Fighting bacteria with bacteria – common nose germ provides new weapon against superbugs | Not Exactly Rocket Science

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Staph

Our bodies are under siege, constantly fighting back assaults from disease-causing bacteria. But we are also home to many harmless bacterial species that are share our bodies to no ill effects. Now, it seems that these ‘commensals’ could be our hidden allies against their harmful cousins. In one such ally, a group of scientists has just discovered a potential new weapon against Staphylococcus aureus.

S.aureus is incredibly common, colonising the noses of a third of people in the USA, UK, Japan and other countries. Often, these colonies do nothing untoward, but if a full-blown infection sets in, the result can include life-threatening diseases like pneumonia, meningitis, toxic shock syndrome, endocarditis and sepsis. With the rise of MRSA and other staph strains that shrug off our most common antibiotics, the threat posed by this common nose bug has never been greater.

But S.aureus doesn’t have our noses to itself. It has to jostle for space with a close relative called Staphylococcus epidermidis. It’s the most common commensal in our noses and, indeed, the most common contaminating bacterium in laboratory equipment. S.epidermidis is harmless, except in people whose immune systems have been compromised. But more interestingly, it has the ability to stunt the growth of its more infamous cousin. Now, Tadayuki Iwase from Jikei University has isolated the protein it uses to do so.

Iwase swapped the noses of 88 volunteers and found that virtually all of them were colonised by S.epidermidis. However, S.aureus had only set up shop in just under a third. On the whole, the two bacteria seem to be able to co-exist in harmony, but Iwase found that some strains of S.epidermidis are anathemas to S.aureus.

Specifically, they caused problems for S.aureus’s ability to set up biofilms, the bacterial equivalent of cities. Thousands of bacteria swarm within these communities, embedded in a slimy matrix of DNA, proteins and sugars. Within biofilms, bacteria are harder to kill, making them an important public health challenge. But according to Iwase, some strains of S.epidermidis not only prevent S.aureus from creating biofilms, they also destroy existing ones. People who were colonised by these defensive strains were around 70% less likely to be colonised by S.aureus.

S.epidermidis

To work out the weapon that was keeping the rival bacteria are bay, Iwase let cultures of S.epidermidis cut a swath through S.aureus biofilms and analysed their secretions when the destruction had reached its peak. He managed to isolate a single protein called Esp or ‘S.epidermidis serine protease’ in full. The protein was absent from strains that couldn’t wipe out S.aureus biofilms and present in strains that could. If Iwase gave the latter bacteria them a chemical that negates the Esp protein, or if he removed the esp gene from them entirely, they lost their competitive edge against S.aureus.

Esp even works in tandem with our own defensive proteins, including one called hBD2 (human beta-defensin 2) that’s secreted by our skin cells. Alone, hBD2 can kill bacteria but it’s a bit of a wimp about it, while Esp (for obvious reasons) has no bacteria-killing ability of its own. But together, their powers are far greater, and they effectively kill S.aureus, even when it was under the protection of biofilms. (The idea that the two proteins have co-evolved with one another is an intriguing question for another time.)

As a final test, Iwase introduced the competitive strains of S.epidermidis into the noses of volunteers who were already colonised by S.aureus. Sure enough, these transplanted bacteria eliminated their evolutionary cousins. Even a purified dose of Esp alone did the trick.

These experiments are very exciting. Humans are fighting a pitched (possibly losing) battle against staph and MRSA in particular, and our antibiotic arsenal is falling short. What better source of new weapons than other bacteria that have been fighting the same fight for millennia? Obviously, there’s a lot of work to do to turn Esp into a viable treatment, but this study is a promising first step.

Even better, it seems that, for some unclear reason, S.aureus can’t evolve resistance to Esp. With its biofilms under attack, you would expect S.aureus to quickly adapt, but after a year of culturing the two species together, Iwase couldn’t find any evidence that of resistance.

Reference: Nature http://dx.doi.org/10.1038/nature09074

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Truce Between Green Groups & Timber Companies Could Save Canadian Forests | 80beats

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CBFA-map-largeIf you need a breather from all the bad news coming out of the Gulf of Mexico, take a look way up north. In Canada this week, environmental groups and big industry—timber, in this case—actually agreed on something. With the Canadian Boreal Forest Agreement, the groups reached a truce in their fight over the forests of Northern Canada. The breakthrough could protect vast swaths of forest that, if added up, would be bigger than the state of Nevada.

Signatories include AbitibiBowater, one of the world’s biggest newsprint producers; Seattle-based Weyerhaeuser, and Canfor, British Columbia’s biggest softwood lumber producer, as well as nine environmental groups such as Greenpeace, the Nature Conservancy and Forest Ethics [Financial Times].

The environmental groups agreed to suspend their “don’t buy” campaigns in exchange for timber firms agreeing not to cut down forests that constitute endangered caribou habitat until at least the end of 2012. In the meantime, the parties will try to hash out a long-term plan. If this step does result in a more permanent conservation plan, it could have benefits not just for the caribou, but for the planet as well.

Over the past decade, boreal-forest preservation has increasingly been seen to be as vital as tropical-forest preservation in efforts to combat global warming. Although tropical forests cover more of Earth’s surface than boreal forests, boreal forests store nearly twice as much carbon, mainly in their soils [Christian Science Monitor].

As you can see in the map here, Canada is home to one of the two great belts of boreal forest in the world; the other stretches across Russia. The timber companies involved in this pact have government-approved leases to 178 million acres of the forests. This agreement covers roughly 72 million acres, and the companies will suspend logging and road-building immediately in 29 million of those acres (the light green portions seen on the map above), with rules for the remaining 43 million acres to come.

While a reasoned truce is nice to see, this fight will go on. Chloe O’Loughlin of Canadian Parks and Wilderness Society argues that the Canadian governments need to restrict other industrial development in the areas to ensure they remain pristine.

She said there was no way forest companies would abide by the new agreement unless oil and gas companies were also required to respect the habitat. “I’m sure they wouldn’t agree to defer something and then see it thrashed by the oil and gas industry,” she said. “Put it off limits to forestry and then put it off limits to oil and gas” [The Province].

Related Content:
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Image: Canadian Boreal Forest Agreement


How Many Sparks in the Genome? | The Loom

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sparksLess than two percent of the human genome is made up of protein-coding genes. Fifty years ago, scientists launched an expedition of the other 98 percent. It has been a slow march for much of that time, but in recent years the pace has picked up, thanks to advances such as new ways to sequence DNA. Scientists are now generally agreed that some of the non-coding DNA falls into several categories, including

–sites where proteins can bind in order to switch nearby genes on and off

–genes for RNA molecules. Instead of just serving as a template for turning genes into proteins, RNA actually plays lots of roles in the cell, such as sensing levels of different molecules in the cell and interfering with other RNA molecules to control levels of protein.

–old viruses and other genomic parasites. Some viruses can insert their genetic material into our genomes so that it becomes a permanent part of our DNA. These viruses and other parasitic stretches of DNA can, from time to time, make copies of themselves, which then get inserted back into the genome. In a few cases, these genomic parasites may be domesticated, evolving to do valuable things like help build placentas or fight off viruses. But for the most part they’re either useless or downright harmful–just like any other source of mutation.

–Hobbled or dead genes. Sometimes mutations strike genes so that they can no longer produce proteins. Sometimes these mutations are fatal. Other times, we’re able to survive without a particular gene. The pseudogene, as it’s known, may linger on in the genome for millions of years. In a few cases, pseudogenes may still be able to produce useful RNA molecules. But for the most part, they’re just baggage.

The first two categories include stretches of DNA that are useful. The second two include stretches that are useless. Now comes the hard part: figuring out just how much of the genome is made up of each. The question goes beyond mere census-taking, because it will help us understand how the genome works, in its entirety. And it will also reveal how much of the genome provides no benefit at all.

I wrote an article about this line of research for the New York Times in November 2008. I described some scientists who were betting that most of the genome wouldn’t be good for much, and others who believed that most of it was serving important functions. The latter group pointed to studies in which scientists tallied up all the RNA transcripts produced by one chunk of the genome. They found that most of the DNA they analyzed produced RNA. John Mattick, a member of the research team who works at the University of Queensland in Australia, claimed that most of that DNA encoded useful molecules. “My bet is the vast majority of it — I don’t know whether that’s 80 or 90 percent,” he said.

But it was just a bet. A lot of work remained to figure out what all that RNA really signified. This week scientists at the University of Toronto published a study that suggests, contrary to Mattick, it’s full of sound and fury, signifying nothing. They used new methods to survey the RNA produced by the genome and compared their results to the ones from older methods. They found that most of their RNA came from regions of the genome that are already known to be protein-coding genes. Very little RNA came from elsewhere in the genome. They argue that the older methods were crude, so studies based on them were loaded with false positives. Protein-coding genes are not the only source of RNA transcripts in the genome, but a lot of the extra ones may just be the result of sloppiness. When proteins slide down DNA, making RNA transcripts, they sometimes grab onto the wrong stretches. The extra RNA gets broken down quickly–as useless and as inevitable as sparks flying off a grinding wheel.

Nature News has a nice write-up, as does PLOS Biology (from which I shamelessly lifted my Macbeth).

[Image: MIT]


Gulf Oil Spill: Fishing Ban Expanded; Endangered Turtles Threatened | 80beats

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100515-N-6070S-056With no end to BP’s gushing oil leak in sight, attention has turned to trying to ascertain just how damaging the spill could be for wildlife in the Gulf of Mexico. Yesterday the National Oceanic and Atmospheric Administration (NOAA) doubled the size of the fishing ban in the Gulf. Now nearly 20 percent of the water is off-limits because of the expanding oil slick.

Because so much oil is under the surface, and diluted but still dangerous, it’s hard to get a handle on just how bad things will be. But turtles seem to be the bellwether for worries about sea life. Since April 30, marine biologists have recorded more than 150 sea turtle deaths, and while they can’t immediately say all those were directly related to the oil spill, it’s a much higher number of deaths that is usual for this time of the year.

Necropsies, the animal equivalent of an autopsy, have been performed on 40 turtles so far. And tissue samples taken from as many specimens as possible are being analyzed for abnormally high chemical levels associated with oil contamination. Initial necropsy results are expected in a few days, but laboratory tests of the tissue samples will likely take weeks to complete. In many cases these results are needed to make a conclusive finding about the cause of an animal’s death [Reuters].

Turtles raise special concern because all five species that live in the Gulf region are endangered. And as spring turns to summer, they could be more in the path of danger.

The nesting season for the sea turtles runs until mid-July, and for most of that time the mothers will remain off Padre Island and the beaches of Mexico, where there is currently no oil. But then things become more chancy, as new sea turtle babies go off to sea, floating on currents in the gulf or on seaweed patches that could be covered by crude [The New York Times].

100517-G-8744K-001Meanwhile, back at the leak site, BP says that the siphon it successfully installed last week is now carrying 2,000 barrels of oil per day to a tanker on the surface. While the company trumpeted this as capturing 40 percent of the estimated 5,000 barrels of oil per day leaking in the Gulf, we noted last week that the 5,000 figure could be a gross underestimation. If the leak is truly 50,000 barrels and not 5,000, then the 2,000 currently being captured is barely a drop in the bucket.

In Washington, Democrats in the Senate are pushing a plan to raise the cap on liability for a spill from its present $75 million to at least $10 billion—a more than 130-fold increase. Republicans have blocked the measure thus far.

And in Florida, people are left to wait and see if Gulf currents bring oil their way.

Florida Democrat Senator Bill Nelson released a forecast by University of South Florida College of Marine Science experts who said part of the oil slick may reach the Keys in five to six days, and possibly Miami five days after that. “While I always hope for the best, this is looking like really out-of-control bad,” Nelson said in a statement before another round of congressional hearings on Tuesday [Reuters].

Recent posts on the BP oil spill:
80beats: Good News: BP’s Oil Siphon Is Working. Bad News: Florida Keys Are in Danger
80beats: Scientists Say Gulf Spill Is Way Worse Than Estimated. How’d We Get It So Wrong?
80beats: Testimony Highlights 3 Major Failures That Caused Gulf Spill
80beats: 5 Offshore Oil Hotspots Beyond the Gulf That Could Boom—Or Go Boom
80beats: Gulf Oil Spill: Do Chemical Dispersants Pose Their Own Environmental Risk?

Image: U.S. Navy photo by Mass Communication Specialist 2nd Class Justin Stumberg; U.S. Coast Guard photo by Petty Officer 3rd Class Patrick Kelley.


The trajectory of American Jews, lessons from history | Gene Expression

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I notice that a peculiar piece of datum from First Things contributor David Goldman is being passed around, repeated by Ross Douthat no less. Goldman states:

Beinart offers a condescending glance at the “warmth” and “learning” of Orthodox Jews, but neglects to mention the most startling factoid in Jewish demographics: a third of Jews aged 18 to 34 self-identify as Orthodox. “Secular Jew” is not quite an oxymoron–the Jews are a nation as well as a religion–but in the United States, at least, secular Jews have a fertility barely above 1 and an intermarriage rate of 50 percent, which means their numbers will decline by 75 percent per generation. It is tragic that the Jewish people stand to lose such a large proportion of their numbers, but they are lost to Judaism in general, not only to Zionism. That puts a different light on the matter.


A reader of Goldman’s who happens not to be stupid and can actually read observes that 34% of Orthodox Jews are 18 to 24 according to the original source Goldman was citing. No surprise that Goldman makes such an error, he has a way with faux erudition which amazes the dull and dumb. In fact, the American Jewish Survey reports that 16% of Jews between the ages of 18 to 29 self-identify as Orthodox.

With that small error out of the way, in regards to the future of the American Jewry I think the story outlined in Amos Elon’s The Pity of It All: A Portrait of the German-Jewish Epoch, 1743-1933 may serve as a possible vision of the future. Elon notes that almost the whole of the German Jewish elite of the late 18th and early 19th century converted to Christianity. Moses Mendelssohn’s last Jewish descendant died before the 20th century; the rest of his descendants had become Christians. Karl Marx and Heinrich Heine were not atypical. But there was a large German Jewish community in the early 20th century, though even that was being eroded by intermarriage and conversion. If Elon is correct that the bulk of the 19th century Jewry became Christian, where did the Jews of the 20th century come from? It seems that as the German Jewish burghers abandoned the Reform temples for Lutheran churches, their spots were filled by assimilating Eastern European Jews who were immigrating into Germany and taking over the institutions which the earlier community had built. They were heirs in spirit, if not blood, to Moses Mendelssohn. In other words, a large bumper crop of Orthodox youth may be the salvation for the Reform and Conservative movements. There may be no third generation Reform, but not all third generations beyond Orthodoxy remain Orthodox either.

The AAAS on Cuccinelli Probe: Scientific Disagreement and Controversy Do Not Imply Fraud (Duh) | The Intersection

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The American Association for the Advancement of Science is now the latest organization to instruct Virginia attorney general Ken Cuccinelli in how science works. In particular, I liked this aspect of the AAAS board statement: Scientists should not be subjected to fraud investigations simply for providing scientific results that may be controversial or inconvenient, particularly on high profile topics of interest to society. The way to resolve controversies of this nature is through scientific review and additional research. In the majority of cases, scientific disagreements are unrelated to any kind of fraud and are considered a legitimate and normal part of the process of scientific progress. The scientific community takes seriously their responsibility for policing scientific misconduct, and extensive procedures exist to ensure the credibility of the research enterprise. Unless founded on some openly discussed evidence of potential misconduct, investigations such as that targeting Professor Mann could have a long-lasting and chilling effect on a broad spectrum of research fields that are critical to a range of national interests from public health to national security to the environment. Unless more clearly justified, Attorney General Cuccinelli’s apparently political action should be withdrawn. That's right--the AAAS just called Cuccinelli's investigation "political." It is, of course--but ...


We live in Utopia! | Gene Expression

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Rod Dreher mulls his bias toward declinism while evaluating Matt Ridley’s new book The Rational Optimist. Here’s a portion of Ridley’s argument:

But with new hubs of innovation emerging elsewhere, and with ideas spreading faster than ever on the Internet, Dr. Ridley expects bottom-up innovators to prevail. His prediction for the rest of the century: “Prosperity spreads, technology progresses, poverty declines, disease retreats, fecundity falls, happiness increases, violence atrophies, freedom grows, knowledge flourishes, the environment improves and wilderness expands.”

Dreher gloomily observes:

Well, I would certainly love to be wrong; neither I nor my descendants gain anything out of a world of decline. But it would be useful to go back and look at how 19th-century progressives expected the 20th century to be a wonderland of peace, prosperity and progress. Didn’t quite work out that way. I suspect the truth is that nobody knows anything about tomorrow, and that we can only make our best educated guesses based on history and the wisdom of experience.

Looking at the imaginings of past futurists is often pretty amusing. And Ridley’s projections of plentitude and prosperity seem to involve an extrapolation of the conditions of the past 200 years, whereby a greater and greater proportion of humanity has broken the shackles of the Malthusian trap. The reality is that for most of human history innovation was always immediately counter-balanced by population growth so that median wealth never increased. Only in the 19th century did a new social pattern and demographic dynamic emerge whereby prosperous individuals did not reproduce to a greater extent in keeping with their greater wealth. Rather, societies went through the “demographic transition”, and greater wealth for future generations became the new norm. There’s no reason that this doesn’t have to be a transient state between long epochs of Malthusianism, so I think assuming that the new normal is the normal forever more is a step too far.

That being said, it seems to me that we do truly live in a utopia in any objective terms when viewed from the 19th or early 20th centuries. The Dickensian lot of the poor no longer characterize the lower classes of the developed world, and obesity is actually a feature of the lives of the poor, as opposed to starvation. The period between 1800 and 1970 witnessed a massive shift in earning power to the working classes, and a closing of the wage gap between skilled and unskilled workers. Infection has not been abolished, but it is no longer so deadly. Violence has decreased, despite the periodic outbreaks of industrialized genocide. And so on.

Utopia is always over the hill, and the new normal was the aspiration of the past, not the bliss of the present. But the past and the present and the future are actually instantiated simultaneously. Consider three airports which I have sharp experiences of. Dhaka airport is the past. John F Kennedy airport is the present. And Munich airport is the future. If you took a flight from Dhaka to Munich you would have thought that you’d been transported to utopia.

I don’t take these utopian dreams as an injunction toward complacency. Rather, we should appreciate all that modern science, technology and government has achieved, and be vigilant. Before we despair at all which might be lost, remember this famous chart:

sala-fig-1-1

Talk Tomorrow in Philly: “Science and Sustainability in the News” | The Intersection

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Tomorrow evening, I'll be appearing at the Philadelphia Academy of Natural Sciences for this event: "Who Will Tell the People? Science and Sustainability in the News” Scientists who study the environment and global warming warn us at every turn that dramatic changes are afoot. Why don’t media headlines convey a sense of urgency? What is the best way to get the climate change message to citizens? What obligations do the media have? What prevents them from telling the story? The May Urban Sustainability Forum will take a look at how the media covers issues of science, how shrinking budgets and disappearing science desks are impacting coverage, and how niche media sources are filling a void in sharing vital information. Beth McConnell, Executive Director of the Media and Democracy Coalition, will be speaking on the topic of media consolidation and its effects on journalism, specifically sustainability. Chris Mooney is a 2009-2010 Knight Science Journalism Fellow at MIT and author of three books, including Unscientific America: How Scientific Illiteracy Threatens Our Future (co-authored by Sheril Kirshenbaum). Mr. Mooney and Ms. Kirshenbaum also co-write The Intersection blog for Discovermagazine.com, a contributing editor to Science Progress, and a senior correspondent for The American Prospect magazine. He has been ...


There Are Several Reasons Not To Fly Any More Ares

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Bolden at odds with Nelson on Ares I tests , Orlando Sentinel

"I can't pay for an Ares I today. It's too expensive," said Bolden, speaking after a meeting of the Commercial Space Transportation Advisory Committee. "That's an easy decision for me because it wipes out everything. My friend Sen. Nelson, and he is my friend to be quite honest, we respectfully agree to disagree on this. It is incredibly costly for me to go off and try a series of Ares I tests to support a heavy-lift at the present cost of solid rocket motors. Now, there is an answer. Get the cost down. And ATK (prime contractor for the Ares I) says they can do that. But we're not there right now."

Keith's note: There is another wrinkle to the whole issue of SRBs, Ares, and Shuttle Derived Launch Vehicles - one that has not gotten much attention - yet: OSTP and others in the White House are concerned that these solid rockets are heavy polluters (1.1 million pounds of propellant each) and that it is time to move to something far less dirty to launch things into space.

When we send things into space, does it affect our atmosphere? ozone layer?, Yahoo ANswers

"... 23 tons of harmful particulate matter settle around the launch area each liftoff, and nearly 13 tons of hydrochloric acid kill fish and plants within half a mile of the site ... the environmental cost per launch is the same as that of New York City over a weekend."

Flagship Technology Demonstrations RFI Is Out

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NASA Request for Information Synopsis for the Flagship Technology Demonstrations

"The National Aeronautics and Space Administration (NASA) is seeking information through this Request for Information (RFI) to identify, improve and/or enhance approaches that will demonstrate the targeted technologies described in this RFI. NASA has defined six (6) targeted technologies that are to be demonstrated via spaceflight in support of the Flagship Technology Demonstration (FTD) effort. Towards this end, four (4) Point of Departure (POD) missions have been identified. While emphasis in the responses should address the existing POD missions, alternate approaches may be suggested in order to more efficiently demonstrate the selected technologies."

Tropical Cyclone 1B (Northern Indian Ocean)

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NASA's Aqua Satellite Sees Tropical Storm 1B Form in Bay of Bengal

The first tropical storm of the Northern Indian Ocean cyclone season has formed and NASA's Aqua satellite captured its birth. Tropical Storm 1B formed in the early morning hours as the convection around the low level circulation center increased since May 17.

NASA's Aqua satellite captured a visible image of 1B from the Moderate Resolution Imaging Spectroradiometer (MODIS) at 7:25 UTC (12:25 p.m. Asia/Kolkata time) today, May 18, where if formed off of India's east coast in the Bay of Bengal.

At 09:00 UTC (5 a.m. EDT or 2 p.m. Asia/Kolkata local time) on May 18, Tropical Storm 1B had maximum sustained winds near 40 knots (46 mph). It was located about 285 nautical miles east-southeast of Chennai, India near 12.4 North and 84.5 East in the Bay of Bengal. It is moving west-northwest near 13 knots (15 mph) and is forecast to continue in that direction, according to the Joint Typhoon Warning Center, the organization the forecasts tropical cyclones in that region.

Tropical Storm 1B is expected to intensify in the next two days as it moves closer to Chennai. It is then forecast to make landfall south of Visakhapatham.

View my blog's last three great articles...

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NASA video explains how to poop in space

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We've been waiting for the answer to this most-popular of space questions: How the heck do you pinch a loaf in microgravity? This detailed video finally answers that question, once and for all.

Of course, positioning is important, and to solve that problem, NASA engineers mounted a video camera so the proper "docking" could take place. But guys, be careful not to "dock" any of your other private parts, or you'll be in an alien world of pain.

View my blog's last three great articles...

Ocean Worlds, Full of Life, Threatened by Oil Drilling

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There is a whole other world beneath the surface of the ocean.  An ocean is not a big reservoir of empty water, of course; it’s swarming with life, and  some people who have never seen it have a hard time imagining how much.   Snorkeling or diving near any barrier reef or off the coast of an island reveals a huge amount of fascinating life.   The first time I went snorkeling in a marine reserve (off the coast of Belize, seen in the video above) I was stunned at what was down there.   It was filled with color and motion and so many varieties of creatures and it seemed endless; truly like being in an alternate universe.  Now imagine that vibrant  alternative universe filled with the dark murkiness of oil.

Endangered sea turtles are washing up dead on the beach in the Gulf. 

“At least 150 sea turtles have washed up dead or dying along the U.S. Gulf Coast since the giant oil spill off Louisiana, a higher number than normal for this time of year, a leading wildlife expert said on Monday.” Read more here.

Below is a report from Wallace J. Nichols, a marine scientist and oceans conservationist who in 1998 founded the Grupo Tortuguero. See more on him here.

My brave friend Leilani Munter called from the field to report that the National Wildlife Federation and CNN had documented the first sea turtle caught in a slick at sea, gasping for air through an iridescent sheen. Tragically, just as nesting season for a number of the Gulf of Mexico’s sea turtle species is set to begin, these highly endangered animals become the poster species of the BP Gulf of Mexico oil spill.

Soon, if not already, adult male and female turtles will gather in shallow coastal waters, mate and prepare to nest, precisely where oil is accumulating. The pregnant females will scuttle across beaches at night to lay eggs, just as they’ve done for millions of years, but these beaches will be different—they will be blacked with oil. In a few short weeks, a new generation of hatchlings will emerge from the sand and make their way across oily beaches to an oily sea where tar balls and slicks will make their already-long odds of survival even longer. As they mature, they will have to rise through oil slicks to breathe and survive by eating oil-coated animals, algae and seagrass. While sea turtle will be among the most recognizable victims, they won’t be alone. Many species of birds, fish, invertebrates and plants will fare just as badly.

Even before the spill, sea turtles had it tough. US and Mexican trawlers drag nets across the sea floor in search of shrimp, but catch thousands of turtles by “accident.” Bright beach [...]

Couldn’t you have picked a better Gene Set Berkeley?

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I admire UC Berkeley for pushing the envelope. They have been doing it for decades. Encouraging risk taking, and defying stereotypes


But when I read about their summer research project I cringed.


Excuse me?

Ok, I get it, poor metabolizers will cut down on drinking so much, The UC saves on risk management insurance, win for the administration and win for the educators who will then "teach" about the findings......

What about that party-hardy freshman who has that timid roommate? well, the roommate just found out that she can process alcohol "just fine"

@KTVU news at 11. UC Berkeley student found dead after party.

"Well, it all started when she found her genetic test results meant that she could handle alcohol just as well as I could"-Dead Student's Roommate

Couldn't they have picked a better gene?

What were they thinking? I dunno, maybe they were blinded by Time Magazine. Well, the good news is that all Berkeley Freshman will all be entered in a drawing to receive a free test from, Guess Who?

23andSerge

The Sherpa Says: First Do No Harm

Proteus Gowanus Benefit/Anniversary Party, Saturday, May 22nd, 7-10 p.m.

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This Saturday May 22, the Morbid Anatomy Library's beloved mother institution Proteus Gowanus will be hosting a benefit party; for the event, I will be on hand to provide wine-soaked tours of the Library and my Observatory exhibition The Secret Museum; there will also be an exciting variety of other events, happenings, workshops, and music, not to mention food and wine. This promises to be a great event! Very much hope to see you there!

Full details follow:

PROTEUS GOWNAUS BENEFIT/ANNIVERSARY CELEBRATION
The Proteus Gowanus Board and Core Collaborators:
Sasha Chavchavadze, Tammy Pittman, Tom LaFarge, Wendy Walker
Julie Freundlich Lang, PK Ramani, Benjamin Warnke, Nick DeFriez
Andrew Beccone, Joanna Ebenstein, David Mahfouda

Invite you to join us for

A Benefit Party
to Celebrate Five Years on the Alleyway

Saturday, May 22nd, 7 - 10 p.m.
RAIN DATE: Sunday, May 23, 7 - 10 p.m.
Featuring

Optiks/Alley
A multimedia installation/performance by Paul Benney and friends
inspired by Newton's Opticks and West Side Story. Viewers will be
transported down the alleyway through a dream-like world
of theatrical lighting, video and an original sound score

And a Laboratory of Protean Workshops:
Rocketworks Countdown 3, a triptych moon launch video
Improvisational Mending with the Fixers Collective: bring a broken object!
Individual and Dual Stunts in the Reanimation Library
A Secret Museum, a private viewing of Morbid Anatomy Library’s collection
The Mysteries of the Gowanus Unveiled in our Hall of the Gowanus
An Oulipian Escapade with our Writhing Society

Music by Union Street Preservation Society
A selection of Thai hors d'oevres by JOYA restaurant
and wine will be served

Tickets $60 each
Space is limited, tickets will be sold
on a first come first served basis

BUY NOW

Or go to http://www.proteusgowanus.com
to buy a ticket or make a donation
718-243-1572
543 Union Street at Nevins Street Gate

You can buy tickets by clicking here; you can find out more about Proteus Gowanus by clicking here, more abou the Morbid Anatomy Library by clicking here, more about Observatory by clicking here, and more about The Secret Museum--which has been extended until June 6th--by clicking here.

Photo: Eric Harvey Brown, for Time Out New York

The Never-Realized Führermuseum, Linz, Austria

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Starting in 1939, Nazi henchmen and art dealers bought and stole thousands of paintings, sculptures, tapestries and other objects from private collections across Europe, then stockpiled them. Hitler helped draw up architectural plans, which megomaniacally grew to include a theater and an opera house, a hotel, a library and parade grounds. Photographs show him, pencil in hand, pondering plans and gazing raptly on the model for the site...

Just in time for International Museum Day (which was yesterday, actually!), a fascinating story in the New York Times which details the ill-fated story of Adolf Hitler's never-realized Führermuseum, an art gallery he planned to establish in his hometown of Linz, Austria.

The article details the surprising importance that collecting artworks and planning the architecture and minutia of a museum held for Hitler even up until the eve of his demise; it also traces the history of a series of intruiguing artifacts related to his pursuit: meticulous scrapbooks containing black and white photos of the projected Führermuseum's collection, scrapbooks which now function as a sort of "museum without walls" for this ill-fated museum that never was. The article also provocatively examines in what ways Hitler's projects of collecting and empire might have been linked.

The article explains:

    It’s hard to overstate how seriously [Hitler] took the whole project. Art collecting obsessed him for years; his staff endured nightly soliloquies, Hitler droning on about art while Germany collapsed around him. He fussed even about how the rooms in the museum should be decorated.

    And goes on to comment:

    The jury is out over whether the 'disproportionate amount of time and energy,' as the head of the Allied art-looting investigation unit put it after the war, that Hitler demanded go to amassing art, diverted German resources from the war effort, hastening its end, or the reverse — whether Hitler’s obsession with Linz, and with collecting generally, in some measure motivated him to press on.

    Full story follows; really fascinating stuff, and well worth a read!

    Strange Trip for a Piece of Nazi Past
    By MICHAEL KIMMELMAN

    BERLIN — Robert Edsel, author of “The Monuments Men,” came to town the other day with a heavy album bound in green Moroccan leather. “Gemäldegalerie Linz XIII” was embossed on the spine. Inside were black-and-white photographs of mostly obscure 19th-century German paintings.

    The album was one of the long-missing volumes cataloging the never-built Führermuseum in Linz, Austria, which Hitler envisioned someday rivaling Dresden and Munich. Starting in 1939, Nazi henchmen and art dealers bought and stole thousands of paintings, sculptures, tapestries and other objects from private collections across Europe, then stockpiled them. Hitler helped draw up architectural plans, which megomaniacally grew to include a theater and an opera house, a hotel, a library and parade grounds. Photographs show him, pencil in hand, pondering plans and gazing raptly on the model for the site.

    “And so they are ever returning to us, the dead,” the German novelist W. G. Sebald wrote in “The Emigrants.” “At times they come back from the ice more than seven decades later and are found at the edge of the moraine, a few polished bones and a pair of hobnailed boots.” He was recalling a long-forgotten Alpine climber, whose remains a glacier in Switzerland suddenly released, 72 years after the man had gone missing.

    But really Sebald was describing the past, which everywhere turns up unexpectedly, jolting us from our historical amnesia. A German publisher, Berliner Verlag, just released a book of photographs of postwar Berlin that had somehow languished in its archives. I know a man in Spain who has been accumulating long-forgotten photographs and other private relics from the war: a mesmerizing and mysterious stash of soldiers’ snapshots and letters, and documents scrawled with Hitler’s notes. The missing Linz album surfaced not long ago outside Cleveland, of all places. An 88-year-old veteran, John Pistone, who fought with Patton’s army, picked it up in 1945 while rummaging through the Berghof, Hitler’s retreat in the Bavarian Alps. Like other soldiers, he wanted a souvenir to prove he’d been there. He didn’t know, or particularly care, what the album was, and only learned its significance when a contractor installing a washer-dryer in his house noticed the volume on a shelf, hunted for information via the Internet, then called Mr. Edsel.

    Mr. Edsel heads the Monuments Men Foundation for the Preservation of Art, an organization dedicated to preserving the legacy of the 350 or so Allied soldiers tasked with looking after cultural treasures in Europe. A 53-year-old, white-haired former oilman, Mr. Edsel isn’t the sort of person who takes no for an answer, and he persuaded Mr. Pistone to relinquish the volume to the German Historical Museum in Berlin , which has the other extant Linz albums. (This makes 20; 11 are still missing.)

    Hitler was presented with the albums every Christmas and on his birthday. They featured reproductions of the latest art to go into the museum. The books were a virtual museum-in-waiting, a museum without walls. You imagine him cradling the bulky volumes, ogling bucolic scenes of a bygone German countryside now in ruins, imagining himself the next Medici.

    It’s hard to overstate how seriously he took the whole project. Art collecting obsessed him for years; his staff endured nightly soliloquies, Hitler droning on about art while Germany collapsed around him. He fussed even about how the rooms in the museum should be decorated.

    “I never bought the paintings that are in the collections that I built up over the years for my own benefit,” he took pains to write in his brief will, just before putting a pistol to his head, “but only for the establishment of a gallery in my hometown of Linz.”

    A model of Linz had already been moved to the bunker in Berlin so it would be among the last things he saw.

    Volume XIII, Mr. Pistone’s album, contains reproductions of 19th-century German and Austrian pictures, the art Hitler admired most. He may have bought some of these works with royalties from “Mein Kampf.” They’re mawkish idylls by painters largely obscure even to Germans and Austrians today. The best pictures are by Adolph von Menzel and Hans Makart, with whose early underappreciation Hitler perversely identified.

    Time whitewashes evil, or not. Mr. Edsel expressed his opinion this week that more and more curios like Mr. Pistone’s album would surface now that the last surviving veterans are dying.

    “Emotional value doesn’t transfer across generations,” is how he put it. “People don’t inherit passions.” One man’s private memento becomes another’s opportunity to sell something on eBay, notwithstanding that German and American authorities insist that artifacts like the Linz album are cultural property that shouldn’t be sold. Regardless, he meant that in the process of passing between generations, the object gains new life.

    In a ceremony on Tuesday, Volume XIII was delivered to the German Historical Museum here, joining other Linz albums on display behind glass, like contaminated evidence. The jury is out over whether the “disproportionate amount of time and energy,” as the head of the Allied art-looting investigation unit put it after the war, that Hitler demanded go to amassing art, diverted German resources from the war effort, hastening its end, or the reverse — whether Hitler’s obsession with Linz, and wi
    th collecting generally, in some measure motivated him to press on.

    Historians can thrash that out. Meanwhile, there are the 11 unaccounted-for albums. Presumably they’re still out there, like Sebald’s polished bones.

    You can view the full article by clicking here, and see the related slide-show--from which the above image, captioned "Hitler at work on plans for his museum in Linz, Austria," was drawn-- by clicking here.

    Epiphany

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    The Institute of Medicine report is a frequent ‘rebuttal’ to science based/real medicine. The argument is usually phrased something to the effect that since medicine can be dangerous, SCAM’s are legitimate. Of course, one does not follow the other. It is the equivalent of saying since you are old, bald and pudgy, I am young, have a full head of hair, and are thin. If every doctor and hospital were to vanish tomorrow like an episode of the Outer Limits, SCAM’s would be just a ineffective.

    Despite the flawed logic of the comparison, I have always had an affinity for the estimates that 44,000 to 98,000 were (note the deliberate use of the past tense) killed each year in hospitals. There may be methodological flaws in the estimate but the ballpark figure is probably correct.

    In 1999 there were 5000 hospitals in the US. Just one death a quarter would bring the number of deaths to 20,000, and one death a quarter is not that many deaths. Lest I sound hardhearted, everyone dies, 2.5 million a year, and often death occurs in the hospital. Against the background of the mortality of existence, a few ‘extra’ deaths would be lost in the background.

    For an individual doctor, it would be indistinguishable against the background death rate in the hospital. What makes it even more difficult to track and recognize excess mortality is that each death may be due to a different breakdown in medical practice.

    Amongst my many jobs is Infection Control. For twenty years I have chaired Infection Control for both the Legacy Health, a collection of 5 hospitals in the Portland-Vancouver area, as well as for Portland Adventist Medical Center. As Chair I get the joy of sitting on many other committees such as Quality Council and Pharmacy. I know all the way hospitals could kill and the endless efforts to try and improve and perfect medical practice to avoid these complications.

    In 20 years of investigating outbreaks, hospital acquired infections, and deaths, I have yet to see two infection related deaths that are due to same cause. Every infection was reviewed and evaluated as a potential for improvement, and I think we practiced the best medicine we knew of at the time.

    With one exception, the universal horse shit compliance with hand washing that was the norm 20 years ago. It always boggled my mind that it was difficult back in the day to get people to wash their hands. The information on efficacy was only 150 years old, after all. But otherwise we practiced state of the art medicine. With the perfect vision of hindsight, I can see that state of the art left much to desired. We didn’t have the studies to guide practice that we have now, and I anticipate that 20 years from now I will be rolling my eyes at how we practiced in 2010. I will sound just like Bones McCoy wandering throughout a 1980’s San Francisco hospital grumping about the butchers of the past and hoping I do not run into T.J. Hooker.

    Unlike the hodgepodge of practices that comprise SCAM, medicine changes and mostly for the better. Change is always slow, and always painful, and more difficult to implement than one could ever anticipate, but if you read the medical literature, you have to change.

    Hospital based medicine is mind bogglingly complex and difficult, and humans are limited in their ability to always function perfectly. The Institute of Medicine knew what it was doing when they entitled their report “To Err is Human.” And all too often we were not able to pinpoint a breakdown that lead to a complication or death

    When I started practice back in the last century, I would have thought that hospital acquired infections were part of the price of taking care of ill and compromised patients. Sure, we can minimize infections, but wound infections, ventilator pneumonias, and line infections are going to happen. You can’t do the things we do to people and NOT get an infection.

    Right?

    Wrong.

    What both administrations at my hospital systems have in common is a commitment to patient safety and over the last decade they have committed considerable time and money to the application of proven procedures to decrease infections and other complications of hospital care.

    You cannot know best practice based on individual experience. I like to tell the residents that the three most dangerous words in medicine are “In my experience.” You need large numbers of patients and studies to guide practice. The last 15 years have seen a large number of clinical trials aimed at discovering what is the best practice to prevent everything from line related infections to deep venous thrombosis. Dozens of science based investigations whose goal was to improve patient care in the hospital, and my hospitals aggressively applied them.

    The first intervention was the use of alcohol foam instead of hand washing. I have in my mind, and cannot find the reference, that if a nurse would wash her hands appropriately after every contact, he would spend 80% of their shift washing hands. Soap and water, it turned out, was not a practical solution to keeping hands clean. It is too time consuming in a busy work day, despite it’s proven efficacy in preventing infections.

    Alcohol foam can be used in a fraction of the time with superior results since it is much easier to foam frequently. And once I discovered it was not to be used orally like cheese whiz, the results were even better.

    The foam is now ubiquitous in the hospitals. Even when the use of the foam was 20%, the overall infection rate in the hospitals fell by half when compared to rates with hand washing. Then, over the next decade, the hand hygiene compliance rate has steady increased to around 90% and there was a corresponding steady decrease in infections. It took over a decade of consistent work and a lot of trial and error to get the rates to 90%.

    At one hospital the limiting problem was no foam outside the rooms. No one would walk an extra few feet to get to the foam. But at another hospital the fire Marshall said alcohol foam in the halls was a fire hazard and we could not put alcohol in the halls. He was eventually overruled, but what are you going to do in the meantime?

    And I could go on for paragraphs about the issue of finding product that minimized the number of HCW’s whose hands where turned raw by the alcohol.

    Ninety percent seems to be the best we can consistently achieve with the current program for hand hygiene, and we are puzzling over how to get the rates to 100%. One approach is the “It’s ok to ask” program, where patients are encouraged to ask their provider if they washed their hands. I asked a series of patients if they would ask, and they uniformly said no, they did not want to risk angering their health care provider. I agree. It is important not to piss off the person providing your morphine. Besides, would you fly on an airline if their motto was “It’s ok to ask if the landing gear is down.”

    Last year I ran a red light. It was 7 am, I was taking the kids to school and I have to make a right then an immediate left across four lanes of traffic. I make this turn everyday. I am talking to the kids and I look several times, no traffic, and make the turns.

    What I did not see was that the light was red nor did I see the cop stopped on my left. I was so intent on the traffic I missed two key features in my environment.

    It is the main reason, I suspect, that we cannot get hand hygiene to 100% every time, every where. The hospital has too many opportunities to focus our attention elsewhere that, for the short term, allows us to forget to foam.

    Somehow, and I do not know how, I suspect we need to make foaming the default rather than optional; then our rates will get to 100%.

    But foam is not the only intervention my hospitals have implemented.

    Surgical check lists, best practice bundles (collections of proven interventions gathered together) to prevent ventilatory pneumonias, to prevent intravenous catheter related infections, to prevent urinary tract infections, to prevent deep venous thrombosis. Innumerable checks and balances with pharmacy to prevent medication errors.

    Simple things to prevent surgical wound infections but logistically difficult to get to 100%: timing of antibiotics to within an hour of cut time, no shaving the surgical site, not letting the patent get cold post op, and tight glucose control were are associated with decreased wound infections. Next up may be no staples with orthopedic cases as a recent meta-analysis demonstrated fewer infections with sutures. That will be fun, getting surgeons to alter practice.

    Over the last year my hospitals have implemented dozens of practice improvements based on the medical literature to improve outcomes and the results have been amazing. Practices that were not effective were abandoned or modified, sometimes going through multiple iterations until were discovered was worked and was practical.

    As a result, at Legacy we have prevented over 200 deaths (12.5% reduction in non-risk-adjusted mortality rate, which is now 1.47% for our system that includes a regional trauma center and regional burn center as well as two NICUs, oncology program, and multiple other high-risk programs) and over 570 prevented infections (39.5% reduction in whole-house infection count) above historical data. And that is over the most recent 24 months. At Legacy it is estimated we have also saved 8 million dollars in associated costs.

    A few of the hospitals have gone a year without a ventilator associated pneumonia or a catheter related infection. Every year has seen a decrease in the healthcare associated infections and other complications.

    That is 100 deaths prevented a year for 5 hospitals. Multiply that for the remaining 4,995 hospitals in the US and the IOM estimates for last century seem reasonable. But not for this century and not for the decades to come.

    I used to think that infections were inevitable, but no longer. There is the occasional patient who will get an infection: the badly burned, the multiple trauma. But even the trauma ICU had a marked decrease in all infections with increased infection control compliance. We had a wound infection in a 400 lib patient who literally had dirt tattooed in the palms and soles and a Hemoglobin A1c of 15 who required emergency surgery. I was not surprised that patient developed an post-op infection. We did everything correctly and still had a complication. Sometimes the barriers we have to overcome to prevent infection may be too great, but it does not stop us from trying.

    But the experience of Legacy and Adventist demonstrates that aggressive adherence to proven infection control works and that the majority of health care associated infections and deaths need not happen.

    I have three epiphanies in my life: my first great meal (at a restaurant called St. Estephe’s), my first great Bordeaux (oddly enough, a St. Estephe’s), and when I realized that most infections in the hospital need not happen.

    This has been a real decrease in infections and death, not just playing with numbers to look better. These hospitals look at every healthcare associated infection (HAI) as an improvement opportunity and do not sweep data under the rug.

    I also know personally that the numbers are real. I used to derive a significant portion of my income from hospital acquired infections. There are many reasons why my income has declined by 60% over the last decade, not the least of which being large numbers of patients that used to make up my practice (HAI’s, AIDS) have disappeared. The majority of those 570 prevented infections would have been consults. I feel like Phillip Morris making stop smoking ads.

    It was not easy making these changes; it took years of committed work. People are like oil tankers and change course slowly. And some are filled with toxic waste. An interesting aspect of instituting the policies and procedures has been who fought against the changes the hardest. Docs. Not all of them, just a small subset. There is a curious subset of MD’s who feel that the data does not apply to them. They do not need to follow infection control procedures, use full barriers when placing a line, or even wash their hands. And I do not get it. I cannot figure out why some docs are so recalcitrant about doing the right thing, the proven thing. Eventually everyone complied, but some people made it more painful than it needed to be.

    My hospitals made a serious commitment to providing the best care as determined by the science. It was not simple and required a surprising amount of creativity and time to apply the evidence to the real world. But the nice thing is that when you apply science to problems, you get results. Science works. Quality initiatives work. Next time you point out the deaths caused by modern medicine, leave my hospitals out of it.

    It makes me wonder. There are numerous naturopathic, chiropractic, and other alternative schools and clinics involved in patient care. I am sure that they too have numerous quality improvement studies to brag about that have improved patient care and outcomes.

    Think of all the practices in medicine that, eventually, have been demonstrated to be worthless, or dangerous, or flawed and that were improved or abandoned for the betterment of patient care.

    So let’s start a list, shall we. The following is the top 10 list of alternative medical practices that have been modified or abandoned because of studies that demonstrated they were ineffective or dangerous and the quality initiatives that have improved patient care:

    1) Disposable acupuncture needles (thanks to wales)

    2)

    3)

    4)

    5)

    6)

    7)

    8)

    9)

    10)

    Sorry. I found nothin’.

    Perhaps it is a reflection of the perfection that is alternative medicine. Alternative medicine practices change based on evidence? No need.

    Of course, I may well be wrong. As the board president of the Oregon Association of Naturopathic Physicians states, “Both MDs and NDs are trained to work from the evidence-based model of medicine, using best practices and standards of care.” I suppose my inability to find examples is due my inadequate Google and Pubmed skills to find the readily available information. I would have my 13 year old do it for me, but he is on a trip. Even if only 25% of medicine is science based, that is still 25% more than alternative practices.

    Please, please, please, someone show me up. Hell, just give me some hand hygiene improvement data and let me know that, if nothing else, there is an understanding of germ theory in the alt med world. Ever since my local paper, the Oregonian, printed a picture of the local Natural Medicine School teaching acupuncture without gloves, I am not so sanguine about that understanding. It still gives me the willies to see that photograph and it looks for all the world that there are two boxes of gloves in the background, so I know they have them. It may be that all the gloves are left handed or right handed and so cannot be worn. Sometimes I pull out a glove for the right hand and it is a lefty glove and then I pull out a glove for the left hand and it is a righty, so I cannot find a pair to wear. It’s a problem.

    Medicine slowly improves, too slowly sometimes. I know that 20 years ago we did not have the information to inform our practice that we do now. We did the best we could with what we knew at the time, and we do the best we can now with the information we have today. Still, despite the impressive improvements, it is a bittersweet victory. I can’t help but think what could have been, if only we had known.


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