Sabin Russell Science Writer



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A World Series, and Entropy Surfing, as Metaphor

Posted by Sabin Russell

A Toshiba Flat-Screen Capture of World Series Entropy

After 162 regular games and three rounds of high-strung playoff baseball, a Season is supposed to end like this: A wave of Giants leaping the dugout rails, streaking toward the mound; grown men hopping around like schoolchildren, tumbling in the grass; hollering, joyful human piles of chaos.

Which is why, of course, I am thinking about entropy.

These days, I think a lot about entropy. Entropy is why things fall apart, why the center cannot hold. It's why a barn door ages and a rock wall falls down. Entropy is a measure of disorder. It's why heat always flows from hot to cold. It's the natural tendency of energy to go to waste.  It's the second law of thermodynamics.

In my scientifically suspect and English Majorly way of thinking, I've come to appreciate entropy as a fundamental property of, well, existence. It's as real, and as directional, as gravity and time. Entropy awareness deepens when the economy goes off track, when oil gushes from a hole at the bottom of the sea, when a pitcher loses his fastball,  and as baby boomers watch themselves fall apart.

But there is no reason to get discouraged or bitter. Entropy may be sweeping us all toward that ultimate rocky shore, but the goal is neither to fight nor submit. There is artistry in cutting back, carving across it, and staying upright. The goal is to surf it, dude.

There is, I think, great beauty in this most natural of processes. Without entropy would a field of grass soothe our eyes with its complexity? Entropy softens the hard edge of order, imparts nuance, bends what is straight, and breaks what is solid. Where we see entropy, we see evidence of life. Entropy imparts the character into a pair of old boots, puts the snap into a well-worn baseball mitt, imparts the fractal shape of mountainsides and fills the beaches with sand.

The “miracle” of life  itself – a process that would appear to be a spontaneous assertion of order – may be just a  gnarly detour in our mutli-billion year cool-down from the birth of the sun.  Bacteria or primate, life is full of order, but living also is a process of energy unwinding, rigidly obedient to the second law of thermodynamics.  We are carried along, sometimes with a sense of control, as the old primal heat does its work and meets its entropic fate.

Perhaps one reason we love the game of baseball it that, as we sit on the edge of our seats, we are watching a spectacle of entropy surfing.  At its best, baseball is a game where the highly skilled slip and slide at the brink of calamity, sometimes succumbing to it, other times inspiring us with their grace and strength. Baseball is an orchestration of statistics, and part of the game is the athletic dance with fate, the calculated pursuit of serendipity, where odds favor failure, collapse, disorder, the triumph of entropy. Yet, for a time, somebody wins. For a time, their artistry seems ageless.  No sport reveres its old-timers – those worn and wizened acrobats of the odds -- as much as baseball. And after game upon game, all the order of the innings ends with a mad, chaotic release. The surfers take up golf. Each season comes with the certainty and unpredictability of waves to a beach, and a good season, like a good life, is wonderful to behold.

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A Voice Fading in the Mist: A Last Blog, on Fake Fog, and Ecstasy Deaths

Posted by Sabin Russell

A scene from the fatal POP2010 at the Cow Palace, May 29, 2010. Photo credit:

There is seldom a single cause of any tragedy or disaster. When the space shuttle Challenger blew up in 1986, it wasn’t just that there was a design flaw in the O-rings that were supposed to seal the hot gases within joints of the solid rocket boosters. It was damn cold that morning, and President Reagan really wanted some good copy to read into his State of the Union address that night. Technicians were advised to “take off their engineering hats,” and act like managers. Launch it! Those fragile, frozen O-rings cracked like crystal ware.

In 2003, when 100 people died at the Station nightclub fire in Rhode Island, it wasn’t just that some idiot thought it would be cool to use indoor fireworks as a special effect for the band Great White. The place was wrapped for sound in cheap plastic foam insulation that ignited, spread the fire, and filled the place with toxic gas. As the crowd surged for the exits, many made a wrong turn for the restrooms.

Now, on a much smaller scale, doctors and lawyers are sorting through the wreckage of lives lost or damaged in a series of giant, commercial dance parties that took place during the New Year’s, Memorial Day, and Fourth of July weekends in Los Angeles and San Francisco. These deaths will likely be called drug overdoses – consumption of illegally manufactured MDMA, or ecstasy, of unknown purity and potency. Combine that with hours of frenetic dancing to techno-pop in hot, crowded venues, and that’s a formula for heatstroke and organ failure.

But I wonder if they are missing one other ingredient: Theatrical fog, of all things.

Laser and strobe lighting effects -- shot through a haze of stage mist and artificial fog -- are as much a part of the rave experience as dreadful electronic techno-music and ecstasy. In this age of environmentalism and health consciousness, it’s worth noting that the entertainment industry is the only one I know of that still deliberately and unapologetically pollutes the air.

During raves, young people in various stages of intoxication dance themselves into a frenzy for hours, hyperventilating a potentially toxic brew of mist – aerosolized particles of mineral oil that linger in the air – and swirling clouds of alcohol-based fogs.

Is it harmless? Opera singers and musicians hate this stuff, and their unions have battled their theater managers about its use for years. Actors’ Equity and production managers have set exposure limits to theatrical fogs and hazes. Singers have claimed that modest exposures to “smoke,” as it is labeled in the stage direction, ended their careers. There have been several serious scientific studies of theatrical fog. They focus on its effects on people singing on stage with it for minutes at a time, or on those sitting in a music pit playing a number as the chemical clouds pour down on them.

The most recent is a five-year-old Canadian study of 101 employees in the entertainment industry. Professor Susan Kennedy and her team at the University of British Columbia School of Occupational and Environmental linked exposure to glycol and mineral oil mists to “acute and chronic adverse effects on respiratory health” of these workers. There was “chronic wheezing and chest tightness,”  “acute cough and dry throat,” and the symptoms increased with increased exposure. Lung function was “significantly lower among those working closest to the fog source.”

On May 29, the Skills DJ Workshop presented an electronic music festival – aka a rave – at the Cow Palace in Daly City. Sixteen thousand people attended, paying as much as $85 a ticket. Two young men died of suspected ecstasy overdoses, and nine other patrons were hospitalized, several in critical condition with kidney failure.

Dr. Kent Olson, medical director of the San Francisco Division of the California Poison Control Center, told me that the most likely cause of death and injury was drug-induced heat stroke: “The recent SF cases and those in LA were most likely due to a combination of higher doses, individual susceptibility, and ambient circumstances (warm environment, intensity of dancing) that would have contributed to drug-induced heat stroke --- which is a well known complication of MDMA alone.” But he also called my notion that stage fog might have contributed to the problem “an interesting hypothesis.”

Skills DJ Workshop spokeswoman Alexis Smith told me that six special effect fog machines were used during the “POP2010: The Dream” festival at the Cow Palace. Together, they consumed 12 gallons of fog fluid. Three of the machines were DF-50’s, which disperse a fine mist of mineral oil that lingers in the air, accentuating the beams of light flashing throughout the venue. Each DF-50 consumed 2 gallons of High Performance fog fluid produced by CITX.

If the claim is accurate, this is certainly interesting. According to the CITX web site , each DF-50 machine is designed to burn one and one half QUARTS of High Performance fluid over 32 HOURS. Now, the Cow Palace is a big place – 85,000 cubic meters, by my estimate – but those machines each generated a week’s worth of aerosolized mineral oil haze during the 10 hour event. Mineral oil is a petroleum distillate so pure that it’s considered safe to rub on a baby’s skin – but can anyone out there tell me what level of atomized oil mist is safe to breathe? What’s the safe level to breathe while dancing, for hours in high heat, high on street drugs?

According to the DF-50 Diffusion Hazer operating instructions , the “hang time” of this sort of haze is 3+ hours. The manufacturer stresses that, because the particles of oil are so tiny, “after a very short period of use the DF-50 will have produced more than a sufficient amount of atmosphere.” There are a few cautions listed: don’t blow the haze through a fan, “as this will result in build-up on the fan blades.” Also: “If the machine is used non-stop (this is NOT recommended) over a long duration, you may create a situation whereby the concentration of smoke is too much, which can result in a build-up of residue in the environment.”

But wait, there’s more…The festival special effects operators also used three G300’s, machines capable of producing either fog or haze. These used 2 gallons a piece of what Ms. Smith described as “water-based” haze fluid. Presuming that the operators used the recommended “C-Beam Fluid” to produce haze in the G300, this is hardly tap water.  According to manufacturer Le Maitre Pyrotechnics and Special Effects:  Do not drink it or use it in smoke machines except in well-ventilated areas. The Materials Safety Data Sheet for C-Beam does not identify the proprietary ingredients, but stresses their non-toxicity. It notes that when they are oxidized they produce pyruvic and acetic acids, which happen to be breakdown products of, respectively, glycol alcohol and mineral oil. Glycol alcohol is the standard ingredient in almost all commercial fog machines. There are food grade versions of it, but it is also an ingredient of antifreeze. It may be safe to swallow, but again – pardon my skepticism – what is the basis for the claim that it is safe to breathe?

One well recognized side effect of breathing theatrical fog is dryness in the throat. That is an interesting condition to add to the rave mix of MDMA, dancing and heat. Dehydration is known side-effect of MDMA. In response, ecstasy users tend to compensate by drinking copious amounts of water.  During a two-day rave festival in Los Angeles, over 114 people were hospitalized.  A 15-year-old girl died from an apparent ecstasy overdose – reports said that she drank cold water before losing consciousness, and an LA Times piece describe her as having symptoms of an electrolyte disturbance. It sounded a lot to me like hyponatremia, a sodium loss associated with athletes who consume too much water.

Two of 18 victims hospitalized during another rave event in Los Angeles, on New Year's Eve, suffered from hyponatremia. One participant at the event died, another suffered severe kidney damage, according to the Centers for Disease Control and Prevention, which coincidentally reported on that incident two weeks after the San Francisco fiasco, and two weeks before the second fatal rave in Los Angeles.

As a science writer, I need to be the first to point out that my “hypothesis” about theatrical fog as a possible contributor to the rave/ecstasy overdose phenomenon is speculation.  It’s not the kind of story I would write for a newspaper, without a great deal more research, but I believe it is appropriate for a personal blog.  (Here's a cavaet, for example: in the most recent instance, the event took place outdoors, in the Los Angeles Coliseum. However, it was in Los Angeles, a town for which the term SMOG was invented…)

I do not claim that the use of this special effect is THE cause of these tragedies. To the extent that accidents and disasters are typically a convergence of unfortunate events, it think there is more than enough reason for people with expertise in these matters to take this into consideration. I just can’t help but wonder if, as we are dazzled by the splendor of these cool special effects, we are figuratively willing to swap our engineering hats for paper party cones and whistles. It's just a commerical music concert. Kids shouldn’t have to die for this.

It seems to me that some classic pump handle epidemiology is in order here: Where in these music venues were the victims doing their dancing – were they in close proximity to any of the fog machines? What were the concentrations of mineral oil and glycol in the air at the time – did they meet the minimum standards demanded by actors and musicians during their brief hours upon the stage? Isn’t a drug overdose a little too easy an answer? If some people are more sensitive to the side effects of heat, or ecstasy, or theatrical fog, would that combination prove dangerous for a small, but real percentage of people at one extreme of the bell curve?

To my former colleagues in legacy media, and in the blogosphere, I hope this little monograph might inspire a little digging, a little real reporting on the nature of these raving tragedies, which seem to be piling up.

I first wrote about the potential adverse health effects of theatrical fog nearly a decade ago, in a front page article in the San Francisco Chronicle . It was one of my favorite pieces during my 22 years as a medical writer at the paper, but as often happens in the journalism world, it landed with an unremarkable thud.

It did not generate a lot of interest then, but I have often thought about it when I read about ecstasy overdoses at fake-fog-shrouded dance clubs. I also think about it when I troll the web and find people hawking fog machines for kids at Halloween parties. Wanna buy some Swamp Juice?  As the ad says, “All Froggys Fog and Haze fluids are made from lab grade UV-filtered de-ionized water and pharmaceutical grade chemicals, each approved by the FDA."

Sure, let’s invite all the neighborhood kids.

I have to end this on a personal note. This is likely my last blog, and my swan song as a journalist of any note. Next week, I will begin a job as a writer at the Lawrence Berkeley National Laboratory. It is an exciting place. I will be surrounded by smart people trying to understand the universe, unravel the meaning of the genome, or trying to save the planet. I’ve also enjoyed my time as a freelancer, with bylines in the New York Times, and it’s been a nice hobby to be a blogger to my faithful audience of…well, let’s not go there. But I have had to face economic reality, and the reality is that, in this dreadful economic climate, with exciting new technologies abounding, at 58 I have aged out of journalism. I feel damn lucky to be working soon at one of the world's greatest laboratories.

A year ago, writer Chris Mooney included me in a piece  he wrote for The Nation, called Unpopular Science, bemoaning the decline in science journalism at the hands of the internet. Having become redundant at the San Francisco Chronicle last year, just as I was finishing up a Knight Science Journalism Fellowship at MIT, I became Chris’ poster boy for exiled science reporters. Here, I’m writing the folo to that part of his story.

Like most veteran science writers, I have at times been saddened and embittered by the loss of a livelihood. More so I mourn the loss of an audience for the stories I wrote about HIV/AIDS, infectious diseases, health policy and general science. More than once, I have seen the web as a techno-kleptocracy, driven by a looting mentality that somehow dazzled my publishers.  My trusty laptop was just a portal to a vaster wasteland – vaster than any imagined by Newton Minow. Yet clearly the changes in media are so large and encompassing that it is foolish to take them personally.  Stories have to be told, and they will be – mostly by a younger generation, willing to work for less, and using tools that today only hint of their future potential.

For me, it has been a thrill to have been a reporter. I’m proud of the work I have done, and now I’m really looking forward to my new job.

So, not with a bang, but a Twitter… it’s -30- for Sabin.

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Sending Spit to Kaiser

Posted by Sabin Russell

Technicians at Kaiser's Oakland lab use a highly automated process to extract DNA from 2,500 samples of saliva per week. Photo by Peter DaSilva appears in May 30, 2010 New York Times

I had one more New York Times story left in me. Click that link and read it. Here's what it's about:

During the past two years, more than 130,000 Northern Californians have sent their saliva to Kaiser Permanente -- not a statement about HMOs or private health insurance -- but to participate in the largest genome scan of its kind. I was not aware that ordinary saliva contains enough white blood cells and cells from the lining of the saliva duct to provide more than enough DNA for modern high speed gene scans. Well, it does.

A spinoff from anti-recessionary spending, the Kaiser/UCSF project was one of those "beaker ready" projects on the wish list of big institutions that qualified for federal stimulus money -- $25 million from the NIH that has to be spent by October 2011. Kaiser had already been busily collecting spit from volunteers. With the stimulus money, they were able to process those samples and run the DNA of each patient over a chip that looks for 675,000 different gene variants. It took a while to set up the robots, but now 2,500 samples are spit are being analyzed each week.

The idea is that, by comparing the genes of healthy people to those of people who have various chronic ailments, they may be able to spot the genetic roots of those diseases. These scans are called genome wide association studies, and for the last several years they've been the hottest thing in molecular biology. The problem is that these scans may not be discerning enough to find faulty genes. It may well be that the genes that contribute to disease are not common. Instead, it is the rare variant that misfires and leads to illness -- and perhaps the only way to find those variants is to sequence the entire genome of affected individuals, rather than scanning their genes for selected variants.

We'll have to wait a couple of years to see if this giant project produces enough data to answer the questions, or strengthens the case that whole genome sequencing, rather than these genome wide association studies, are needed to yield the information researchers believe they can find. In the meantime, Dr. Elizabeth Blackburn and her lab will also be analyzing the DNA of these same volunteers to measure the length of telomeres (tee-lo-meers), which are wads of repeating sequences of DNA that bind the ends of chromosomes like the tips on shoelaces, so the the DNA chains don't unravel every time a cell divides. Long telomeres are associated with longer lifespan, shorter teleomeres with shorter longevity. Blackburn will be analyzing telomere length simultaneously with the data from the high speed gene scans.

The first results of this giant study won't be ready until 2011. Until then, read what you can about this technology, which represents in many ways the leading edge of modern genetics. As this story demonstrates, it is has already reached into the homes of 130,000 Northern Californians, who have sent their spit to Kaiser. In time, Kaiser expects to have DNA stored from spit or blood of 500,000 members.   It's where soft, wet chemistry (what is wetter than spit or blood? ) meets the hard dry edge of statistics. Whether or not studies like this one  will solve the genetic puzzles surrounding chronic illness and longevity remains to be seen. Regardless, this spit-propelled project will build up an enormous bank of information that will keep the dry scientists -- those sifters of epidemiological data -- and their computers busy for decades to come.

Read the whole story in the New York Times.

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Posted by Sabin Russell

Yellow Legged Frog Credit:USGS

For people looking for the proverbial "canary in the coal mine," frogs offer plenty of fodder for the dark imagination. A 2004 study by the International Union for the Conservation of Nature and Natural Resources (IUCN) found that 43 percent of 5,743 amphibian species worldwide were in decline; one third of the total met the IUCN's "Red List" criteria of being vulnerable, endangered or critically endangered.    

In California, the loss of the Sierra Nevada frog population has been phenomenal, and the once ubiquitous mountain yellow-legged frogs are today's classic example -- in just a few decades they have disappeared from 93 percent of their range in the high mountain lakes. Two closely related species  are listed as "critically endangered."  

Vance Vredenburg of San Francisco State University and his colleagues have been studying the mountain frogs, and this week published a pair of papers in the Proceedings of the National Academy of Sciences based on 13 years of observations. (; Vredenburg previously has identified a fungal infection known as chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), as the primary culprit. This is no ordinary fungus. Chytridiomycosis has been blamed for "the greatest loss of vertebrate biodiversity attributable to disease in recorded history" -- in other words, this is a genocidal bug.     

In his latest work, Vredenburg studied three mountain watersheds in Sequoia and Kings Canyon National Parks. Initially, all three were Bd-free, and home to thriving populations of yellow-legged frogs in 88 different lakes. But his meticulous observations tracked how Bd eventually appeared in each watershed, and chytrid swept like waves through various frog colonies, leading to "extirpation" -- a clinically precise word for "wiped out."  His study of the extirpation process showed how it was a function of  "fungal load," the average amount of spores on the frogskin surfaces. Fungal load would rise and reach a threshold, at which point the frog populations were quickly...extirpated. He even mapped the pace of this grisly extinction -- about 688 meters per year -- similar to the range of individual frogs, indicating the fungus was spreading frog to frog.    

What's unusual and unsettling about this is that, as Vredenburg  points out, "disease is generally not a driving force in extinctions," because typically a pathogen fades away as it knocks down the host population. The dynamics of this fungal infection in the Sierra lakes and ponds are different. Fungal load could soar to the lethal threshold in less than 50 days, causing mass mortality, a die-off so quick and complete that mitigating factors such as an immune response or "density dependence" -- that loss of virulence due to thinning of the host population -- could not kick-in. This is extirpation, disease-driven extinction -- very creepy to contemplate. So intent is this organism on eliminating its host that it lingers over the long winters, when tadpoles of yellow-legged frogs slumber under the ice. When summer arrives and they metamorphose into frogs, the fungus strikes again. Yellow-legged frogs are unusual in that they can remain in the tadpole state for three successive winters. Extirpation, therefore, is not instantaneous. It comes in three genocidal cycles.    

A second Vredenburg paper explains an exception to this dreadful scenario. There are lakes where hobbled populations of frogs seem to live if, and only if, circumstances conspire to lower the fungal load below the lethal threshold -- it's a natural strategy not unlike harm reduction. These are not happy frogs, but a few of them live on, like bunker survivalists.  

What to make of all this? Why fungus? Should we be thinking of patterns, when we also read of the devastating impact of white nose fungus on bat populations, a mammalian species? Some bat populations in Vermont are down 90 percent.     

Fungi may also be playing a role in another genocidal disease that goes under the name Colony Collapse Disorder, which is wreaking havoc in the honey bee population. A suspect -- by no means proven the culprit -- is the parasitic fungus Nosema ceranae.  

There's even a fungus that has clipped the occasional healthy human being. Cryptococcus gattii is a tropical airborne fungus that turned up in British Columbia in 1999, and has drifted south into Oregon.  A paper about this particularly virulent C. gattii strain (, published in the April 22, 2010 issue of PLoS Pathogens is extremely dense reading and a bit unsettling. An excerpt:     

 The continued expansion of C. gattii in the United States is ongoing, and the diversity of hosts increasing. Cases have been observed in urban and rural areas, and have occurred in a range of mammals. On Vancouver Island and the mainland of British Columbia, cases have been documented in marine and terrestrial mammals including cats, dogs, porpoises, ferrets, and llamas. This trend has continued in the United States, with several cases in agrarian, domestic, and wild terrestrial mammals, as well as marine mammals, adding elk, alpacas, and sheep to the aforementioned list. The co-expansion of the outbreak among mammals and humans is significant for several reasons. Non-migratory mammals serve as sentinels for disease expansion, particularly given that isolation of C. gattii from the environment is difficult, and not yet successful at all in Oregon. Additionally, the threat to agricultural and domestic animals is significant and thus the need for cooperation among health officials is critical. Finally, the widespread spectrum of disease illustrates that the organism is likely to be pervasive in the environment, and that physicians and veterinarians should be well informed of symptoms to facilitate early diagnoses, and successful isolate collection and tracking.   

Since 2004, it has been implicated in 21 human cases in the U.S., causing five deaths -- a 25 percent mortality rate. Not quite extirpation. Infectious disease experts, including lead study author Edmond J. Byrnes, say the yeast-like bug with a penchant for eucalyptus trees is so rare that it is not a significant threat to public health -- more of a scientific curiosity, for now.     

 So... no need to panic about C. gattii.   

But it does cause one to ponder, in our very scientific way... what did we and the frogs and the bats and the bees do to the 'shrooms to make them so pissed off at us?

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Wrinkles in Time — Stephen Hawking Dives into the Quantum Foam

Posted by Sabin Russell

Stephen Hawking Credit: Getty Images

Since it is Sunday, a day for secular humanists to reflect, I was delighted to read a very accessible discourse on time and space by Stephen Hawking in -- of all places -- the Daily Mail, a UK tabloid. 

Hawking has been in the news lately, making the observation that maybe it would not be a good ideas to contact space aliens, as they would more or less give us the Christopher Columbus treatment. This is really sort of ...obvious, and makes me worry a little bit about Dr. Hawking, as he is better known for really clear descriptions of things that aren't obvious at all, such as the bendable nature of space and time. He's wonderfully sympathetic to those of us who can grasp the importance of what deep physics is telling us, but really can't explain it to ourselves. 

So I was pleased to read this essay on line in the Daily Mail. I'll excerpt bits of it, but I encourage all of you to read it, cause it's just plain cosmic fun. It's called: How to Build a Time Machine, All you need is a wormhole, the Large Hadron Collider or a rocket that goes really, really fast. 

If I can't convince you to jump right in and read the whole thing, I at least hope you will read a few of his more interesting paragraphs. Hawking is at his popular best when he is explaining Einstein. He's like a Sunday School teacher in the Church of Relativity. Some day, if I read my Book often enough, I might actually grok it. 

So here are a few clips from the article. First, describing wormholes, which like time tunnels of science fiction, are indeed a kind of portal within the fourth dimension: 

"Physicists have been thinking about tunnels in time too, but we come at it from a different angle. We wonder if portals to the past or the future could ever be possible within the laws of nature. As it turns out, we think they are. What's more, we've even given them a name: wormholes. The truth is that wormholes are all around us, only they're too small to see. Wormholes are very tiny. They occur in nooks and crannies in space and time. You might find it a tough concept, but stay with me... 

Nothing is flat or solid. If you look closely enough at anything you'll find holes and wrinkles in it. It's a basic physical principle, and it even applies to time. Even something as smooth as a pool ball has tiny crevices, wrinkles and voids. Now it's easy to show that this is true in the first three dimensions. But trust me, it's also true of the fourth dimension. There are tiny crevices, wrinkles and voids in time. Down at the smallest of scales, smaller even than molecules, smaller than atoms, we get to a place called the quantum foam. This is where wormholes exist. Tiny tunnels or shortcuts through space and time constantly form, disappear, and reform within this quantum world. And they actually link two separate places and two different times. 

Unfortunately, these real-life time tunnels are just a billion-trillion-trillionths of a centimetre across. Way too small for a human to pass through - but here's where the notion of wormhole time machines is leading. Some scientists think it may be possible to capture a wormhole and enlarge it many trillions of times to make it big enough for a human or even a spaceship to enter..." 

In another section of the essay, Hawking once again goes to the Einstein, explaining the plasticity of time with a nice water metaphor, and then going into a real world example of just how close relativity comes to home -- how the GPS system in our Garmins and iPhones has to take gravity's brake on time into account. That river of time runs just a tad more quickly in satellites circling the earth -- and if they did not calibrate their internal clocks to take this relativistic phenonmenon into account, our GPS's would miss their coordinates by...six miles a day

"Time flows like a river and it seems as if each of us is carried relentlessly along by time's current. But time is like a river in another way. It flows at different speeds in different places and that is the key to travelling into the future. This idea was first proposed by Albert Einstein over 100 years ago. He realised that there should be places where time slows down, and others where time speeds up. He was absolutely right. And the proof is right above our heads. Up in space. 

This is the Global Positioning System, or GPS. A network of satellites is in orbit around Earth. The satellites make satellite navigation possible. But they also reveal that time runs faster in space than it does down on Earth. Inside each spacecraft is a very precise clock. But despite being so accurate, they all gain around a third of a billionth of a second every day. The system has to correct for the drift, otherwise that tiny difference would upset the whole system, causing every GPS device on Earth to go out by about six miles a day. You can just imagine the mayhem that that would cause. 

The problem doesn't lie with the clocks. They run fast because time itself runs faster in space than it does down below. And the reason for this extraordinary effect is the mass of the Earth. Einstein realised that matter drags on time and slows it down like the slow part of a river. The heavier the object, the more it drags on time. And this startling reality is what opens the door to the possibility of time travel to the future..." 

So, time travelers, read the Daily Mail: 


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Dueling Bugs: Giga- and Nano-scale Ant-iBodies

Posted by Sabin Russell

Menzel 3, aka The Ant Nebula

Well, it is good to be back in action. The engineers at Network Solutions finally (see prior post) got on the case, and solved it. For the techies out there, here is the Dx/Rx: "Our Engineers have identified and corrected the issue of file permissions being set incorrectly for file uploads." A Hearty Thank You! (freelance wages) to them.

As a reward to my patient followers, I am presenting here on the left, Planetary Nebula Menzel 3, AKA the Ant Nebula, in honor of our recent bug. Truth be told, it was my first attempt to upload this cosmological bug that seemed to have brought about the recent unpleasantness. A non-scientist would suspect some sort of Karmic connection; a Jungian, a bit of synchronicity; a scientist, an association, not causality, and undoubtedly the result of chance.  I, of course, attribute it to bad luck and the gremlin that sits on my shoulder, ready to pounce and foul up my bytes whenever he/she/it is hungry or feeling frisky.

My original intent in posting the beautiful Ant Nebula -- a computer composite of Hubble images produced by the Hubble Heritage project -- was to say something profound about the the tendency of nature to produce varying degrees of dual symmetry, in this case the structure of the death throes of a star quite like our own Sun. That was meant to be a rough segway to the posting of my latest freelance work, a piece in MIT's Technology Review (June 2010) about dual specific antibodies.

Antibodies are Y-shaped structures, about 10 nanometers long, that are one of the immune system's primary weapons against invading...bugs.  My piece, commissioned by the good folks at Technology Review, was to look at a technology developed by Genentech Inc. scientist Germaine Fuh and her team to cause a single antibody to attach to two different targets. These dual-specific antibodies were chosen by the editors of Technology Review as one of the TR 10 -- the top ten emerging technologies of the year.

 The dual action takes place at the tips of the symetrical Y-shaped wings, a region called the paratope, which connects to the...epitope -- a receptor on a cell or bacteria or virus. Drugs can be made by producing engineered antibodies that latch onto specific receptors, such at the HER2 receptor on the surface of some breast cancer cells. The receptor acts like a faulty accelerator pedal on a 2010 Prius. Your breast cancer cells just take off. The Genentech drug that blocks this accelerator pedal, Herceptin, is worth billions. So is another monoclonal antibody, Avastin, that jams a mechanism cancer cells use to promote blood vessel growth -- angiogenesis.

 Fuh's team tinkered with the tips of the Herceptin and Avastin antibodies and produced a new antibody that attaches to either receptor -- a two-for-one drug. The cynic in me would say this is just a scheme to stretch the patent life of the two drugs, which last year generated worldwide sales of $11 billion for Roche, the Swiss drug company that now owns Genentech. Probably true, but the combined drug might also genuinely work better at half the cost to produce than using both in the same patient. And the real story is that Fuh's technology can be applied to entirely new monoclonal drugs, so you might be able to produce a beneficial two-for-one combination antibody right out of the chute, which would require only one regulatory process instead of at least two.

I've written all this so you won't have to read the article itself, but it's short, and if you want to see it, here is the link:

Photo credit: From Astronomy Picture of the Day, April 25, a composite image produced by the Hubble Heritage Project. Credit:  R. Sahai (JPL) et al., Hubble Heritage Team, ESA, NASA.

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A Spot of Bother

Posted by Sabin Russell

Spot of Bother: Eyjafjallajokull Volcano, as seen from space


"Ladies and Gentlemen, we are in a spot of bother." 

 So said Capt. Eric Moody, addressing his passengers as pilot of British Airways Flight 009, enroute to New Zealand from Heathrow Airport in London, when just west of Jakarta, at 37,000 feet, all four engines stopped. It was June 24, 1982.    

  Long before Capt. "Sully" Sullenberger pulled off his Miracle on the Hudson, Capt. Moody landed The City of Edinburgh and 240 passengers and crew safely in Jakarta after flying through a cloud of volcanic ash over the Indian Ocean. The unexpected encounter in the middle of the night clogged all four engines of the 747, and the plane glided silently to 13,000 feet before one engine, then two, three and four restarted. With three still going, their electronic instruments failing and a windshield sand-blasted opaque, the crew threaded through a mountain range and made their happy landing in Indonesia.

  The current spot of bother, of course, is the Eyjafjallajokull Volcano, the laughably unprounceable spewer of ash in Iceland that has shut down air traffic all over Europe. It was the experience of Flight 009 -- and a repeat performance in 1989, when KLM 867 glided for five minutes with all four engines out after a run-in with the plume from the Redoubt volcano over Alaska -- that led international air traffic controllers to take the latest navigation hazard so seriously.    

I still remember the quote from from 28 year old wire service accounts of Capt. Moody's awesome display of British reserve in a crisis.  "We're in a spot of bother." It's a silly and ironic turn of phrase, and it strikes a chord for that coolness under fire that we admire about Brits. Capt. Sully didn't have time for irony when he struck that flock of Canada geese over New York City, but we admire that same sense of cool command and decisiveness.  And let's face it, in all these kinds of situations, we tend to feel we are witnessing something miraculous, something lucky. Luck, we hope, is something contagious. We love it when we see it. Think about buzzer beaters in basketball.   

When the Barack Obama presidency was six months old, he paid a visit to the troops in Iraq-- another spot of bother.  In an Army base gymnasium, he shot some hoops with soldiers in front of TV cameras. There's a well-known clip of him snapping the net, with a perfectly aimed shot from the three-point line. Coolness under pressure. Lucky. 

     Photo: NTV/EPA

Not every encounter with a spot of bother has a happy ending. There is a place in Russia known as Katyn Forest. It was a very unlucky place for 22,000  Polish Army officers in 1940. When the President Lech Kaczynski of Poland, his wife and 94 others were killed in a plane crash there last week on their way to an April 10th commemoration of the massacre, luck did not favor the pilot or the President. The Poles once again refer to the place as "cursed."    

 The results of the investigation of the Polish air disaster are still pending, but it is not hard to imagine the pressure the pilots were under to land the plane in time for the ceremony, despite the wave off from the Russian air controllers. No comments about "spot of bother here." There probably wasn't time for reflection. Yet I doubt this was an example of coolness under pressure, of decisiveness and command. Kaczynski had raised hell with Polish pilots earlier, when they refused to land him in Georgia, during the conflict there with Russia.   

According to Egyptian backgammon players, luck is "the just and inevitable reward of the skillful." Baseball wise man Branch Rickey called it "the residue of design." To put a little science in this, Louis Pasteur famously said "Fortune favors the prepared mind."  If I ever encountered a spot of bother, would I have the coolness and command of a Capt. Moody or Sullenberger? I doubt it.  That's why we admire people who do. We call them Lucky. We call them heroes. They are leaders we tend to follow. I guess we harbor the hope that, in our spots of bother, a little of their luck will rub off on us.  

If we were to pan out from the satellite photograph of  Eyjafjallajokull, we'd eventually see another spot of bother: 

  Here is a place that is heating up, and cries out for coolness under fire. It's a place where people are trying to wave us away from danger, while others are denying or belittling the risk and demanding that we press on. It will take the right kind of leadership to get us through this jam, to  remain calm, and make the right decisions. It's reassuring to think we still have the capacity to choose between a a safe landing and a rising plume. We will need some skilled leadership, some good design, and as the great scientist once said, "the prepared mind." 

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Space for Space

Posted by Sabin Russell

Astronomy Picture of the Day

I have laid down quite a bit of grey type in the last several posts, so I thought it was time to put a little more color back into this Blog, and give a plug to Astronomy Picture of the Day, a site that my four avid readers may already know can be accessed any time by clicking on the link to the right under the Blogroll label.

So, take a look at the Orion Nebula, in all its glory.

This is actually a bit of a phony photograph because it uses special "false color" processing to make visible the infrared images gathered from the Spitzer Space Telescope. If this was photojournalism, fingers would be wagging, because authenticity is paramount. Tinkering with images is tantamount to fraud. But in this picture from space, a little fraud helps us see what otherwise we would not. And since, if we looked up and tried to see this with the naked eye, we would not, we have to have a little inauthenticity to comprehend the almost incomprehensible. Too bad Spitzer is giving this a bit of a bad name. It is a pretty picture.

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It’s the Virus, Stupid

Posted by Sabin Russell

A story by me in the Sunday, April 4, 2010 Bay Area section of the New York Times. I think it is new, and interesting, and important, which as my four avid readers know, is my standard for what is news worth reading.  This one is about San Francisco taking the lead in adopting the most aggressive option for treating HIV -- a patient should start taking the antiviral meds as soon as he or she tests positive. It's controversial still, but the evidence points to a model of HIV disease in which the virus causes permanent damage while T-cell counts are still high. There was a time when an argument could be made that the medications were worse the the bug. I'm inclined to side with Dr. Follansbee's analysis below, or as he also explained it to me: "It's the virus, stupid."

City Endorses New Policy for Treatment of H.I.V.


In a major shift of H.I.V. treatment policy, San Francisco public health doctors have begun to advise patients to start taking antiviral medicines as soon as they are found to be infected, rather than waiting — sometimes years — for signs that their immune systems have started to fail.

The new, controversial city guidelines, to be announced next week by the Department of Public Health, may be the most forceful anywhere in their endorsement of early treatment against H.I.V., the virus that causes AIDS.

Ever since combinations of antiviral drugs were found to slow progression of the disease in the mid-1990s, doctors and patients have wrestled with the question of when to begin a lifetime regimen of costly and sometimes toxic medicines. The answer remains in dispute, but public health leaders here are now making a case for a change.

Behind the policy switch is mounting evidence that patients who start early are more likely to live longer, and less likely to suffer a variety of ailments — including heart disease, kidney failure and cancer — that plague long-term survivors. Studies suggest that in the early years of infection, when a patient may show few signs of immune system failure, the virus is in fact causing permanent damage that becomes evident later.

For instance, in older patients who finally start taking the drugs, the effects of chronic inflammation take their toll.

“The impact on health risk is comparable to that of diabetes,” said Dr. Steven G. Deeks, a researcher at the University of California, San Francisco. “Their immune system may look like that of someone 30 years older.”

Dr. Diane V. Havlir, chief of the H.I.V./AIDS division at San Francisco General Hospital, said the new policy was already in effect for her patients. Although a decision whether or not to take the medicine rests with the patient, all those testing positive for H.I.V. will be offered combination therapy, with advice to pursue it.

“The history of H.I.V. disease has always been about change,” she said. “We pride ourselves on working quickly with new data.”

 Or read the whole thing:

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