Thursday, May 28, 2015

Pathological science journalism: chocolate edition

Science journalist John Bohannon reports on an experiment he conducted. On science journalists.
“Slim by Chocolate!” the headlines blared. A team of German researchers had found that people on a low-carb diet lost weight 10 percent faster if they ate a chocolate bar every day. It made the front page of Bild, Europe’s largest daily newspaper, just beneath their update about the Germanwings crash. From there, it ricocheted around the internet and beyond, making news in more than 20 countries and half a dozen languages. It was discussed on television news shows. It appeared in glossy print, most recently in the June issue of Shape magazine (“Why You Must Eat Chocolate Daily”, page 128). Not only does chocolate accelerate weight loss, the study found, but it leads to healthier cholesterol levels and overall increased well-being. The Bild story quotes the study’s lead author, Johannes Bohannon, Ph.D., research director of the Institute of Diet and Health: “The best part is you can buy chocolate everywhere.”
I am Johannes Bohannon, Ph.D. Well, actually my name is John, and I’m a journalist. I do have a Ph.D., but it’s in the molecular biology of bacteria, not humans. The Institute of Diet and Health? That’s nothing more than a website.
Other than those fibs, the study was 100 percent authentic. My colleagues and I recruited actual human subjects in Germany. We ran an actual clinical trial, with subjects randomly assigned to different diet regimes. And the statistically significant benefits of chocolate that we reported are based on the actual data. It was, in fact, a fairly typical study for the field of diet research. Which is to say: It was terrible science. The results are meaningless, and the health claims that the media blasted out to millions of people around the world are utterly unfounded.
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Here’s a dirty little science secret: If you measure a large number of things about a small number of people, you are almost guaranteed to get a “statistically significant” result. Our study included 18 different measurements—weight, cholesterol, sodium, blood protein levels, sleep quality, well-being, etc.—from 15 people. (One subject was dropped.) That study design is a recipe for false positives.
Think of the measurements as lottery tickets. Each one has a small chance of paying off in the form of a “significant” result that we can spin a story around and sell to the media. The more tickets you buy, the more likely you are to win. We didn’t know exactly what would pan out—the headline could have been that chocolate improves sleep or lowers blood pressure—but we knew our chances of getting at least one “statistically significant” result were pretty good.
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 It was time to share our scientific breakthrough with the world. We needed to get our study published pronto, but since it was such bad science, we needed to skip peer review altogether. Conveniently, there are lists of fake journal publishers. (This is my list, and here’s another.) Since time was tight, I simultaneously submitted our paper—“Chocolate with high cocoa content as a weight-loss accelerator”—to 20 journals. Then we crossed our fingers and waited.
....................

Our paper was accepted for publication by multiple journals within 24 hours. Needless to say, we faced no peer review at all. The eager suitor we ultimately chose was the the International Archives of Medicine. It used to be run by the giant publisher BioMedCentral, but recently changed hands. The new publisher’s CEO, Carlos Vasquez, emailed Johannes to let him know that we had produced an “outstanding manuscript,” and that for just 600 Euros it “could be accepted directly in our premier journal.”
...............
 Onneken wrote a German press release and reached out directly to German media outlets. The promise of an “exclusive” story is very tempting, even if it’s fake. Then he blasted the German press release out on wire service based in Austria, and the English one went out on NewsWire. There was no quality control. That was left to the reporters.
............
 We landed big fish before we even knew they were biting. Bild rushed their story out—”Those who eat chocolate stay slim!”—without contacting me at all. Soon we were in the Daily Star, the Irish Examiner, Cosmopolitan’s German website, the Times of India, both the German and Indian site of the Huffington Post, and even television news in Texas and an Australian morning talk show.
When reporters contacted me at all, they asked perfunctory questions. “Why do you think chocolate accelerates weight loss? Do you have any advice for our readers?” Almost no one asked how many subjects we tested, and no one reported that number. Not a single reporter seems to have contacted an outside researcher. None are quoted.
Fake science meets fake science journal meets fake science journalism. Stir, pour and enjoy.

Tuesday, May 26, 2015

The dark side of philosophy

Anil Gomes points to a troubling side of philosophical sophistication.
Prime amongst the ‘transferable skills’ so lauded by philosophy’s proselytisers are those of drawing careful distinctions, of paying attention to small but subtle differences between cases.
The development of these skills is thought to be central to a philosophical education. (‘Oxford Philosophy: training tomorrow’s thinkers today.’) And when used effectively, they allow a clarity of thought shocking in its brilliance and precision.
But they sometimes lapse into institutionally sanctioned pedantry. And when they do, they have analogues in a particular kind of self-deception, that involved in rationalising our bad behaviour. It is easy for a philosopher, trained in the making of distinctions, to distinguish lying from reticence, as Kant did, when writing to a suicidal correspondent. Lying is contrary to the moral law, he claimed; reticence on the other hand…
Here is one use for philosophical thinking: to draw distinctions that make one’s immoral conduct seem permissible, even praiseworthy. It is the kind of thinking which justifies claiming light bulbs on expenses or pressuring one’s spouse into taking one’s speeding points.
It is as if philosophy provides the tools which enable us to do all that we do whilst looking in the mirror and saying: yes, you’ve done good.
Unhappily, the recent spate of cases of philosophers cleverly "justifying" their own and others' appalling behavior provides support for Gomes's bleak view. Maybe it is past time to love wisdom a little more and cleverness a little less.
(h/t DailyNous)

Monday, May 25, 2015

Memorializing the Forever War

I am old enough that my then elderly elementary school teachers (you know, the ones who had gone to 'Normal School' and tucked lace handkerchiefs into the sleeves of their dresses) referred to Memorial Day as 'Decoration Day', as in 'decorate civil war graves'.Counterpunch is good enough to remind us of how many new graves we have been manufacturing for future decoration.

Permanent War
Since 1980 the US has engaged in aggressive military action in 14 countries in the Islamic world alone, according to research published in the Washington Post: Iran (1980, 1987-1988), Libya (1981, 1986, 1989, 2011), Lebanon (1983), Kuwait (1991), Iraq (1991-2011, 2014-), Somalia (1992-1993, 2007-), Bosnia (1995), Saudi Arabia (1991, 1996), Afghanistan (1998, 2001-), Sudan (1998), Kosovo (1999), Yemen (2000, 2002-), Pakistan (2004-) and now Syria. In this hemisphere, US military forces invaded Grenada (1983) and Panama (1989), and landed 20,000 military forces in Haiti (1994).
US Global War Machine
The US has 1.3 million people in the military and another million serve in the military reserves. The US has over 700 military bases in 63 countries across the world deploying over 255,000 US military personnel there. The Department of Defense officially manages over 555,000 buildings on 4400 properties inside the US and in over 700 properties across the globe.   The US has over 1500 strategic nuclear warheads, over 13,000 military aircraft, dozens of submarines, many of which carry nuclear weapons, and 88 huge destroyer warships.
Global Harm
Nearly 7000 US military people died as a result of the wars waged by the US since 9/11. Just as important, in Iraq over 216,000 combatants, most of them civilians, have died since the 2003 invasion.  No one even counted civilian deaths in Afghanistan for the first five years of our war there. Our drone attacks have murdered hundreds of children and hundreds of civilian adults in Pakistan and dozens more in Yemen.
World Leader in War Spending
US military spending is about the same as the total of military spending by the next eight largest countries combined, that is more than China, Russia, Saudi Arabia, France, UK, India and Germany combined.
Since 9/11 US spending on our military cost well over $3 trillion. Direct combat and reconstruction costs for wars in Afghanistan and Iraq since 9/11 have officially cost US taxpayers $1.6 trillion dollars according to the Congressional Research Service.   Additional trillions have been spent on growing the Pentagon budget and for present and future increased health and disability benefits for veterans.
The US military captures 55 percent of our national discretionary spending and spending on veterans benefits is another 6 percent. Since 9/11 military spending has increased by 50 percent while spending on other discretionary domestic spending increased by 13 percent according to the National Priorities Project.
Read the rest here.

Saturday, May 23, 2015

German octomom

My first thought is that this is a new form of child abuse:
A 65-year-old teacher from Berlin has given birth to quadruplets after a pregnancy that was widely criticized by medical professionals because of her age, RTL television said Saturday.
Annegret Raunigk, gave birth to a girl - Neeta - and three boys - Dries, Bence and Fjonn - by cesarean section at a Berlin hospital Tuesday, RTL said. The newborns weighed between 655 grams (1 lb., 7 ounces) and 960 grams (2 lbs., 2 ounces) each.
A spokeswoman for RTL said the babies stood a strong chance of survival but possible complications couldn't yet be ruled out, because they were born in the 26th week of pregnancy. Their mother was doing well, the spokeswoman said.
"Ms. Raunigk basically has no medical risk anymore," Heike Speda told The Associated Press. She said the woman had signed a contract granting RTL exclusive access in return for an undisclosed sum.
Raunigk already had 13 children ranging in age from 9 to 44, from five fathers. She told Germany's Bild newspaper last month that she decided to become pregnant again because her 9-year-old daughter wanted a younger sibling. She also has seven grandchildren.
Raunigk traveled abroad to have donated, fertilized eggs implanted - a procedure that is illegal in Germany.
My second thought, consistent with the first, is that this is a new form of mental illness, ("Suleman syndrome"), aided and abetted by 'doctors' and by television programmers, in either case.

Tuesday, May 19, 2015

Obama's failed presidency

At Harper's, David Bromwich reflects on the failed Obama presidency, something that started even as his presidency did. Case in point: the failure to close Guantanamo in the face of opposition.
To declare the argument over in the midst of a debate is to confess that you are lacking in resources. This defect, a failure to prepare for attacks and a corresponding timidity in self-defense, showed up in a capital instance in 2009. Obama had vowed to order the closure of the prison at Guantánamo Bay as soon as he became president. He did give the order. But as time passed and the prison didn’t close of its own volition, the issue lost a good deal of attraction for him. The lawyer Obama had put in charge of the closure, Greg Craig, was sacked a few months into the job (on the advice, it is said, of Obama’s chief of staff, Rahm Emanuel). Guantánamo had turned into baggage the president didn’t want to carry into the midterm elections. But the change of stance was not merely politic. For Obama, it seemed, a result that failed to materialize after a command had issued from his pen was sapped of its luster.
Yet as recently as March of this year, Obama spoke as if the continued existence of the prison were an accident that bore no relation to his own default. “I thought we had enough consensus where we could do it in a more deliberate fashion,” he said. “But the politics of it got tough, and people got scared by the rhetoric around it. Once that set in, then the path of least resistance was just to leave it open, even though it’s not who we are as a country and it’s used by terrorists around the world to help recruit jihadists.” One may notice a characteristic evasion built in to the grammar of these sentences. “The politics” (abstract noun) “got tough” (nobody can say why) “and people” (all the people?) “got scared” (by whom and with what inevitability?). Adverse circumstances “set in” (impossible to avoid because impossible to define). In short, once the wrong ideas were planted, the president could scarcely have done otherwise.
The crucial phrase is “the path of least resistance.” In March 2015, in the seventh year of his presidency, Barack Obama was presenting himself as a politician who followed the path of least resistance. This is a disturbing confession. It is one thing to know about yourself that in the gravest matters you follow the path of least resistance. It is another thing to say so in public. Obama was affirming that for him there could not possibly be a question of following the path of courageous resistance. He might regret it six years later, but politics set in, and he had to leave Guantánamo open — a symbol of oppression that (by his own account) tarnished the fame of America in the eyes of the world.
It wasn't just Guantanamo:
 In responding to the opportunities of his first years in office, Obama displayed the political equivalent of dead nerve endings. When the news broke in March 2009 that executives in AIG’s financial-products division would be receiving huge bonuses while the federal government paid to keep the insurance firm afloat, Obama condemned the bonuses. He also summoned to the White House the CEOs of fifteen big banks. “My administration,” Obama told them, as Ron Suskind reported in Confidence Men, “is the only thing between you and the pitchforks.” But the president went on to say that “I’m not out there to go after you. I’m protecting you.” Obama was signaling that he had no intention of asking them for any dramatic sacrifice. After an embarrassed reconsideration, he announced several months later that he had no use for “fat cats.” But even that safe-sounding disclaimer was turned upside down by his pride in his acquaintance with Lloyd Blankfein, of Goldman Sachs, and Jamie Dimon, of JPMorgan Chase: “I know both those guys; they are very savvy businessmen.” His attempt to correct the abuses of Wall Street by bringing Wall Street into the White House might have passed for prudence if the correctives had been more radical and been explained with a surer touch. But it was Obama’s choice to put Lawrence Summers at the head of his economic team.
And then there was the continuing disaster of Afghanistan:
In foreign policy, Afghanistan was the first order of business in Obama’s presidency. His options must have appeared exceedingly narrow. During the campaign, he had followed a middle path on America’s wars. He said that Iraq was the wrong war and that Afghanistan was the right one: Bush’s error had been to take his eye off the deeper danger. By early spring of 2009, Obama knew that his judgment — though it earned him praise from the media — had simply been wrong. The U.S. effort in Afghanistan was a shambles, and nobody without a vested interest in the war was saying otherwise.
Two incidents might have been seized on by a leader with an eye for a political opening. The first arrived in the form of diplomatic cables sent to the State Department in early November 2009 by Karl W. Eikenberry, the ambassador to Afghanistan and, before that, the senior commander of U.S. forces there. Eikenberry’s length of service and battlefield experience made him a more widely trusted witness on Afghanistan than General David Petraeus; his cables said that the war could not be won outside the parts of the country already held by U.S. forces. No more troops ought to be added. Eikenberry recommended, instead, the appointment of a commission to investigate the state of the country. Any reasonably adroit politician would have made use of these documents and this moment. With a more-in-sorrow explanation, such a leader could have announced that the findings, from our most reliable observer on the ground, compelled a reappraisal altogether different from the policy that had been anticipated in 2008. Though Obama had his secretary of state, Hillary Clinton; his secretary of defense, Robert Gates; and the chairman of the joint chiefs, Michael Mullen, arrayed against him, he also had opponents of escalation, including Vice President Biden and others, at the heart of his policy team. He chose to do nothing with the cables. A lifeline was tossed to him and he treated it as an embarrassment.
Nor did he take advantage of the opportunity the assassination of Bin Laden afforded him:
 But Obama made no such gesture. He held on to his December 2009 plan, which had called for an immediate escalation in Afghanistan to be followed by de-escalation on a clock arbitrarily set eighteen months in advance. The days after the killing saw the White House inflating and deflating its accounts of what happened in Abbottabad, while Obama himself paid a visit to SEAL Team 6. A truth about the uses of time in politics — as Machiavelli taught indelibly — is that the occasion for turning fortune your way is unlikely to occur on schedule. The delay in withdrawing from Afghanistan was decisive and fatal, and it is now a certainty that we will have a substantial military presence in that country at the end of Obama’s second term.
Bromwich explains this and other failings (health care!) by pointing both to Obama's personal predilection to avoid conflict, but more significantly, the the functioning of the embedded and entrenched bureaucracy and its mindset: the deep state:
 However one reads the evidence, there can be no doubt that Obama’s stance toward the NSA, the CIA, and the intelligence community at large has been the most feckless and unaccountable element of his presidency. Indeed, his gradual adoption of so much of Cheney’s design for a state of permanent emergency should prompt us to reconsider the importance of the Deep State — an entity that is real but difficult to define, about which the writings of James Risen, Mike Lofgren, Dana Priest, William Arkin, Michael Glennon, and others have warned us over the past several years. There is a sense — commonly felt but rarely reflected upon by the American public — in which at critical moments a figure like John Brennan or Victoria Nuland may matter more than the president himself. There could be no surer confirmation of that fact than the frequent inconsequence of the president’s words, or, to put it another way, the embarrassing frequency with which his words are contradicted by subsequent events.
Bureaucracy, by its nature, is impersonal. It lacks an easily traceable collective will. But when a bureaucracy has grown big enough, the sum of its actions may obstruct any attempt by an individual, no matter how powerful and well placed, to counteract its overall drift. The size of our security state may be roughly gauged by the 854,000 Americans who enjoy top-secret security clearances, according to the estimate published by Priest and Arkin in the Washington Post in 2010. The same authors reported that nearly 2,000 private companies and 1,300 government organizations were employed in the fields of counterterrorism, intelligence gathering, mass surveillance, and homeland security.
When Obama entered the White House, it was imperative for him to rid the system of the people who would work against him. Often they would be people far back in the layers of the bureaucracy; and where removal or transfer was impossible, he had to watch them carefully. But in his first six years, there was no sign of an initiative by Obama to reduce the powers that were likeliest to thwart his projects from inside the government. On the contrary, his presumption seems to have been that all the disparate forces of our political moment would flow through him, and that the most discordant tendencies would be improved and elevated by this contact as they continued on their way.
---a presumption that has been falsified again and again. The function of the deep state is to continue, to retain power, to expand power. Elected officials simply wave to the masses as the locomotive roars down the tracks on autopilot settings programed and tweaked by others. Folks at DKos and elsehwere get pissed off when they are reminded that it really doesn't matter who gets to sit and wave at the front of the locomative.But they delude themselves by shutting their eyes to the evidence.

Saturday, May 9, 2015

Wildlife decline at Fukushima

Ornithologists have been studying birds in the exclusion zone around Fukushima's melted down reactors. Here's what they have found so far.
Now, after four years surveying bird populations in 400 sites around Fukushima-Daiichi, Mousseau and his team have assembled a grim portrait of the disaster’s impact on local wildlife, using bird populations as a model system. Even though radioactivity has dropped throughout the region, their data show that bird species and abundances are in sharp decline, and the situation is getting worse every year.
“At first only a few species showed significant signs of the radiation’s effects,” Mousseau says. “Now if you go down and around the bend maybe five or ten kilometers [from a safe zone] to where it’s much, much hotter, it’s dead silent. You’ll see one or two birds if you’re lucky.”
Mousseau’s team conducted almost 2,400 bird counts in total and gathered data on 57 species, each of which showed specific sensitivity to background radiation. Thirty of the species showed population declines during the study period, the team report in the March issue of the Journal of Ornithology. Among these, resident birds such as the carrion crow and the Eurasian tree sparrow demonstrated higher susceptibility than migratory species, which didn’t arrive in the region until a few weeks after the partial meltdown in early March.
Nuclear accidents are rare in human history, so we have very little data about such radiation’s direct effects on wildlife. Mousseau has spent the past 15 years drawing comparisons between nuclear events to help build up our knowledge base and fill in the gaps. For instance, while there are no official published records of the Chernobyl disaster’s early impact on wildlife, plenty of work has been done in recent years to assess Chernobyl's ecosystem post-accident, from local birds to forest fungi.
When Mousseau returned to Fukushima in 2012, he began capturing birds in irradiated zones that had patches of bleach-white feathers. It was a familiar sign: “The first time I went to Chernobyl in 2000 to collect birds, 20 percent of the birds [we captured] at one particularly contaminated farm had little patches of white feathers here and there—some large, some small, sometimes in a pattern and other times just irregular.”
His team thinks these white patches are the result of radiation-induced oxidative stress, which depletes birds’ reserves of the antioxidants that control coloration in their feathers and other body parts. In Chernobyl, the patches have a high coincidence with other known symptoms of radiation exposure, including cataracts, tumors, asymmetries, developmental abnormalities, reduced fertility and smaller brain size.
By 2013, the birds Mousseau was counting in Fukushima had white patches big enough to be seen through binoculars.
Presented together, Mousseau thinks such data sets on Chernobyl and Fukushima could offer significant evidence for radiation’s prolonged, cumulative effects on wildlife at different stages after a nuclear disaster. But other experts have a completely different take on the available information.
“I’m not convinced about the oxidative stress hypothesis, full stop,” says Jim Smith, editor and lead author of Chernobyl: Catastrophe and Consequences and an expert on pollution in terrestrial and aquatic ecosystems. “The radiation levels in both Fukushima and Chernobyl are currently low-dose, and the antioxidant capacity of a cell is way, way bigger than the oxidizing capacity of the radiation at those levels,” he says. This would mean the white feather patches—and perhaps the overall bird declines—are being caused by something other than radiation.
His is just one of several scientific voices raised in objection.
Prum says he had heard the ecosystem at Chernobyl was doing quite well, an opinion defended by Mousseau’s critics. Back at the University of Portsmouth in the U.K., Smith primarily studies aquatic invertebrates, and in some of Chernobyl’s most contaminated lakes he has actually observed increased levels of biodiversity following the accident.
“Many of the literature studies on animals find it difficult to distinguish between the early effects of high doses shortly after the accident and later effects of much lower subsequent doses,” Smith says. “Plus some of them don’t properly account for the ecosystem impacts of removal of humans.”
Back in 2000, Robert Baker and Ron Chesser of Texas Tech University published a paper characterizing Chernobyl as a wildlife preserve, established thanks to the absence of humans since the accident. Both scientists have maintained that biodiversity and species abundance in Chernobyl and Fukushima are, in the long term, not adversely affected by radiation.
“Despite our best efforts, post-accident field studies aren’t sufficient to give us a clear picture,” says Chesser. “They offer no good controls, because we aren’t working with data from before the accident.” Chesser suggests that physiological aberrations of the sort Mousseau has observed are not conclusive results of chronic radiation exposure. Instead, they reflect other sources of oxidative stress including reproduction, immune response to infection and disease and strenuous physical activity such as migration.
“All the evidence that I grew up with and read in the last 60 years tells me [Mousseau’s findings] are probably wrong,” Chesser says, explaining why he disputes radiation as the cause behind the bird declines in Japan. “I don’t intend to cast aspersion on anyone, but if your evidence is really outside the norm, you better have some extraordinary data to back that up.”
Mousseau acknowledges that his research methods deviate from those of “old-school radiation biologists,” whose work has typically measured responses to radiation based on Geiger counter readings of individual animals. Not caring about the exact levels of radioactivity, as Mousseau says he does not, understandably ruffles some feathers.
“We’re strictly motivated by measurements of ecological and evolutionary response,” Mousseau says. “Our extraordinary evidence relates to these censuses, these massively replicated bionic inventories across a landscape scale and in both locations, and that has not been done in any rigorous way by any of these other groups.

Thursday, May 7, 2015

Appeals court declares NSA bulk collection illegal

Whoa:
A federal appeals court in New York on Thursday ruled that the once-secret National Security Agency program that is systematically collecting Americans’ phone records in bulk is illegal. The decision comes as a fight in Congress is intensifying over whether to end and replace the program, or to extend it.
In a 97-page ruling, a three-judge panel for the United States Court of Appeals for the Second Circuit held that a provision of the USA Patriot Act permitting the Federal Bureau of Investigation to collect business records deemed relevant to a counterterrorism investigation cannot be legitimately interpreted to permit the systematic bulk collection of domestic calling records.
The ruling was certain to increase the tension that has been building in Congress because the provision of the Patriot Act that has been cited to justify the bulk data collection program will expire in June unless lawmakers pass a bill to extend it.
It is the first time a higher-level court in the regular judicial system has reviewed the program, which since 2006 has repeatedly been approved in secret by a national security court.
The court, in a decision written by Judge Gerard E. Lynch, held that the Patriot Act provision, known as Section 215, “cannot bear the weight the government asks us to assign to it, and that it does not authorize the telephone metadata program.”
In declaring the program illegal, the judges said, “We do so comfortably in the full understanding that if Congress chooses to authorize such a far‐reaching and unprecedented program, it has every opportunity to do so, and to do so unambiguously.”
Let's see what happens next. Meanwhile, there is this:
Germany’s secret service has greatly restricted its cooperation with the US National Security Agency following a row about their alleged joint spying on European officials and companies, reports say.
The foreign intelligence agency BND stopped sharing internet surveillance data with the NSA, passing on only fax and phone intercepts, according to German media on Thursday.
Berlin now demands that the NSA provide a justification for each online surveillance request, reported the Süddeutsche Zeitung, public broadcasters NDR and WDR, and the news agency DPA.
The cynic in me thinks that there is too much money at stake for agencies and their contractors for them to simply acquiesce---they'll figure out some kind of end run.

Wednesday, May 6, 2015

Yikes: Three Mile Island edition

Yikes.
People living near the Three Mile Island nuclear plant may have heard a loud release of steam at 1 a.m. Wednesday as the plant was shut down after an electrical issue developed in the reactor. The plant was taken out of service after a problem developed with an electrical component that operates one of the control rods in the reactor. The control rods control the nuclear reaction in the reactor.
“The issue with the control rod presented no danger or issue with controlling the reactor,” said Exelon spokesman Ralph DeSantis.
He said the release of steam when the plant was being taken off-line was audible to nearby residents. Any radioactivity in the steam was too low to detect so there was no threat to the public or the environment,” DeSantis said.
Why would there be any radioactivity in the steam release? The steam running the turbines is supposed to be isolated from the radioactive water in the core. Is something going wrong with the Areva steam generators again?