pretend that they had something important to do.

The Chron's food section is entirely devoted to lipids today, and if you bother to read it, it will say, I can only imagine, that every single "nutritionist" is full of shit. Knowing the Chron, they'll probably fuck it up.

Someone named Mike Steinberger mocked the Olympian pronouncecments occasioned by Loiseau's suicide in Slate

It's not a little ironic that Bocuse has been doing most of the finger-pointing during the past week, since no one has prospered more than he from Michelin's imprimatur. Initially awarded three stars in 1965, he was the first chef to use the guide's stamp of approval as a ticket to universal celebrity, becoming a globe-trotting icon with lucrative consulting and endorsement deals.
Fair enough. But then he goes on, with unwitting irony, to compare Michelin to the Olympics. It's important to have standards, I guess, but the systematic fetishization of the absurd extravagances of haute cuisine is possibly even worse than Zagat's relentless assault on the lowest common denominator.

via Sauté Wednesday, which also has a nice appreciation of Steingarten's latest.

Speaking of which, the Times fawns over Hélène Darroze, who just got her second star, for serving carrots with confit. Incroyable!

This can't be a good sign [NYT]:

HEIR TO AUSTRIAN THRONE IS SLAIN WITH HIS WIFE BY A BOSNIAN YOUTH TO AVENGE SEIZURE OF HIS COUNTRY

Francis Ferdinand Shot During State Visit to Sarajevo.

TWO ATTACKS IN A DAY

Archduke Saves His Life First Time By Knocking Aside a Bomb Hurled at Auto.

SLAIN IN SECOND ATTEMPT

Lad Dashes at Car as the Royal Couple Returns from Town Hall and Kills Both of Them.

LAID TO A SERVIAN PLOT

Heir warned Not to Go to Bosnia, Where Populace Met Him with Servian Flags.

AGED EMPEROR IS STRICKEN

Shock of Tragedy Prostrates Francis Joseph -- Young Assassin Proud of His Crime.

[I have a pdf of the front page, if you want it].

Farmers beg the USDA to perform a glaringly obvious impact statement to find out how much money they'll lose when Roundup-Ready wheat is introduced [Cropchoice | Reuters].

UPDATE [3/13]: Looks like Iowa State already did it [Reuters]:

"Important market indicators point to a high risk that up to 30 to 50 percent of the foreign market for U.S. HRS wheat and even more of the U.S. durum wheat exports could be lost if HRS GMO wheat is introduced into the U.S. now or in the next two to six years," the report states.

The study estimated that prices will drop at least 32 percent for hard red spring wheat as it would move into animal feed marketing channels.

Tuesday, March 11, 2003

ahem. back to business:
The Rockefeller Foundation, Monsanto, DuPont, Syngenta and Dow establish new foundation to improve African agriculture based on donated patents [Post].

NRDC et al. sue gov't over new factory farm "effluent"rules [ENS].

Department of Stupidity
Notwithstanding the recent (conservative) estimate that 85% of people are morons, the level of stupidity revealed by Jane Mayer's NewYorker article* on Jihad Johnny Walker was disturbing. The astonishing stupidity of Mr. Walker was always apparent by his actions (though it doesn't mean other stupid people should beat him), so one was (somewhat) prepared for his shock and dismay at learning that he was a stooge for the expansionists fantasies of the ISI instead of a martyr for the coming theocratic paradise in Kashmir. But the waves of stupidity that swirled around him, from the "intelligence" "analyst" who did not understand the words "al-Ansar" while he was interrogating Walker, so simply replaced them with "al-Qaeda", to the Justice Dept. hacks who based their prosecution on that interrogation, destroyed internal documents pointing out the manifold stupidities of the prosecutions approach, then fired and crudely intimidated the only woman smart enough to protest -- this stupidity seems unbelievable, unacceptable in the career professionals on whom we must increasingly rely to get anything substantial done by our government. We all know about the theocratic thuggery of the boss, but doesn't he have professional lawyers to actually execute the law, or whatever it is they do? Or were all the competent people working on those crucial bong cases?

Ashcroft's stupidity springs from the same source as Johnny's, namely, religion -- and the latter's is only a predictable perversion of that American "moral compass" that has always plagued us, described by Simon Schama in the very same issue of the New Yorker:

�If there be an object truly ridiculous in nature, it is an American patriot, signing resolutions of independency with the one hand, and with the other brandishing a whip over his affrighted slaves.� After the Civil War, European critics pointed to the unprotected laborers in mines and factories as industrial helots. Just as obnoxious as the fraud of liberty was the fraud of Christian piety, a finger-jabbing rectitude incapable of asserting a policy without invoking the Deity as a co-sponsor. This hallelujah Republic was a bedlam of hymns and hosannas, but the only true church was the church of the Dollar Almighty. And how could the cult of individualism be taken seriously when it had produced a society that set such great store by conformity?
Attention fanatical douchebags: the American Revolution was the fruit of the enlightenment, which means that our sham republic is supposed to represent the application of reason to public life. However provincial and hypocritical our american enlightenment, however discredited and forlorn its ideal of reason, the puerile cruelty and simplistic chiliasm of the crimes against humanity that constitute your contribution to our society make Jefferson look like Mahatma fucking Gandhi. Your "belief" "system" is a bankrupt fraud, which is too bad because there is no hell to torment you for eternity. Except the one you're about to unleash on the rest of us.**

* Published in the New Yorker (home of terrorists like Sy Hersh) -- not online, but see this TalkLeft description -- and I've been waiting for it to pop up on Lexis-Nexis, but it hasn't, and presumably won't, so the details above are dredged from memory.

** If you didn't hear Col. Mike Turner on NPR this morning, lucidly describing the end-times shitstorm we're about to unleash, listen to it now.

Why Zagat sucks (aside from relying on the opinions of the star-fucker unwashed): they censor the best comments, like
If you were on fire, they wouldn't even throw a drink on you

I cannot give credit to [this place] other than to praise them for hiring the mentally handicapped

[Via Gawker, which also reports on an unspeakable Puma ad campaign that is cerainly fake, whatever may seem plausible in NYC].

Monday, March 10, 2003

FoodRoutes points out some problems with that StarLink settlement:
"As best I can tell," says one knowledgeable source, "the attorneys on both sides worked out this deal without letting any farmer be part of the discussions."

Second, the amount of money contained in the settlement appears to less than actual damages incurred by non-StarLink growers. Farmers, including some who had outside attorneys review the proposed settlement, say the money they will receive amounts to "a penny a bushel or maybe $1 per acre" in damages.

Anecdotal evidence, says one farmer, points to actual market damages of "more than 15-cents a bushel and maybe as much as 40-cents a bushel." Another farmer notes that farmers who grew StarLink "got 25-cents a bushel from Aventis, but we who didn't grow it are going to get just a fraction of that amount. It's not right."

Further down the page, the pork and beef checkoff cases head to appeals court [background].
Another avian influenza outbreak in the Netherlands [ScienceNOW -- don't know if this requires a subscription, but feel free to tell me].

Friday, March 07, 2003

Holy shit: Skimble reports, from the WSJ, that Halliburton "lost" the Nigerian "radioactive material".
trans-atlantic relations
J forwards this sweet popup from the Hotel Sainte-Beuve's homepage:
Dear American Friends,

These last few months, politicians and the mass media on both sides of the Atlantic have been bashing us with two versions of the same story: Frenchies are arrogant traitors poking America in the eye! Americans are a bunch of war-happy loonies looking for world domination!

Baloney.

Folks, let's put the show on hold, and think together for a minute: who is holding the microphone for dear life, and pounding the message with a tremendous whack?

Not you, not us. Not the little people. But journalists and politicians.

Politicians will always put their own interests before yours - remember 'Follow the money trail' - and journalists love the sound of their own voices, and a good controversy - whether rooted in fact, or totally fabricated....

The truth is we, French people, like American folks. Beyond our pride of being French, we greatly admire the American people. We always have.

Over the years, we took notice of your commendable efforts to speak French. Yes, some of us won't tell you, but we generally appreciate your efforts to address us in our language. We also try to better our English skills (please don't laugh at our accent).

We appreciate your polite, non-intrusive behavior when you come to visit. We cannot say that all of us Frenchies behave as well when we visit you. We gotta try harder.

All of us who have travelled abroad know that the cultural differences which exist between Americans and Frenchies can be resolved with a smile and a good word. There cannot be any lasting misunderstanding between two peoples of goodwill.

You are very welcome in our country. We have many good things to offer, we hope some of them appeal to your hearts and interests.

You are welcome in France. Don't listen to tall tales to the contrary. We the people are not our 'governing elites'. You folks are not your government or the press.

Let's remain friends.

Grovelling frog. I mean, lets go to Paris!
Connecticut quarantines 4.7 million chickens for avian influenza:
Gresczyk would not disclose the name of the farm, but the apparent outbreak occurred at Kofkoff Egg Farm, said Michael Darre, a state poultry specialist and animal science professor at the University of Connecticut. The farm controls more than 90 percent of the state's egg market and produces 12 million eggs every week.
Thus proving the value of factory farming.

Meanwhile, a really scary bug in HK [Science]

Last month in Hong Kong, a 33-year-old man died and his 9-year-old son fell seriously ill after contracting an avian influenza virus from a source that remains mysterious.

Initial genetic sequencing suggests that the virus may be descended from one found in wild birds. If so, it could be difficult to contain. In all previously known cases of an avian flu jumping to humans, the source is believed to have been poultry. But "this virus hasn't been seen in domestic poultry," says Robert Webster, director of the World Health Organization's (WHO's) collaborating laboratory on animal influenza at St. Jude Children's Research Hospital in Memphis, Tennessee. However, authorities have not ruled out the possibility that the virus came from chickens on a relative's farm in mainland China.

Most flu viruses are adapted for a particular group of animals, although pigs can mix and match viruses from birds and humans. And on seemingly rare occasions, flu viruses have jumped the species barrier from other animals to humans. The last two human influenza pandemics, or worldwide flu epidemics, were caused by viruses that incorporated both human and avian flu genes. Because humans have no immunity to many strains of avian influenza, such viruses have deadly potential if they acquire the ability to infect human cells and move easily from one human host to another. However, Hong Kong health officials say that thus far there is no indication that the latest avian virus can spread from person to person.

All the same, WHO has declared an influenza alert, and its collaborating laboratories have moved into high gear. "We don't know what the consequence of this virus will be. I wouldn't trust it," says Webster. He points out that in the most similar case known--an avian influenza virus that jumped from chickens to humans in 1997, infecting 18 people in Hong Kong and killing six--there was a 6-month lag between the first death and those that followed.

Further complicating the current case is the fact that the Hong Kong family had recently visited relatives who keep chickens in Fujian Province in mainland China. The man's 8-year-old daughter died from an undiagnosed respiratory infection while there. And the deaths in this family coincide with an unidentified virus sweeping nearby Guangdong Province, infecting more than 500 people and killing at least seven. Researchers aren't sure if the family has the same illness as those in Guangdong. Webster says the nature of the Guangdong outbreak is still unknown, but "WHO has a team investigating there now."

The virus in the 1997 avian flu outbreak, labeled H5N1 for the particular forms of its surface molecules ("H" stands for hemagglutinin and "N" for neuraminidase), didn't spread beyond those who'd had direct contact with infected birds. All 1.4 million chickens in Hong Kong were slaughtered with the hope of stamping out the virus (Science, 16 January 1998, pp. 324 and 393). But despite the massive slaughter, the virus survived--perhaps in backyard poultry or in other domestic or wild bird hosts--and has continued to evolve. The latest virus, also an H5N1 subtype, is believed to be its most recent descendant.

And it ain't just the birds [also Science]
It seems that after years of stability, the North American swine flu virus has jumped onto an evolutionary fast track, churning out variants every year. Changes in animal husbandry, including increased vaccination, may be spurring this evolutionary surge. And researchers say that the resulting slew of dramatically different swine flu viruses could spell danger for humans, too. The evolving swine flu "increases the likelihood that a novel virus will arise that is transmissible among humans," says Richard Webby, a molecular virologist at St. Jude Children's Research Hospital in Memphis, Tennessee....

Most genetic changes in the flu viruses--human, pig, and bird--are small and subtle point mutations in the virus's RNA. Less common but more alarming are sudden, wholesale changes that replace entire genes and are more likely to circumvent the immune system. This process, called genetic shift, is exactly what is now occurring in North American pigs. Thus, the latest swine influenza virus is a curious hybrid: The genes that code for its coat proteins derive from classical swine influenza, but half of its internal genes have been snatched whole from avian and human viruses.

The structure of the influenza virus lends itself to such radical changes. The virus is made of eight single-stranded segments of RNA that together code for 10 proteins (see illustration). If two or more different viruses infect the same host cell, they can swap segments, creating new viral types....

The "classical" swine influenza virus discovered in 1931 is an H1N1 virus, related to the H1N1 that caused the 1918 pandemic. But in the past 5 years, a quick succession of progeny, which now include at least three additional virus subtypes and four genotypes, have all but supplanted that classical swine virus in North American pigs.

The first new virus, the one that struck the North Carolina hogs in 1998, was an H3N2; in this case, genes had crossed from human viruses to pig viruses. By late 1999, the novel viruses could be found wherever there were pigs in North America and so were presumably spread by cross-country transport. Webby and St. Jude colleague Robert Webster, together with Olsen and others at UW Madison, traced these viruses' evolutions. They found both "double reassortant" viruses, with human and swine flu genes, and "triple reassortants," containing genes from human, swine, and avian influenza viruses....

In the past decade, big swine producers have gotten bigger, and many small producers have gone out of business. The percentage of farms with 5000 or more animals surged from 18% in 1993 to 53% in 2002, according to Rodger Ott, an agricultural statistician at the National Agricultural Statistics Service in Washington, D.C. Having more pigs under one roof makes it more likely that a rogue virus can take hold. "With a group of 5000 animals, if a novel virus shows up, it will have more opportunity to replicate and potentially spread than in a group of 100 pigs on a small farm," Rossow says. On the other hand, pigs in outside pens, as is common on small farms, can be exposed to the droppings of migratory waterfowl, which may contain infectious viruses; large-scale confinement agriculture may prevent such exposure, points out Liz Wagstrom, director of veterinary science at the National Pork Board in Clive, Iowa.

Another crucial change has been the recent wide-scale vaccination for swine influenza. In less than a decade, vaccination has become the norm for breeding sows, which in turn pass their maternal antibodies on to their progeny. In 1995, swine flu vaccination was so new that the National Swine Survey conducted by the United States Department of Agriculture didn't bother to assess its extent. In 2000, the same survey showed that 44.1% of breeding females received a vaccine. Today, more than half of all sows are vaccinated against both H1N1 and H3N2 viruses, says Robyn Fleck, a veterinarian at Schering-Plough, one of the nation's three producers of swine influenza vaccine. But the vaccine is not protecting against all new strains. "We're seeing clinical disease in vaccinated pigs," says Rossow. Flu is also showing up in piglets thought to be protected by maternal antibodies passed on from vaccinated sows, such as those on the Minnesota farm.

Widespread vaccination may actually be selecting for new viral types...

It gets worse, so much worse, but in the interest of supporting the Digital Millennium Cpoyright Act and The American Academy for the Advancement of Science, I'm going to truncate the story here. Both stories written by Bernice Wuethrich, by the way.
I've stopped noting every time Krugman writes an editorial because I figure all of you should be reading it automatically, but just in case you forgot today:
Last week The Economist quoted an American diplomat who warned that if Mexico didn't vote for a U.S. resolution it could "stir up feelings" against Mexicans in the United States. He compared the situation to that of Japanese-Americans who were interned after 1941, and wondered whether Mexico "wants to stir the fires of jingoism during a war."

Incredible stuff, but easy to dismiss as long as the diplomat was unidentified. Then came President Bush's Monday interview with Copley News Service. He alluded to the possibility of reprisals if Mexico didn't vote America's way, saying, "I don't expect there to be significant retribution from the government" � emphasizing the word "government." He then went on to suggest that there might, however, be a reaction from other quarters, citing "an interesting phenomena taking place here in America about the French . . . a backlash against the French, not stirred up by anybody except the people."

And Mr. Bush then said that if Mexico or other countries oppose the United States, "there will be a certain sense of discipline."

All you corn farmers who read this page need to mosey over to this site to get in on the Starlink class-action settlement.
Maybe Iowans should privatize their investments [NYT]
USDA announces (slightly less crippling than necessary) new rules, as predicted in the immediately preceeding post:
The rules do not outlaw biopharming in the heart of the Corn Belt. The biotechnology industry had proposed that idea, but Midwest politicians opposed it, saying it would deny farmers an opportunity to grow what could be lucrative crops.

Ms. Smith said increasing the distance between pharmaceutical and conventional crops would make it much less practical to grow such corn in the Corn Belt. Corn with pharmaceuticals that is allowed to pollinate freely will have to be kept one mile from other corn, double the previously required distance.

Thursday, March 06, 2003

Eternal vigilance...
The Des Moines Register finally realizes that Iowa has a $25 million stake in ProdiGene:
Regardless of where the crops are grown, the fund hopes to use the leverage of its financial stake in ProdiGene to get some of the company's research and processing done in Iowa, said officials with the fund.
That sounds like a good idea, considering how successful they've been. And there are no questions about legality or crippling regulation to worry about. I guess Iowans don't have the compunctions of this Colorado farmer, who recently wrote to his legislature:
[T]he US GMO regulatory system, which describes itself as being transparent, is about as transparent as a brick wall. Because it won't tell us the precise location of field trials and production fields of drug and chemical crops, nor will it tell us the precise nature of those crops (what they are modified to produce), we farmers do not have the right to know such crops are in our neighborhoods and what they might be producing.

This is appalling! Is our regulatory system supposed to operate in secrecy?

The biotech companies and the regulators say there are concerned about vandals and protecting "confidential business information." Well, how about protecting farmers growing ordinary crops? While I know of no farmers who would vandalize someone else's crops, I do many who would at least like to know that the growers of such crops have adequate liability insurance to cover any damages from contamination.

Which legislature, by the way, presumably has better things to do than sink $25 million of taxpayer money into companies like Prodigene. You have to respect the guy for being appalled, as opposed to unsurprised, which is about all I can muster.
Lots of news today:
1.
The San Diego biotechnology company Diversa has received government approval to market a feed additive the company says will make poultry and swine waste less offensive, at least to the environment....

The enzyme allows the livestock to digest phosphorous that occurs naturally in feed but cannot be broken down in the animals' systems, Short said. If the feed is not treated with digestion-aiding enzymes, farmers often add a supplemental phosphorous that can be digested to the livestock's food.

But adding more phosphorous to the front end means more at the tail end....

Agricultural products such as Phyzyme XP can get to market much faster than pharmaceuticals, which can take more than a decade to develop and cost hundreds of millions of dollars.

Phyzyme XP made it to market eight months after the application was submitted to federal regulators.

[SDU-T via Corante]

2. In the continuing saga of of the WTO case against Europe over GM food, xenophobe trade rep. Robert Zoellick was badgered by the bigger rednecks on the Senate finance committee [FT]:

Charles Grassley, the Republican committee chairman, said he was "profoundly disappointed" that the administration had not brought a WTO case against the European Union's moratorium on approving new biotechnology products. US farmers say the ban costs them about $300m (�192m, �276m) in lost sales to Europe. "The status quo in this area is totally unacceptable," he said. "The administration must do something and do it soon."
[I have refrained from posting the endless non-stories on this for some time, because the case has been dead in the water for over a month, which various zealots and crazy people just can't seem to accept.]

3. University of Rochester lost a huge patent suit covering Celebrex, among other things [NYT; academic IP background below]

"While courts are comfortable with narrow patents, there is widespread interest among research universities in ensuring that our broader, more basic research work is likewise protected by the nation's patent laws," Thomas H. Jackson, the university's president, said in a statement.
Annals of Bad Taste
James Stewart's article on Kozlowski in the 2/17 New Yorker quotes a description of the infamous Sardinian birthday party from a Tyco email:
Guests arrive at the club starting at 7:15 p.m. The van pulls up to the main entrance. Two gladiators are standing next to the door, one opens the door, the other helps the guests. We have a lion or horse with a chariot for shock value. The guests proceed through the two rooms. We have gladiators standing guard every couple feet and they are lining the way. The guests come into the pool area, the band is playing, they are dressed in elegant chic. Big ice sculpture of David, lots of shellfish and caviar at his feet. A waiter is pouring Stoli vodka into his back so it comes out his penis into a crystal glass. Waiters are passing cocktails in chalices. They are dressed in linen togas with fig wreath on head. A full bar with fabulous linens. The pool has floating candles and flowers. We have rented fig trees with tiny lights everywhere to fill some space. 8:30 the waiters instruct that dinner is served. We all walk up to the loggia. The tables are all family style with the main table in front. The tables have incredible linens with chalices as wineglasses. The food is brought out course by course, family style, lots of wine, and it's starting to get dark. Everyone is nicely buzzed, LDK [L. Dennis Kozlowski] gets up and has a toast for K [Karen]. Everyone is jumping from table to table. E Cliff has continued to play light music through dinner. They kick it up a bit. We start the show of pictures on the screen, great background music in sync with the slides. At the end Elvis is on the screen wishing K a Happy Birthday and apologizing that he could not make it. It starts to fade and Elvis is on stage and starts singing happy birthday with the Swingdogs [a Nantucket band often hired for Tyco events]. A huge cake is brought out with the waiters in togas singing and holding the cake up for all to see. The tits explode. Elvis kicks it in full throttle. Waiters are passing wine, after dinner drinks, and there is dancing. 11:30 light show starts. HBK [Happy Birthday Karen] is displayed on mountain, fireworks coming from both ends of the golf course in sync with music. Swingdogs start up and the night is young.
Stoli?
Would it be less offensive if these assholes weren't funding such comically nouveau riche excesses with our pension plans?

[Actually, I guess we have to blame the Stoli on the shortcomings of the New Hampshire State Liquour Store. Elvis is another story.]

Wednesday, March 05, 2003

Pew has a debate on IP issues in biotech.
Technical shit
New Nature article measures the movement of chloroplast DNA into the cell nucleus:
Thus, we provide a quantitative estimate of one transposition event in about 16,000 pollen grains for the frequency of transfer of cpDNA to the nucleus. In addition to its evident role in organellar evolution, transposition of cpDNA to the nucleus in tobacco occurs at a rate that must have significant consequences for existing nuclear genes.
Also, "Nature this week finds itself in the unenviable (and unprecedented) position of formally retracting seven papers".[history]

Using gene silencing to eradicate pests in New Scientist, which also reports:

The MRSA bacterium, or methicillin-resistant Staphylococcus aureus, can be resistant to many antibiotics. It has long been a serious problem in hospitals and nursing homes, where it infects the wounds of patients weakened by disease or injury. But it now appears that a new strain is emerging that spreads through skin contact and can even infect healthy people.
In the latest Journal of Agricultural and Food Chemistry: Spanish scientists use PCR to detect fraudulent meats in foie gras; the last issue's article showing that organic fruit and vegetables are healthier than conventionally-grown is starting to get some play (specifically, "total phenolic levels" were ~ 15-60% higher). This is presented as a health issue, but let's also consider that these phenolic compounds include flavonols, which, unsurprisingly, affect the taste.

Monday, March 03, 2003

Justin Gillis's Post article on the demise of Prodigene's CEO featured this priceless line
[Board member] Thomas L. Steen.... said the board was seeking a chief executive with extensive experience in complying with government regulations on pharmaceutical production, experience that Laos did not have.
Evidently.

He sneaks this bombshell in later:

Steen acknowledged that some money invested in ProdiGene -- he would not say how much -- came from a state-sponsored agricultural fund in Iowa that he helps run. It is, in other words, Iowa taxpayers' money.

This fact, known to some people in Iowa but not to those in Washington who have been following the issue, raises the question of whether ProdiGene will be free to pull its production out of Iowa if that turns out to be the safest way to grow pharmaceutical corn.

Nature Biotechnology publishes a proposal for "DNA barcoding." The authors have this to say about potential undesireable effects:
It is evident that adding a noncoding, technical label to a transgene is unlikely to have important biological consequences for the GM organism, in that there should be no increased mutability (in particular no recombination hotspots within the technical label or the "linker" between the label and the transgene), no effect of the label on the stability or expression of the transgene per se, and no changes in overall biological fitness of the organism.

To avoid a functional conflict defined early by von Neumann in his theory of self-replicating automata, the proposed information message would be placed outside of the transgene itself; alternatively, it can be placed on an intron inside the linear molecule of the transgene. To remain linked to the transgene during organism reproduction, the DNA encoding the accompanying technical message has to be closely or directly linked to the transgene DNA, a requirement that is easy to accommodate without complicating the engineering process. Given the rate of genome evolution of multicellular organisms such as animals and plants, such a linkage will certainly be maintained for a technologically relevant period of time, provided the added segment has been engineered so as not to cause increased recombination.

To avoid any serious effect of the label on the neighboring transgene or the organism itself, the introduced segment should be engineered without the use of sequences that are known as mutation hotspots (repeats, palindromes, recombination sites, etc.) or transcription elements ("hairpins" affecting transcription, enhancers, etc.). Ultimate proof will most likely be gained only through a practical evaluation of the specific label sequences.

With regard to the potential biological implications of introducing an additional DNA fragment into an organism, we see no obvious negative consequences. The added DNA fragment of proposed size (300 or so nucleotides) will increase the total length of the DNA construct to be integrated into an organism's genome by no more than 10-20%. Unlike accompanying selectable or phenotypic markers used for genetic transformation, it does not contain information expressed by the organism, and in this regard, it should be as harmless as other noncoding DNA that is abundant in genomes of most eukaryotes.

So we'll have to see.
Do you think it ever occurred to the douchebag trying to genetically engineer non-allergenic prawns that making his work useful would require altering the entire population of a wild species to make it more digestible to humans? Probably won't be a problem, since prawns are on the low end of practically every marine food chain that we're decimating from the top down.
You have a problem:
A billion-dollars-worth of beef gets thrown away every year by U.S. supermarkets, say meat industry experts. It happens because beef that sits in the meatcase too long, exposed to the natural atmosphere, begins to lose its bright cherry-red color, and turns brown. This natural oxidation process doesn't necessarily mean there's anything wrong with the meat, but health-conscious consumers will likely pick over it in favor of something that looks fresher. Eventually, the discolored meat gets thrown out � at a billion-dollar loss!
Is the solution to stop shipping slaughterhouse-packed subprimals straight to the market? No (it would raise supermarket labor costs intolerably if they had to retain skilled workers who knew anything about meat); instead we are going to force-feed the cows vitamin E at the feedlot, then use modified atmosphere packaging to "give the meat a few extra days to find a shopper."

Hungry?

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