building better bacteria

The Scientist | Researchers from the J. Craig Venter Institute have developed a technique for generating modified strains of bacteria with novel, genetically engineered properties, they report online today (August 20) in Science. The advance could help scientists tweak microorganisms to more efficiently produce biofuels, the researchers say.

"I think it's an important and interesting advance," said James Collins, a bioengineer at Boston University who was not involved in the study. "I suspect this will turn out to be quite important for bioengineering and bioenergy systems."

Last year, Venter, an author on the paper (and a member of The Scientist's editorial board), reported that he and his collaborators had created a synthetic bacterial genome and cloned it into a yeast cell. However, they were unable to transfer the genome into a cell that would use the genetic code to produce a functioning version of the organism. In the current paper, the researchers present a technique for doing just that.

The Venter team first cloned the genome of the bacterium Mycoplasma mycoides into a yeast cell. They then altered the genome, using the myriad tools available for yeast gene manipulation. In the procedure's trickiest step, they transplanted the yeast-bound bacterial genome into a closely related bacterium, Mycoplasma capricolum, coaxing it to "take this bacterial genome and boot it up" and generate their mutant strain, said Sanjay Vashee, a synthetic biologist at the institute and the corresponding author on the paper.

The hurdle Vashee and his team had to overcome to achieve this feat involved bypassing the bacterial equivalent of an immune system -- essentially a collection of restriction enzymes. These enzymes, thought to have evolved to chew up the genomes of viruses infecting bacterial cells, were preventing the successful transplantation of the modified M. mycoides genome into wild-type M. capricolum. So the group developed two fixes, which together solved the problem: First, they inactivated M. capricolum's restriction enzymes. Then, they chemically modified their mutant M. mycoides genome where these enzymes typically cleave the genomes of intruders.

Decades of research on yeast genetics have yielded the know-how to do extensive genomic manipulations in yeast, but that capability doesn't exist for other microorganisms. "There are so many organisms in nature that we cannot manipulate," said Vashee. "If we can extend this -- and put those genomes into yeast, to manipulate them there -- we've got a new technology that can bring genomics to a wide host of organisms." (Vashee noted that the current study was conducted in a natural Mycoplasma genome -- not the synthetic genome the group assembled last year.)

virus benefits insect hosts

The Scientist | Bacteria-infecting viruses, generally thought to be harmful to their hosts, can also be surprisingly beneficial.

A bacteriophage infecting a bacterium living in the cells and body cavity of a small, plant-eating insect protects the insect from attack by a deadly wasp predator, reports a study published online in Science today (August 20). The discovery may help create more effective methods of pest control, the authors say.

"This is a wonderful paper," Christoph Vorburger, an ecologist at the University of Zurich, told The Scientist. "It is important because it shows clearly that genetic elements such as bacteriophages are vehicles for transmitting resistance to predators," added Vorburger, who was not involved in the study.

Small insects called pea aphids are parasitized by a species of wasp, Aphidus ervi. The wasp injects its eggs into the aphids, and the eggs develop, pupating and eventually killing the insects. Earlier work has shown that the symbiotic relationship between aphids and a species of bacteria called Hamiltonella defensa can keep the insect safe, but no one understood exactly how the bacterium offered protection.

Using genetic sequencing tests, Kerry Oliver from the University of Georgia and his colleagues determined that Hamiltonella harbors a bacteriophage. To find out whether the phage is what safeguards the insect, they then generated three aphid--lines one without the bacterium, one with the bacterium infected by the phage, and one with the uninfected bacterium. The team found that only aphids with the phage were protected from the wasps' egg.

swiss bunkers

Polarinertia | For over four years, I have developed a photographic documentary work on Swiss fortified constructions – bunkers. Each element of these photographs has a relation with Switzerland and particularly the mountain landscape that is an inherent part of our identity. The bunkers are a integral part of a finely developed popular defense military system in Switzerland, a military with historically strong links to the landscape.

After the cold war ended many of the bunkers became obsolete. The tendency is to forget them or even to renounce them, my approach on the contrary, aims to expose them from a new angle. This approach has led me to discover a great number of bunkers, some in remote areas, sometimes difficultly accessible, covering the whole of the Swiss territory. The relations between these basic shaped bunkers and the often-sumptuous landscape surrounds them became an essential part of the study. I looked for the most spectacular bunkers, notable for their camouflage devices, true theatre scenery made with the utmost care. A quality indeed fully Swiss.

open letter to the queen

Abundancy Partners | We live in tumultuous times. Many developed world citizens are losing their livelihoods. The effects on the world's poorest will, as ever, be dreadful. However we are surprised that the Academy has not addressed anything outside the narrow remit their letter covered. Far greater insecurities threaten the world's poorest due to our effects on the natural world.

The letter ignores the physical constraints which are central to this bubble and indeed most bubbles. It speaks of "the bigger picture" and of "individual risks being small" and "the system as a whole being vast", yet, for us has a limited horizon.

Our premise is that our current economic malaise is symptomatic of a far more serious systemic failure to acknowledge what Archbishop Rowan Williams has identified in saying "It has been said that 'the economy is a wholly-owned subsidiary of the environment'. The earth itself is what ultimately controls economic activity because it is the source of the materials upon which economic activity works".

Energy underlies everything – Scylla and Charybdis of peak oil and climate change. The underlying cause of the current economic meltdown is a multi-generational debt-binge inextricably linked to a concomitant multi-generational energy-binge. The Academy's letter focuses on some "imbalances in the global economy". However, the key to addressing our current situation is to recognise the far more serious imbalances between our insatiable hunger for energy, its finite nature and the environmental pollution in its use.

Energy is the lifeblood of any economy. Our exponential debt-based money system is in turn based on exponentially increasing energy supplies. It is therefore clear that the supply of that energy deserves our very highest attention. That this attention doesn't appear in the Academy's analysis is deeply worrying.

The impending peaking of production of oil and other hydrocarbons, along with the resulting peak in food production and everything on which oil relies, is now widely accepted. Leading UK companies including Arup, Scottish and Southern Energy, Solarcentury and Virgin have warned that a peak in cheap, easily available oil production is likely to hit by 2013, posing a grave risk to the economy. On 2nd August 2009, the International Energy Association's Chief Economist, Dr Fatih Birol, warned of an oil crisis in 2010.

The letter refers to the "overheating economy" but gives no mention of the effect and cause of the overheating of planet Earth. Climate change is now recognised by the world's scientists, political and business leaders as the most serious threat to mankind and is described by Sir Nicholas Stern as "the greatest market failure of our times". On an almost daily basis we get increasingly urgent signals that unstoppable, runaway climate chaos is almost upon us.

natural gas not so sustainable

Examiner | It does not appear that Mr. Podesta's plan addresses the number one concern regarding the expansion of natural gas drilling domestically, and that is the over 300 compound chemical cocktail that is injected into the ground to force the gas to the surface. (for a list of 54 known chemicals in the fracking fluids and their effects, check HERE). His suggestion of public disclosure by gas producers does not go far enough. So what if gas developers disclose the chemical cocktail that they use; they still inject it into the ground where it seeps into our domestic freshwater supply. Even if the fracking goes on far below the groundwater table level, the tailing ponds on the surface have the potential to leak topdown into the water supply. Look at the map below where they want to drill (click for enlargement):

Do we really have the luxury of poisoning this much of our freshwater suply in the name of natural gas development? The question needs to be asked again: What do we value more, energy to run our machines or water to sustain human life?

Fracking processes are improving. There are best practices that use non-toxic cocktails, but these methods are employed in areas few and far between. Perhaps in the future, they will become standard.

What happens when the domestic natural gas wells run dry, though? Won't we simply be in the same position we find ourselves currently today? At least both Podesta and Chu refer to natural gas as a transition fuel (Pickens for that matter too), but our money, time, and effort could be better spent expanding clean energy in the form of wind, solar, biofuels, and geothermal as well as energy efficiency measures.

Drilling for more natural gas simply ruins more landscapes and runs the risk of poisoning our entire domestic freshwater supply. Is this the lowest level of risk our society can muster?

Is there any point in fighting to stave off industrial apocalypse?

Guardian | The collapse of civilisation will bring us a saner world, says Paul Kingsnorth. No, counters George Monbiot – we can't let billions perish.

The root cause of all these trends is the same: a rapacious human economy bringing the world swiftly to the brink of chaos. We know this; some of us even attempt to stop it happening. Yet all of these trends continue to get rapidly worse, and there is no sign of that changing soon. What these graphs make clear better than anything else is the cold reality: there is a serious crash on the way.

Yet very few of us are prepared to look honestly at the message this reality is screaming at us: that the civilisation we are a part of is hitting the buffers at full speed, and it is too late to stop it. Instead, most of us – and I include in this generalisation much of the mainstream environmental movement – are still wedded to a vision of the future as an upgraded version of the present. We still believe in "progress", as lazily defined by western liberalism. We still believe that we will be able to continue living more or less the same comfortable lives (albeit with more windfarms and better lightbulbs) if we can only embrace "sustainable development" rapidly enough; and that we can then extend it to the extra 3 billion people who will shortly join us on this already gasping planet.

I think this is simply denial. The writing is on the wall for industrial society, and no amount of ethical shopping or determined protesting is going to change that now. Take a civilisation built on the myth of human exceptionalism and a deeply embedded cultural attitude to "nature"; add a blind belief in technological and material progress; then fuel the whole thing with a power source that is discovered to be disastrously destructive only after we have used it to inflate our numbers and appetites beyond the point of no return. What do you get? We are starting to find out.

megacities

Physorg | Charles Kolb, Ph.D., reports that the concept of urban metabolism has existed for decades. It views large cities as living entities that consume energy, food, water, and other raw materials, and release wastes. The releases include carbon dioxide, the main greenhouse gas; air pollutants, sewage and other water pollutants; and even excess heat that collects in vast expanses of concrete pavement and stone buildings. Humans directly produce a significant share of this waste, but emissions from industrial, power generation and transportation systems respire the largest quantities of greenhouse gases and other air pollutants. Other urban metabolizers include sewage systems, landfills, domestic pets and pests like rats, which in some cities outnumber people.

During the last five years, this body of knowledge has drawn into sharper focus the hazards of poor air quality in megacities, not just on the large local populations but also on population centers, agricultural activities and natural ecosystems located downwind from these sprawling areas, Kolb said. He is with the Center for Atmospheric and Environmental Chemistry and the Center for Aerosol and Cloud Chemistry of Aerodyne Research Inc. in Billerica, Mass.

"Carbon dioxide and other pollutants in megacities make them immense drivers of climate change," he said. "They impact climate on both a regional and global level because these long-lived greenhouse gases are dispersed around the world."

More than half the world's population today lives in cities, and the world's largest urban areas are growing rapidly. The number of megacities — metropolitan areas with populations exceeding 10 million — has grown from just three in 1975 to about 20 today.

Kolb said that the most highly polluted megacities are in developing countries. They include Dhaka, Bangladesh; Cairo, Egypt; and Karachi, Pakistan. Some megacities in less developed regions have recently mounted air quality management campaigns that have resulted in lower levels of pollution; they include Mexico City, Mexico; Beijing, China; Sao Paulo, Brazil; and Buenos Aires, Argentina. Even the cleanest megacities like Tokyo/Osaka in Japan and New York City and Los Angeles in the United States — all in the developed world — still have serious problems, Kolb said.

what's really wrong with american healthcare?

The Atlantic | After the needless death of his father, the author, a business executive, began a personal exploration of a health-care industry that for years has delivered poor service and irregular quality at astonishingly high cost. It is a system, he argues, that is not worth preserving in anything like its current form. And the health-care reform now being contemplated will not fix it. Here’s a radical solution to an agonizing problem.

How does a nation that might close down a business for a single illness from a suspicious hamburger tolerate the carnage inflicted by our hospitals? And not just those 100,000 deaths. In April, a Wall Street Journal story suggested that blood clots following surgery or illness, the leading cause of preventable hospital deaths in the U.S., may kill nearly 200,000 patients per year. How did Americans learn to accept hundreds of thousands of deaths from minor medical mistakes as an inevitability?

My survivor’s grief has taken the form of an obsession with our health-care system. For more than a year, I’ve been reading as much as I can get my hands on, talking to doctors and patients, and asking a lot of questions.

Keeping Dad company in the hospital for five weeks had left me befuddled. How can a facility featuring state-of-the-art diagnostic equipment use less-sophisticated information technology than my local sushi bar? How can the ICU stress the importance of sterility when its trash is picked up once daily, and only after flowing onto the floor of a patient’s room? Considering the importance of a patient’s frame of mind to recovery, why are the rooms so cheerless and uncomfortable? In whose interest is the bizarre scheduling of hospital shifts, so that a five-week stay brings an endless string of new personnel assigned to a patient’s care? Why, in other words, has this technologically advanced hospital missed out on the revolution in quality control and customer service that has swept all other consumer-facing industries in the past two generations?

I’m a businessman, and in no sense a health-care expert. But the persistence of bad industry practices—from long lines at the doctor’s office to ever-rising prices to astonishing numbers of preventable deaths—seems beyond all normal logic, and must have an underlying cause. There needs to be a business reason why an industry, year in and year out, would be able to get away with poor customer service, unaffordable prices, and uneven results—a reason my father and so many others are unnecessarily killed.

Before exploring alternative policies, let’s reexamine our basic assumptions about health care—what it actually is, how it’s financed, its accountability to patients, and finally its relationship to the eternal laws of supply and demand. Everyone I know has at least one personal story about how screwed up our health-care system is; before spending (another) $1trillion or so on reform, we need a much clearer understanding of the causes of the problems we all experience.

supreme post crowley-gates symbolic hack...,

Fist tap P6 and Plantsmantx

Carefully orchestrated, but from a symbolic perspective, this strikes me as an exceptionally well crafted piece of libertarian agitprop. So I take back my initial "bookerrising surrealism" critique.

"We worked with the Phoenix police department. They came down to our studio on Friday. We've gone through this with them for 15 years."

"They have a squad - used to be called the confrontation prevention squad, now called community service. We told them that we're going to come down, I'm going to do the radio show live, we're going to be broadcasting it, and I'm going to have a firearm. I had a 9 millimeter on myself..."

"It was Thursday that I called and talked to Al Ramirez, the representative from the Phoenix police department, and we were discussing - we've been around this rhetoric that was building up around William Kostric, who did this in New Hampshire. We knew this from 15 years ago when Janet Napolitano was a U.S. Assistant Attorney and prosecuted the Viper Militia out of Arizona, and how that was generated into something it wasn't. We talked to Al and we were like, look, we know where this is going and we want to make sure, we come down, we're peaceful, and we demonstrate the right of the people to carry their firearms. And the police protected our right."

"They wanted to help - they assigned him [a police officer] to me. He was never more than 4-5 feet away from me. We had law enforcement around us to protect our rights to protect this firearm."

why the tea tastes like pee

Fist tap BTx3.

NHS drawn into u.s. healthcare reform debate

Pro:


Con:

Corporate Health Insurance is damning Obama's attempt to extend health care to the poor. As the process of demonizing the president's attempts grow, it has spawned an opportunistic attack on the British National Health Service (NHS), as well.

oil industry backs protests of emissions bill

NYTimes | Hard on the heels of the health care protests, another citizen movement seems to have sprung up, this one to oppose Washington’s attempts to tackle climate change. But behind the scenes, an industry with much at stake — Big Oil — is pulling the strings.

Hundreds of people packed a downtown theater here on Tuesday for a lunchtime rally that was as much a celebration of oil’s traditional role in the Texas way of life as it was a political protest against Washington’s energy policies, which many here fear will raise energy prices.

“Something we hold dear is in danger, and that’s our future,” said Bill Bailey, a rodeo announcer and local celebrity, who was the master of ceremonies at the hourlong rally.

The event on Tuesday was organized by a group called Energy Citizens, which is backed by the American Petroleum Institute, the oil industry’s main trade group. Many of the people attending the demonstration were employees of oil companies who work in Houston and were bused from their workplaces.

This was the first of a series of about 20 rallies planned for Southern and oil-producing states to organize resistance to proposed legislation that would set a limit on emissions of heat-trapping gases, requiring many companies to buy emission permits. Participants described the system as an energy tax that would undermine the economy of Houston, the nation’s energy capital.

when most powerful masquerade as grass roots...,

Washington Post | A petroleum industry trade group is asking oil companies to recruit employees and retirees to attend rallies attacking climate-change legislation, an approach to grass-roots politics that resembles strategies used recently by some opponents of health-care reform.

In a memo this month, American Petroleum Institute President Jack Gerard detailed plans for "Energy Citizen" rallies to be held in 20 states during the final two weeks of Congress's August recess. Gerard wrote that the intent was to put a "human face on the impacts of unsound energy policy," including a climate-change bill passed by the House in June.

"Please indicate to your company leadership your strong support for employee participation in the rallies," Gerard wrote in the memo, saying that contractors and suppliers should also be recruited.

Environmental groups on Saturday criticized the rallies, which they described as manufactured events intended to pass as organic assemblies of concerned citizens. Greenpeace activists said they saw parallels to the health-care debate, where opponents of reform -- including some organizations that receive heavy funding from industry groups and individuals -- have organized efforts to shout down lawmakers at "town hall" meetings.

"It's the most powerful among us, masquerading as grass-roots outrage to stifle debate on global warming," Michael Crocker, a spokesman for Greenpeace, said of the oil group's plans. "These are manufactured concerns, and the people who get involved in this are paid to put on this theater."

The memo, obtained by Greenpeace, was first reported on by the Financial Times Saturday.

cap and rage...,

Washington Post | The fight over health-care reform could hobble climate-change legislation. The rancorous debate over health reform has given voice to considerable uneasiness among Americans. Many are worried about how a new system will be paid for in an economy that has unraveled, and they are anxious about a kudzu-like expansion of an already unwieldy bureaucracy. Given the herculean effort it will take to get President Obama's vision of reform through Congress, we're not convinced that the Senate will have the stomach to tackle cap-and-trade legislation this fall. The growing agitation within the chamber over the creation of another complex system to buy, sell and trade pollution credits only adds to our doubts.

If Congress fails to pass cap-and-trade legislation, it will rapidly approach a fork in the road in addressing global warming. Members can sit back while unelected bureaucrats at the Environmental Protection Agency follow through on their moves toward regulating greenhouse gas emissions as a pollutant under the Clean Air Act. Or they can entertain a carbon-based tax designed to reduce emissions and give the money back to taxpayers in an equitable manner. A decision on which path to take is bearing down upon us. Not only are the global warming dangers facing the planet reaching the tipping point, but there will also be no climate agreement in Copenhagen without strong leadership in words and deeds from the United States. As the Senate forges ahead, nothing should be off the table.

the more things change.....,

Fist tap Denmark Vesey.

corporations co-opt craziness...,

Washington Post | Before the "black helicopters" of the 1990s, there were right-wingers claiming access to secret documents from the 1920s proving that the entire concept of a "civil rights movement" had been hatched in the Soviet Union; when the landmark 1964 Civil Rights Act was introduced, one frequently read in the South that it would "enslave" whites. And back before there were Bolsheviks to blame, paranoids didn't lack for subversives -- anti-Catholic conspiracy theorists even had their own powerful political party in the 1840s and '50s.

The instigation is always the familiar litany: expansion of the commonweal to empower new communities, accommodation to internationalism, the heightened influence of cosmopolitans and the persecution complex of conservatives who can't stand losing an argument. My personal favorite? The federal government expanded mental health services in the Kennedy era, and one bill provided for a new facility in Alaska. One of the most widely listened-to right-wing radio programs in the country, hosted by a former FBI agent, had millions of Americans believing it was being built to intern political dissidents, just like in the Soviet Union.

So, crazier then, or crazier now? Actually, the similarities across decades are uncanny. When Adlai Stevenson spoke at a 1963 United Nations Day observance in Dallas, the Indignation forces thronged the hall, sweating and furious, shrieking down the speaker for the television cameras. Then, when Stevenson was walked to his limousine, a grimacing and wild-eyed lady thwacked him with a picket sign. Stevenson was baffled. "What's the matter, madam?" he asked. "What can I do for you?" The woman responded with self-righteous fury: "Well, if you don't know I can't help you."

The various elements -- the liberal earnestly confused when rational dialogue won't hold sway; the anti-liberal rage at a world self-evidently out of joint; and, most of all, their mutual incomprehension -- sound as fresh as yesterday's news. (Internment camps for conservatives? That's the latest theory of tea party favorite Michael Savage.)
---------------------------------------------------
Rick Perlstein will be online today at 11:00am ET to discuss this article. Outlook: In America, Crazy Is a Pre-existing Condition
' ... the crazy tree blooms in every moment of liberal ascendancy ...'

forgery...,

American Prospect | Before the big House vote on the American Clean Energy and Security Act (ACES), Rep. Tom Perriello had a tough choice to make. Perriello won his seat by a small margin and worried about attacks from Republicans campaigning against the bill. Ultimately, he voted for it, in part because he believes a sustainable energy industry is the future of his district's economy.

But even as he was considering how to approach the legislation, he received at least five letters from local constituency groups opposing the bill, including a local Hispanic advocacy organization and the area branch of the NAACP. There was just one one small problem: The letters were forgeries; at least one came from Washington, D.C.-based lobbyists Bonner & Associates.

“They stole our name. They stole our logo. They created a position title and made up the name of someone to fill it. They forged a letter and sent it to our congressman without our authorization,” said Tim Freilich, who sits on the executive committee of Creciendo Juntos, a nonprofit network that tackles issues related to Charlottesville’s Hispanic community. “It’s this type of activity that undermines Americans’ faith in democracy.”

For all the reprehensible shenanigans that lobbying firms involve themselves in, forging letters from civil-rights groups to oppose this legislation is still pretty outrageous -- in fact, the NAACP even supports the legislation. Members of Congress are already very skeptical of constituent communications in this day of Internet-organized communications blitzes; the possibility that they may take these messages even less seriously due to fraud is a very disheartening one. Hopefully the reporting on this story will spur an investigation by legal authorities and some serious punishment for the perpetrators.

surreal bookerrising moment...,

game over - payer profits prevail

Washington Post | The president has said that creating a nonprofit, government-sponsored insurance plan -- competing alongside private insurers -- would provide a lower-cost alternative for consumers and keep the industry "honest." In Colorado on Saturday, the tone was more conciliatory.

"The public option, whether we have it or we don't have it, is not the entirety of health-care reform," Obama said. "This is just one sliver of it."

The proposal has become a lightning rod, particularly in the Senate, where Finance Committee members are seeking bipartisan consensus.

"The fact of the matter is there are not the votes in the United States Senate for the public option," said Conrad, one of six panel members involved in the talks. "There never have been. So to continue to chase that rabbit, I think, is just a wasted effort."

Sen. Orrin G. Hatch (R-Utah) said Democrats are moving toward a European-style, single-payer system. "And this public plan, this public government plan, don't think for a minute that that will not destroy the current insurance system," he said on ABC's "This Week."

Sebelius and other administration aides have said Obama is open to a nonprofit cooperative model as an alternative to the public option and the existing private plans. Finance Committee members have been studying utility co-ops as a possible model.

Liberal leaders reacted strongly to the idea that Obama would walk away from what they consider a central element of reform.

"I don't think this bill is worth passing without a public option," said Howard Dean, head of the grass-roots group Democracy for America.

mining the technosphere

Mining the Technosphere: a Solution for the Industrial Ecosystem? from Rembrandt Koppelaar on Vimeo.