Last year's Contact conference was one of my favorite conferences of all time.

The focus of Contact is really hard to explain, but I'll try: Space Exploration, Artificial Intelligence, Music, Science Fiction, Film making, Singularity stuff, Robot stuff, Artificial Life, Virtual Worlds, Virtual Reality, Space Colonization, Astrobiology, Astropsychology, Astrosociology, Biotech, Bioinformatics... -- and *really* on all of it! (and I'm sure I'm forgetting something) -- ALL this stuff is covered -- and well!

Just go if you can. Registration is a bargain, and there's a student rate!

Check out the speaker list.

Aw come on -- we just went through all this trouble to take over Iraq, and now we find out we can make oil out of... anything?

Anything into
Oil Technological savvy could turn 600 million tons of turkey guts and other waste
into 4 billion barrels of light Texas crude each year
By Brad Lemley for Discover Magazine.

In an industrial park in Philadelphia sits a new machine that can change almost anything into oil.

Really.

...Because depolymerization takes apart materials at the molecular level, Appel says, it is "the perfect process for destroying pathogens." On a wet afternoon in Carthage, he smiles at the new plant—an artless assemblage of gray and dun-colored buildings—as if it were his favorite child. "This plant will make 10 tons of gas per day, which will go back into the system to make heat to power the system," he says. "It will make 21,000 gallons of water, which will be clean enough to discharge into a municipal sewage system. Pathological vectors will be completely gone. It will make 11 tons of minerals and 600 barrels of oil, high-quality stuff, the same specs as a number two heating oil." He shakes his head almost as if he can't believe it. "It's amazing. The Environmental Protection Agency doesn't even consider us waste handlers. We are actually manufacturers—that's what our permit says. This process changes the whole industrial equation. Waste goes from a cost to a profit."

...Chemistry, not alchemy, turns (A) turkey offal—guts, skin, bones, fat, blood, and feathers—into a variety of useful products. After the first-stage heat-and-pressure reaction, fats, proteins, and carbohydrates break down into (B) carboxylic oil, which is composed of fatty acids, carbohydrates, and amino acids. The second-stage reaction strips off the fatty acids' carboxyl group (a carbon atom, two oxygen atoms, and a hydrogen atom) and breaks the remaining hydrocarbon chains into smaller fragments, yielding (C) a light oil. This oil can be used as is, or further distilled (using a larger version of the bench-top distiller in the background) into lighter fuels such as (D) naphtha, (E) gasoline, and (F) kerosene. The process also yields (G) fertilizer-grade minerals derived mostly from bones and (H) industrially useful carbon black...

Feedstock is funneled into a grinder and mixed with water to create a slurry that is pumped into the first-stage reactor, where heat and pressure partially break apart long molecular chains. The resulting organic soup flows into a flash vessel where pressure drops dramatically, liberating some of the water, which returns back upstream to preheat the flow into the first-stage reactor. In the second-stage reactor, the remaining organic material is subjected to more intense heat, continuing the breakup of molecular chains. The resulting hot vapor then goes into vertical distillation tanks, which separate it into gases, light oils, heavy oils, water, and solid carbon. The gases are burned on-site to make heat to power the process, and the water, which is pathogen free, goes to a municipal waste plant. The oils and carbon are deposited in storage tanks, ready for sale.

Here is the full text of the article in case the link goes bad:

http://www.discover.com/may_03/gthere.html?article=featoil.html

Anything into Oil Technological savvy could turn 600 million tons of turkey guts and other waste into 4 billion barrels of light Texas crude each year

By Brad Lemley Photography by Tony Law

Gory refuse, from a Butterball Turkey plant in Carthage, Missouri, will no longer go to waste. Each day 200 tons of turkey offal will be carted to the first industrial-scale thermal depolymerization plant, recently completed in an adjacent lot, and be transformed into various useful products, including 600 barrels of light oil.

In an industrial park in Philadelphia sits a new machine that can change almost anything into oil. Really. "This is a solution to three of the biggest problems facing mankind," says Brian Appel, chairman and CEO of Changing World Technologies, the company that built this pilot plant and has just completed its first industrial-size installation in Missouri. "This process can deal with the world's waste. It can supplement our dwindling supplies of oil. And it can slow down global warming." Pardon me, says a reporter, shivering in the frigid dawn, but that sounds too good to be true. "Everybody says that," says Appel. He is a tall, affable entrepreneur who has assembled a team of scientists, former government leaders, and deep-pocketed investors to develop and sell what he calls the thermal depolymerization process, or TDP. The process is designed to handle almost any waste product imaginable, including turkey offal, tires, plastic bottles, harbor-dredged muck, old computers, municipal garbage, cornstalks, paper-pulp effluent, infectious medical waste, oil-refinery residues, even biological weapons such as anthrax spores. According to Appel, waste goes in one end and comes out the other as three products, all valuable and environmentally benign: high-quality oil, clean-burning gas, and purified minerals that can be used as fuels, fertilizers, or specialty chemicals for manufacturing. Unlike other solid-to-liquid-fuel processes such as cornstarch into ethanol, this one will accept almost any carbon-based feedstock. If a 175-pound man fell into one end, he would come out the other end as 38 pounds of oil, 7 pounds of gas, and 7 pounds of minerals, as well as 123 pounds of sterilized water. While no one plans to put people into a thermal depolymerization machine, an intimate human creation could become a prime feedstock. "There is no reason why we can't turn sewage, including human excrement, into a glorious oil," says engineer Terry Adams, a project consultant. So the city of Philadelphia is in discussion with Changing World Technologies to begin doing exactly that. "The potential is unbelievable," says Michael Roberts, a senior chemical engineer for the Gas Technology Institute, an energy research group. "You're not only cleaning up waste; you're talking about distributed generation of oil all over the world." "This is not an incremental change. This is a big, new step," agrees Alf Andreassen, a venture capitalist with the Paladin Capital Group and a former Bell Laboratories director. The offal-derived oil, is chemically almost identical to a number two fuel oil used to heat homes.

Andreassen and others anticipate that a large chunk of the world's agricultural, industrial, and municipal waste may someday go into thermal depolymerization machines scattered all over the globe. If the process works as well as its creators claim, not only would most toxic waste problems become history, so would imported oil. Just converting all the U.S. agricultural waste into oil and gas would yield the energy equivalent of 4 billion barrels of oil annually. In 2001 the United States imported 4.2 billion barrels of oil. Referring to U.S. dependence on oil from the volatile Middle East, R. James Woolsey, former CIA director and an adviser to Changing World Technologies, says, "This technology offers a beginning of a way away from this." But first things first. Today, here at the plant at Philadelphia's Naval Business Center, the experimental feedstock is turkey processing-plant waste: feathers, bones, skin, blood, fat, guts. A forklift dumps 1,400 pounds of the nasty stuff into the machine's first stage, a 350-horsepower grinder that masticates it into gray brown slurry. From there it flows into a series of tanks and pipes, which hum and hiss as they heat, digest, and break down the mixture. Two hours later, a white-jacketed technician turns a spigot. Out pours a honey-colored fluid, steaming a bit in the cold warehouse as it fills a glass beaker. It really is a lovely oil. "The longest carbon chains are C-18 or so," says Appel, admiring the liquid. "That's a very light oil. It is essentially the same as a mix of half fuel oil, half gasoline." Private investors, who have chipped in $40 million to develop the process, aren't the only ones who are impressed. The federal government has granted more than $12 million to push the work along. "We will be able to make oil for $8 to $12 a barrel," says Paul Baskis, the inventor of the process. "We are going to be able to switch to a carbohydrate economy."

Making oil and gas from hydrocarbon-based waste is a trick that Earth mastered long ago. Most crude oil comes from one-celled plants and animals that die, settle to ocean floors, decompose, and are mashed by sliding tectonic plates, a process geologists call subduction. Under pressure and heat, the dead creatures' long chains of hydrogen, oxygen, and carbon-bearing molecules, known as polymers, decompose into short-chain petroleum hydrocarbons. However, Earth takes its own sweet time doing this—generally thousands or millions of years—because subterranean heat and pressure changes are chaotic. Thermal depolymerization machines turbocharge the process by precisely raising heat and pressure to levels that break the feedstock's long molecular bonds. Many scientists have tried to convert organic solids to liquid fuel using waste products before, but their efforts have been notoriously inefficient. "The problem with most of these methods was that they tried to do the transformation in one step—superheat the material to drive off the water and simultaneously break down the molecules," says Appel. That leads to profligate energy use and makes it possible for hazardous substances to pollute the finished product. Very wet waste—and much of the world's waste is wet—is particularly difficult to process efficiently because driving off the water requires so much energy. Usually, the Btu content in the resulting oil or gas barely exceeds the amount needed to make the stuff. That's the challenge that Baskis, a microbiologist and inventor who lives in Rantoul, Illinois, confronted in the late 1980s. He says he "had a flash" of insight about how to improve the basic ideas behind another inventor's waste-reforming process. "The prototype I saw produced a heavy, burned oil," recalls Baskis. "I drew up an improvement and filed the first patents." He spent the early 1990s wooing investors and, in 1996, met Appel, a former commodities trader. "I saw what this could be and took over the patents," says Appel, who formed a partnership with the Gas Technology Institute and had a demonstration plant up and running by 1999. Thermal depolymerization, Appel says, has proved to be 85 percent energy efficient for complex feedstocks, such as turkey offal: "That means for every 100 Btus in the feedstock, we use only 15 Btus to run the process." He contends the efficiency is even better for relatively dry raw materials, such as plastics. So how does it work? In the cold Philadelphia warehouse, Appel waves a long arm at the apparatus, which looks surprisingly low tech: a tangle of pressure vessels, pipes, valves, and heat exchangers terminating in storage tanks. It resembles the oil refineries that stretch to the horizon on either side of the New Jersey Turnpike, and in part, that's exactly what it is. Appel strides to a silver gray pressure tank that is 20 feet long, three feet wide, heavily insulated, and wrapped with electric heating coils. He raps on its side. "The chief difference in our process is that we make water a friend rather than an enemy," he says. "The other processes all tried to drive out water. We drive it in, inside this tank, with heat and pressure. We super-hydrate the material." Thus temperatures and pressures need only be modest, because water helps to convey heat into the feedstock. "We're talking about temperatures of 500 degrees Fahrenheit and pressures of about 600 pounds for most organic material—not at all extreme or energy intensive. And the cooking times are pretty short, usually about 15 minutes." Once the organic soup is heated and partially depolymerized in the reactor vessel, phase two begins. "We quickly drop the slurry to a lower pressure," says Appel, pointing at a branching series of pipes. The rapid depressurization releases about 90 percent of the slurry's free water. Dehydration via depressurization is far cheaper in terms of energy consumed than is heating and boiling off the water, particularly because no heat is wasted. "We send the flashed-off water back up there," Appel says, pointing to a pipe that leads to the beginning of the process, "to heat the incoming stream." At this stage, the minerals—in turkey waste, they come mostly from bones—settle out and are shunted to storage tanks. Rich in calcium and magnesium, the dried brown powder "is a perfect balanced fertilizer," Appel says. The remaining concentrated organic soup gushes into a second-stage reactor similar to the coke ovens used to refine oil into gasoline. "This technology is as old as the hills," says Appel, grinning broadly. The reactor heats the soup to about 900 degrees Fahrenheit to further break apart long molecular chains. Next, in vertical distillation columns, hot vapor flows up, condenses, and flows out from different levels: gases from the top of the column, light oils from the upper middle, heavier oils from the middle, water from the lower middle, and powdered carbon—used to manufacture tires, filters, and printer toners—from the bottom. "Gas is expensive to transport, so we use it on-site in the plant to heat the process," Appel says. The oil, minerals, and carbon are sold to the highest bidders. Depending on the feedstock and the cooking and coking times, the process can be tweaked to make other specialty chemicals that may be even more profitable than oil. Turkey offal, for example, can be used to produce fatty acids for soap, tires, paints, and lubricants. Polyvinyl chloride, or PVC—the stuff of house siding, wallpapers, and plastic pipes—yields hydrochloric acid, a relatively benign and industrially valuable chemical used to make cleaners and solvents. "That's what's so great about making water a friend," says Appel. "The hydrogen in water combines with the chlorine in PVC to make it safe. If you burn PVC [in a municipal-waste incinerator], you get dioxin—very toxic." Brian Appel, CEO of
Changing World Technologies, strolls through a thermal depolymerization plant in Philadelphia. Experiments at the pilot facility revealed that the process is scalable—plants can sprawl over acres and handle 4,000 tons of waste a day or be "small enough to go on the back of a flatbed truck" and handle just one ton daily, says Appel.

The technicians here have spent three years feeding different kinds of waste into their machinery to formulate recipes. In a little trailer next to the plant, Appel picks up a handful of one-gallon plastic bags sent by a potential customer in Japan. The first is full of ground-up appliances, each piece no larger than a pea. "Put a computer and a refrigerator into a grinder, and that's what you get," he says, shaking the bag. "It's PVC, wood, fiberglass, metal, just a mess of different things. This process handles mixed waste beautifully." Next to the ground-up appliances is a plastic bucket of municipal sewage. Appel pops the lid and instantly regrets it. "Whew," he says. "That is nasty." Experimentation revealed that different waste streams require different cooking and coking times and yield different finished products. "It's a two-step process, and you do more in step one or step two depending on what you are processing," Terry Adams says. "With the turkey guts, you do the lion's share in the first stage. With mixed plastics, most of the breakdown happens in the second stage." The oil-to-mineral ratios vary too. Plastic bottles, for example, yield copious amounts of oil, while tires yield more minerals and other solids. So far, says Adams, "nothing hazardous comes out from any feedstock we try." "The only thing this process can't handle is nuclear waste," Appel says. "If it contains carbon, we can do it." à This Philadelphia pilot plant can handle only seven tons of waste a day, but 1,054 miles to the west, in Carthage, Missouri, about 100 yards from one of ConAgra Foods' massive Butterball Turkey plants, sits the company's first commercial-scale thermal depolymerization plant. The $20 million facility, scheduled to go online any day, is expected to digest more than 200 tons of turkey-processing waste every 24 hours.

The north side of Carthage smells like Thanksgiving all the time. At the Butterball plant, workers slaughter, pluck, parcook, and package 30,000 turkeys each workday, filling the air with the distinctive tang of boiling bird. A factory tour reveals the grisly realities of large-scale poultry processing. Inside, an endless chain of hanging carcasses clanks past knife-wielding laborers who slash away. Outside, a tanker truck idles, full to the top with fresh turkey blood. For many years, ConAgra Foods has trucked the plant's waste—feathers, organs, and other nonusable parts—to a rendering facility where it was ground and dried to make animal feed, fertilizer, and other chemical products. But bovine spongiform encephalopathy, also known as mad cow disease, can spread among cattle from recycled feed, and although no similar disease has been found in poultry, regulators are becoming skittish about feeding animals to animals. In Europe the practice is illegal for all livestock. Since 1997, the United States has prohibited the feeding of most recycled animal waste to cattle. Ultimately, the specter of European-style mad-cow regulations may kick-start the acceptance of thermal depolymerization. "In Europe, there are mountains of bones piling up," says Alf Andreassen. "When recycling waste into feed stops in this country, it will change everything." Because depolymerization takes apart materials at the molecular level, Appel says, it is "the perfect process for destroying pathogens." On a wet afternoon in Carthage, he smiles at the new plant—an artless assemblage of gray and dun-colored buildings—as if it were his favorite child. "This plant will make 10 tons of gas per day, which will go back into the system to make heat to power the system," he says. "It will make 21,000 gallons of water, which will be clean enough to discharge into a municipal sewage system. Pathological vectors will be completely gone. It will make 11 tons of minerals and 600 barrels of oil, high-quality stuff, the same specs as a number two heating oil." He shakes his head almost as if he can't believe it. "It's amazing. The Environmental Protection Agency doesn't even consider us waste handlers. We are actually manufacturers—that's what our permit says. This process changes the whole industrial equation. Waste goes from a cost to a profit." He watches as burly men in coveralls weld and grind the complex loops of piping. A group of 15 investors and corporate advisers, including Howard Buffett, son of billionaire investor Warren Buffett, stroll among the sparks and hissing torches, listening to a tour led by plant manager Don Sanders. A veteran of the refinery business, Sanders emphasizes that once the pressurized water is flashed off, "the process is similar to oil refining. The equipment, the procedures, the safety factors, the maintenance—it's all proven technology." And it will be profitable, promises Appel. "We've done so much testing in Philadelphia, we already know the costs," he says. "This is our first-out plant, and we estimate we'll make oil at $15 a barrel. In three to five years, we'll drop that to $10, the same as a medium-size oil exploration and production company. And it will get cheaper from there." "We've got a lot of confidence in this," Buffett says. "I represent ConAgra's investment. We wouldn't be doing this if we didn't anticipate success." Buffett isn't alone. Appel has lined up federal grant money to help build demonstration plants to process chicken offal and manure in Alabama and crop residuals and grease in Nevada. Also in the works are plants to process turkey waste and manure in Colorado and pork and cheese waste in Italy. He says the first generation of depolymerization centers will be up and running in 2005. By then it should be clear whether the technology is as miraculous as its backers claim.

EUREKA:

Chemistry, not alchemy, turns (A) turkey offal—guts, skin, bones, fat, blood, and feathers—into a variety of useful products. After the first-stage heat-and-pressure reaction, fats, proteins, and carbohydrates break down into (B) carboxylic oil, which is composed of fatty acids, carbohydrates, and amino acids. The second-stage reaction strips off the fatty acids' carboxyl group (a carbon atom, two oxygen atoms, and a hydrogen atom) and breaks the remaining hydrocarbon chains into smaller fragments, yielding (C) a light oil. This oil can be used as is, or further distilled (using a larger version of the bench-top distiller in the background) into lighter fuels such as (D) naphtha, (E) gasoline, and (F) kerosene. The process also yields (G) fertilizer-grade minerals derived mostly from bones and (H) industrially useful carbon black.

Garbage In, Oil Out

Feedstock is funneled into a grinder and mixed with water to create a slurry that is pumped into the first-stage reactor, where heat and pressure partially break apart long molecular chains. The resulting organic soup flows into a flash vessel where pressure drops dramatically, liberating some of the water, which returns back upstream to preheat the flow into the first-stage reactor. In the second-stage reactor, the remaining organic material is subjected to more intense heat, continuing the breakup of molecular chains. The resulting hot vapor then goes into vertical distillation tanks, which separate it into gases, light oils, heavy oils, water, and solid carbon. The gases are burned on-site to make heat to power the process, and the water, which is pathogen free, goes to a municipal waste plant. The oils and carbon are deposited in storage tanks, ready for sale. — Brad Lemley

I was able to capture a "before" clip on NBC news and an "after" clip from the Jim Lehrer News Hour on PBS.

The clips show an interview with the girls and explain the nature of the surgery involved (and what went wrong).

I've edited them together into a single news reel:

NBC and PBS On The Conjoined Twins. (Small - 6 MB)

So they died from blood loss -- most likely when the makeshift grafted brain arteries didn't hold. Perhaps they should have waited another couple of years. (When we will be growing arteries whole :)

Tim O'Reilly Explains Why He's Excited About Bioinformatics:
Audio Tim O'Reilly On Bioinformatics (MP3 - Hi-Res - 4 MB)

Tim O'Reilly On Bioinformatics (Hi-Res - 73 MB)

Tim O'Reilly On Bioinformatics (Lo-Res - 31 MB)

Tim O'Reilly On Bioinformatics Part 1 of 2 (Lo-Res - 15 MB)

Tim O'Reilly On Bioinformatics Part 2 of 2 (Lo-Res - 16 MB)

I really regretted not going to last year's O'Reilly Bioinformatics Conference -- so when it became time for this year's conference, I remembered not going to make the same mistake twice.

Jim Kent (who rocked last year's OSCON will be one of the Keynote's next week.

I'll be there Tuesday-Thursday next week and video taping the keynotes and some of the speakers and press conferences.

If you're interested in learning how to use your computer programming skills to like, save the world and stuff, you might want to check it out.

Oh yeah -- these companies are hiring too. They're always hiring, and growing.

Friendly bunch too :-)

Anyway, I'll be posting some pre-conference info here after I finish my other back up of projects (like the radio show on crowd control, which I am still working on, but which turned out to be more work than I bargained for editing everything together nicely and providing good information about who's on the tape, etc.)

For Wired News by one of my favorite journalists, Kristen Philipkoski:
Getting a Closer Look at the Eye

Eye diseases such as glaucoma and macular degeneration often aren't discovered until a patient is well on his way to blindness. But a new imaging technology promises to deliver diagnoses at critically early stages.

The technology, called adaptive optics, was originally developed for peering into outer space. It made headlines most recently for giving astronomers rare views of Saturn's largest moon, Titan...

In 1953, an astronomer named Horace Babcock first proposed using adaptive optics for looking at stars and planets without atmospheric distortion, but the technology was not developed until the late '60s and early '70s by the military and aerospace industry, mainly in conjunction with developing high-powered lasers to destroy satellites. The technology remained classified until 1991.

It wasn't applied to medical research until about five years ago when David Williams of the University of Rochester noticed that eliminating distortions in the earth's atmosphere was probably a similar endeavor to eliminating distortions caused by the human eye when trying to use a microscope to see inside it.

Researchers at the University of Heidelberg in Germany had made the same observation, but never succeeded in proving that adaptive optics could work in the eye.

Now, at the Indiana University School of Optometry in Bloomington, Indiana, researchers are utilizing adaptive optics with another technique called optical coherence tomography, which allows doctors to capture images deep inside tissue.

By combining these two powerful technologies, an ophthalmologist might be able to not only find damaged cells in the retina, but also to precisely map the aberrations inside the eye that make eyesight less than perfect.

The new technology would replace the archaic phoropter (the part of the exam when the eye doctor says does it look better here, or here, and you usually can't tell) and give a theoretically precise diagnosis.

With an exact map of the eye, they could precisely plan laser correction surgery, or create customized contact lenses, Olivier said.

Several combinations of adaptive optics with other imaging technologies are in the works, but the technology is still too expensive and the mirrors too large to enable widespread use.

Here is the full text of the article in case the link goes bad:

http://wired.com/news/technology/0,1282,57332,00.html

Welcome to Wired News. Skip directly to: Search Box, Section Navigation, Content.

Wired News

Search:
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Getting a Closer Look at the Eye

By Kristen Philipkoski | Also by this reporter Page 1 of 1

02:00 AM Jan. 23, 2003 PT

Eye diseases such as glaucoma and macular degeneration often aren't discovered until a patient is well on his way to blindness. But a new imaging technology promises to deliver diagnoses at critically early stages.

The technology, called adaptive optics, was originally developed for peering into outer space. It made headlines most recently for giving astronomers rare views of Saturn's largest moon, Titan.

However, researchers studying the human eye are discovering the technology has applications in their field as well.

Adaptive optics uses mirrors to eliminate the visual distortion caused by the earth's atmosphere. Ophthalmologists, it turns out, encounter a similar distortion when looking inside the human eye, which prevents them from seeing the minute details of the retina.

Those details can indicate when someone is developing glaucoma or macular degeneration, which are often diagnosed when it's no longer possible to do something about it.

Centers for adaptive optics around the world are developing ways to use the technology to see individual cells in the retina, which would help diagnose potential eye diseases early enough to prevent them.

"Adaptive optics showed that you could image the individual cells in the eye, particularly the cone photo receptors, which are responsible for color vision and high-resolution vision in humans," said Scot Olivier, adaptive optics group leader at the Lawrence Livermore National Laboratory. "These are cells that are mostly invisible in the retinal diseases that cause blindness in this country."

In 1953, an astronomer named Horace Babcock first proposed using adaptive optics for looking at stars and planets without atmospheric distortion, but the technology was not developed until the late '60s and early '70s by the military and aerospace industry, mainly in conjunction with developing high-powered lasers to destroy satellites. The technology remained classified until 1991.

It wasn't applied to medical research until about five years ago when David Williams of the University of Rochester noticed that eliminating distortions in the earth's atmosphere was probably a similar endeavor to eliminating distortions caused by the human eye when trying to use a microscope to see inside it.

Researchers at the University of Heidelberg in Germany had made the same observation, but never succeeded in proving that adaptive optics could work in the eye.

Now, at the Indiana University School of Optometry in Bloomington, Indiana, researchers are utilizing adaptive optics with another technique called optical coherence tomography, which allows doctors to capture images deep inside tissue.

By combining these two powerful technologies, an ophthalmologist might be able to not only find damaged cells in the retina, but also to precisely map the aberrations inside the eye that make eyesight less than perfect.

The new technology would replace the archaic phoropter (the part of the exam when the eye doctor says does it look better here, or here, and you usually can't tell) and give a theoretically precise diagnosis.

With an exact map of the eye, they could precisely plan laser correction surgery, or create customized contact lenses, Olivier said.

Several combinations of adaptive optics with other imaging technologies are in the works, but the technology is still too expensive and the mirrors too large to enable widespread use.

"It looks like there will be a large explosion of this in the next few years," said Donald Miller, a professor in the Visual Sciences Group at the Indiana University School of Optometry. "Right now, there are about five operational systems in the world in laboratories, including here at IU."

Olivier's lab is working on a MicroElectricalMechanical system, or MEM, a device to build tiny and less expensive mirrors using the same technique that's employed for building integrated circuits.

"We are now applying these to the adaptive optics for human vision, which will allow us to build a much more compact and inexpensive system," Olivier said.

Out-of-body operation banishes tumours
By Sergio Pistoi for New Scientist.

Instead the surgeons decided to remove the entire liver. The organ was placed in a Teflon bag that neutrons can pass through and taken to a research reactor nearby, where it was irradiated with neutrons. It was then re-implanted, just as in a normal liver transplant operation.

"By explanting the organ, we could give a high and uniform dose to all the liver, which is impossible to obtain inside the body without serious risk to the patient," says Tazio Pinelli, a physicist who coordinated the work together with liver surgeon Aris Zonta.

"It was a bold stroke and has stirred the interest of many in the field," says Paul Busse, a neutron radiology expert at Harvard Medical School in Boston.

The technique has been dubbed TAORMINA after the Italian for "advanced treatment of organs by means of neutron irradiation and autotransplant". But with only one person treated so far, it is too early to judge how safe and effective it is.

Here is the full text of the article in case the link goes bad:

http://www.newscientist.com/news/news.jsp?id=ns99993193

Out-of-body operation banishes tumours

19:00 18 December 02

Exclusive from New Scientist Print Edition

For the first time, cancer has been treated by removing an organ from the body, giving it radiotherapy and then re-implanting it. The out-of-body operation allows doctors to administer high doses of radiation to widespread tumours without affecting other organs.
Surgeons remove a liver during a normal transplant operation (Image: AURORA/KATZ)
Surgeons remove a liver during a normal transplant operation (Image: AURORA/KATZ)

Doctors in Italy used the technique to treat a 48-year-old man with multiple tumours in his liver. One year after the operation, which took 21 hours, the man is alive and well. His liver is functioning normally and the latest scans have not revealed any signs of tumours.

The team, which consists of surgeons at the San Matteo Hospital in Pavia and physicists from the local division of the National Institute of Nuclear Physics, is now waiting for approval to treat another six patients with multiple liver tumours. If these are successful, the technique could one day be used to tackle hard-to-treat cancers in other organs that can be transplanted, such as the lungs or pancreas.

The patient they have treated had had a colon tumour removed, but the cancer spread to his liver. Scans revealed no fewer than 14 tumours there, and many smaller ones were discovered during the operation. Such diffuse cancers are very difficult to treat by conventional means.

Neutron capture

The tumours proved resistant to chemotherapy. And there was little hope of killing such widespread growth with conventional radiotherapy - which usually involves focusing X-ray beams onto the target - without destroying the liver.

So doctors decided to try a method called boron neutron capture therapy, first attempted in the 1950s, in which boron atoms are attached to the amino acid phenylalanine and injected into a patient. Because they are growing quickly, tumours take up more of the compound than normal cells.

The team has been working on the method since 1987 and has done extensive studies to work out the optimum dose. Two to four hours after the compound is given, a low-energy neutron beam is directed at the organ, splitting the boron into high-energy particles that mainly kill the cancer cells.

But to ensure that all cancerous cells are destroyed, an even dose of neutrons has to be given to the entire organ. That's not easy to do in the body, where obstructions such as bones block the neutron beam. And the tissues surrounding the organ inevitably receive a large dose of radiation.

Teflon bag

Instead the surgeons decided to remove the entire liver. The organ was placed in a Teflon bag that neutrons can pass through and taken to a research reactor nearby, where it was irradiated with neutrons. It was then re-implanted, just as in a normal liver transplant operation.

"By explanting the organ, we could give a high and uniform dose to all the liver, which is impossible to obtain inside the body without serious risk to the patient," says Tazio Pinelli, a physicist who coordinated the work together with liver surgeon Aris Zonta.

"It was a bold stroke and has stirred the interest of many in the field," says Paul Busse, a neutron radiology expert at Harvard Medical School in Boston.

The technique has been dubbed TAORMINA after the Italian for "advanced treatment of organs by means of neutron irradiation and autotransplant". But with only one person treated so far, it is too early to judge how safe and effective it is.

Brain tumours

Even if the method proves effective against liver and other cancers, such a drastic operation would be reserved for patients with the worst outlook, and could only be carried out while they were still strong enough to survive the long operation.

It could also be used only in cases where the spreading cancer is restricted to one organ. Once cancers spread widely, there is little that can be done. Another problem is that there are few reactors capable of producing suitable neutron beams.

But the work could also help improve normal boron neutron capture therapy, Busse says, by improving our knowledge of what doses are safe and effective. The technique is currently being tested on patients with otherwise untreatable brain tumours - obviously without removing the organ in question.

Sergio Pistoi, Rome

Here's the skinny from my one of my favorite journalists, Kristen Philipkoski:

Stem Cells Key to Diabetes Cure.

Dr. Fred Levine, an associate professor of pediatrics at the University of California at San Diego, is doing similar work.

"There's a lot of ambiguity about what constitutes a stem cell, and it's becoming less and less clear, rather than more, in this field," Levine said.

He and his colleagues have succeeded in forcing insulin-secreting beta cells to grow in culture, which causes them to revert to an earlier stage of development.

The problem is, cells like to do one of two things: revert to an earlier stage of development and replicate indefinitely, or differentiate into a specific type of cell.

Here's the full text of the article in case the link goes bad:

http://www.wired.com/news/medtech/0,1286,55239,00.html

Stem Cells Key to Diabetes Cure
By Kristen Philipkoski

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2:00 a.m. Sep. 20, 2002 PDT
Diabetes sufferer Bob Marks may never again have to stick himself with an insulin injection.

Marks is part of a lucky group of about 100 diabetes patients chosen for a University of Pennsylvania clinical trial of a new procedure called islet cell transplantation. Still, Marks waited a year before doctors called to tell him they'd found a matching donor who could give him islet cells -- the cells in the pancreas that secrete insulin.

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But the 31-year-old attorney from Danville, Pennsylvania, says it was worth the wait. And even though he takes 18 pills a day to prevent the cells from being rejected, Marks has no regrets.

"Almost right away after the surgery I felt better than I have in years," he said. "I could concentrate better and my mind was clear because my sugars weren't going high, then super low."

Marks still has to inject three-quarters the amount of insulin he needed before the surgery, but the life change is extreme, he said.

The biggest plus: Since the cells were transplanted into his liver, his body now gives him warning signs when his blood sugar is low. Before, it could sneak up on him. He no longer fears blacking out while driving his 11-year-old son to school, or arguing a case in court.

Marks is waiting for a second donor, which could eliminate his need to inject insulin, as it has for many other clinical trial participants.

Unfortunately, there are not nearly enough donors to go around. Seven hundred thousand people in the United States have type 1 diabetes (islet cell transplantation can't treat most cases of type 2 diabetes).

Meanwhile, only 6,000 donor organs were available last year -- 2,500 of which were not viable for donation. Moreover, most patients need two transplantations to get off insulin injections.

"Islet cell transplantation is wildly successful in the sense that it's been done in living people who are off insulin and leading a normal life. But it can only help a few people as opposed to many," said Dr. Robert Goldstein, chief scientific officer of the Juvenile Diabetes Research Foundation.

If the FDA approves islet cell transplantation, which could take three more years, doctors and hospital administrators will have to find a fair way to decide who will qualify for the procedure first.

"The bad news is that with this protocol, there are only enough donor pancreases in the country to meet the needs of 0.2 to 0.5 percent of those who need them. It's an ethical issue who gets them," said Dr. Joel Habener, director of the molecular endocrinology laboratory at Massachusetts General Hospital and Harvard Medical School.

Habener has an answer. Unfortunately it's unattainable, at least for now.

"The solution is to make islets in the lab," he said.

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Stem Cells Key to Diabetes Cure
2:00 a.m. Sep. 20, 2002 PDT

(page 2)

No one has figured out how, but they've gotten closer using stem cells -- both the controversial embryonic stem cells, and the kind taken from adults.

The political and ethical debate surrounding stem cells has been widely reported. People who believe that life begins at conception oppose embryonic stem cell research because the cells are extracted from human embryos, which are destroyed in the process.

Embryonic stem cells have not yet "differentiated" into mature human cells, and they have the ability to become any of the 200,000 types of cells in the human body: hair, blood, skin, toenail and so on.

Embryonic stem cell opponents cite adult stem cells, taken from adult bone marrow, blood or brains, as an answer to the ethical conundrum. But a study published recently in Science by Stanford researchers raised serious questions about the viability of these cells as therapies.

In August 2000, President Bush limited federally funded stem cell research to cells that had already been taken from 64 embryos; that number was bumped up to 72 stem cell "lines" (called that because they can replicate indefinitely) a year later.

Amidst the political and ethical controversy, scientists like Habener continue the search for a diabetes cure.

In July, he and his colleagues reported a study in which an intestinal hormone caused stem cells taken from a pancreas to become the islet cells that secrete insulin, called beta cells, and to proliferate.

"We discovered a totally unexpected population of cells in islets and we can grow and keep them in culture for as long as we want to keep them," he said.

Not surprisingly, scientific controversy exists on top of the ethical one.

Since Habener's research has not yet been replicated, it's not certain that stem cells even exist in the pancreas, let alone whether they can really proliferate new insulin-producing cells.

Dr. Fred Levine, an associate professor of pediatrics at the University of California at San Diego, is doing similar work.

"There's a lot of ambiguity about what constitutes a stem cell, and it's becoming less and less clear, rather than more, in this field," Levine said.

He and his colleagues have succeeded in forcing insulin-secreting beta cells to grow in culture, which causes them to revert to an earlier stage of development.

The problem is, cells like to do one of two things: revert to an earlier stage of development and replicate indefinitely, or differentiate into a specific type of cell.

"We force (beta cells) to grow, then we will try to do our best using various tricks of genetic modification to try to keep that growing cell in a state such that it remembers that it was a beta cell," Levine said.

In the meantime the Juvenile Diabetes Research Foundation (JDRF) -- which is free of President Bush's stem cell research restrictions because it raises money privately -- has funded several embryonic stem cell studies around the world.

The studies are in the early stages, but many scientists think they hold the most promise for success because they say embryonic stem cells are the most flexible kind.

"The field of (embryonic) stem cell research is clearly one of the most promising because it has such a wide impact. We're not just studying stem cells for one disease, it has broad implications for treating disease and understanding human development," said the JDRF's Goldstein.

And the success of islet cell transplantation only gives researchers another reason to hope for the same success with stem cell research.

"It gives us the clinical success story, it provides the basis for us wishing to do stem cell research," Goldstein said, "so we can get an unlimited supply (of islets), instead of a limited supply."

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See the Wired article by Wil McCarthy:
Strange Blood
--Cataclysmic shortages. Tainted supplies. There is a solution: artificial blood..

To truly end blood shortages and the fears that help produce them, hospitals would need a fluid that's laboratory pure, universally compatible with any human blood or tissue type, and indefinitely storable at room temperature. Most important, it would have to perform the function of oxygen delivery, so far the most elusive function to mimic in efforts to create fake blood. Simply adding oxygen-carrying hemoglobin to a substance like saline won't work - the raw hemoglobin molecule turns out to be both short-lived and toxic to the kidneys and liver unless surrounded by the fatty envelope of the red cell. And numerous other creative workarounds - like encapsulating the molecules in tiny globs of fat or chaining them together into polymers - have failed. Oxygen and CO2 can be dissolved directly into droplets of liquid perfluorocarbon, which holds and releases the two gases about as efficiently as hemoglobin does; when oxygenated, this liquid is even breathable - remember the rat in The Abyss ? This approach too, however, produces side effects, from toxicity to allergies to exhaling an ozone-depleting gas.

Only one oxygen-carrying blood substitute has ever been approved by the FDA. That was Fluosol, a perfluorocarbon additive developed in the US and marketed by Japan's Green Cross corporation from 1989 to 1993, during which time it was infused into some 13,000 patients in the US annually. Unfortunately, Fluosol was a frozen, two-part drug that had to be thawed and mixed immediately prior to use, and in large doses it required patients to breathe pure oxygen (potentially toxic) for the weeks it took their natural blood supply to recover. Meanwhile, doctors had to keep pumping the stuff in every 12 hours or the patient would die, bloodless in a cloud of exhaled fluorocarbons. Fluosol was eventually pulled off the market.

That hasn't stopped others from trying. Today around 10 companies are pushing blood substitutes through the FDA approval process.

Although I just heard about the Spider Goat story yesterday for the first time, it turns out that Forbes had written a full story on it over a year ago. ABC News also covered the story in detail a while back.

(And here's the poop straight from the source at Nexia Biotech.)

Here's the Forbes story by Christopher Helman:
Charlotte's Goat.

Nexia is tackling a materials-science conundrum that has stumped even DuPont for 20 years: how to synthesize spider silk. Milking the spiders themselves is out of the question—they're cannibals. "Put a bunch of them together and soon you end up with one big, fat, happy spider. It's like trying to farm tigers," says Turner.

By injecting the orb weaver gene into the father of Mille and Muscade, Nexia bred she-goats whose mammary glands are able to produce the complex proteins that make up spider silk. Their milk looks and tastes like the real thing, but once its proteins are filtered and purified into a fine white powder, they can be spun into tough thread.

Here's the ABC.com story:
Here Comes Spider-Goat?: Genetically Altered Goats May Lead to Strong Silk-like Threads.

Ounce for ounce, spider silk is five times stronger than steel and about three times tougher than man-made fibers such as Kevlar. And that makes the material ideal for all sorts of interesting uses — from better, lighter bulletproof vests to safer suspension bridges.

But "harvesting" spider silk hasn't been easy. Unlike silkworms, spiders aren't easy to domesticate. "Spiders are territorial carnivores, they eat each other if placed in contact of in close proximity," says Jeffrey Turner, president and CEO of Nexia Biotechnoloies, Inc. "It's like trying to farm tigers."

Now, researchers at the Quebec-based Nexia along with scientists at the U.S. Army's Soldier Biological Chemical Command (SBCCOM) in Natick, Mass., say they may have figured a way out of the sticky situation.

Some agricultural biotechnology interests (Monsanto and Syngenta) have found a new humanitarian ways of dodging the real concerns surrounding the use of biogenetically-altered plants in food crops.

See:
Cultivating a New Image: Firms Give Away Data, Patent Rights on Crops,
by Justin Gillis for the Washington Post.

But the long-term environmental impact of the crops remains a serious question. Many scientists wonder whether foreign genes inserted into crops can spread to the wild relatives of those plants, doing some kind of unforeseen environmental damage.

In fact, several incidents have suggested that the ag bio companies, whatever their intentions, won't be able to control where their altered genes wind up. Agricultural biotechnology's biggest debacle to date occurred when an altered crop called Starlink corn, approved only for use as animal food, turned up in the human food supply, forcing widespread recalls of taco shells and other products.

That mess forced all the biotechnology companies to pledge never to put a crop on the market for animal use only, because it would be certain to wind up in the human food supply. For similar reasons, many American farmers are worried about Monsanto's efforts to commercialize a genetically engineered wheat. The farmers, though they may support biotechnology in principle, are afraid the altered wheat will taint the entire American crop in the eyes of foreign buyers.

Rose-tinted help with reading

A breakthrough in biomarkers was revealed at an oncology conference last week in San Francisco. See:
New biomarkers for ovarian, breast, and head and neck cancers identified.

Researchers have identified new biomarkers for ovarian, breast, and head and neck cancers that could lead to earlier detection of these malignancies and improved treatment outcomes, according to study findings presented this week at a major oncology meeting in San Francisco.

See the story by Alex Kirby for the BBC:
Blind gorilla sees again.