Is this new? Oh, well, time to catch up with those forward thinkers at the Pentagon then. Surely govt intelligence uses these resources too - it cannot be news that strategic collecting of brainpower needs to look outside the Physics department, can it?

Here's something four-year-olds know: A screen that ships without a mouse ships broken. Here's something four-year-olds know: Media that's targeted at you but doesn't include you may not be worth sitting still for. Those are things that make me believe that this is a one-way change. Because four year olds, the people who are soaking most deeply in the current environment, who won't have to go through the trauma that I have to go through of trying to unlearn a childhood spent watching Gilligan's Island, they just assume that media includes consuming, producing and sharing.

It's also become my motto, when people ask me what we're doing--and when I say "we" I mean the larger society trying to figure out how to deploy this cognitive surplus, but I also mean we, especially, the people in this room, the people who are working hammer and tongs at figuring out the next good idea. From now on, that's what I'm going to tell them: We're looking for the mouse. We're going to look at every place that a reader or a listener or a viewer or a user has been locked out, has been served up passive or a fixed or a canned experience, and ask ourselves, "If we carve out a little bit of the cognitive surplus and deploy it here, could we make a good thing happen?" And I'm betting the answer is yes.

 This is the wrap-up but the whole article is worth reading. It's about the way that society responds to cognitive surpluses created by innovation. He's got his cause and effect a bit mangled, I think, but it's an interesting viewpoint. His point is that when a technological or societal change occurs that frees up human capacity in some way, that capacity is absorbed at first in what might be seen as bad ways. In the 18th century as the industrial revolution created an unprecedented urban population boom in London, some of that brainpower was taken up by gin (see Hogarth pics etc) and the pursuit of gin and the recovery from gin and the procurement of yet more gin. In post-war America, the changes created by labour-saving devices and other tech innovations meant there was lots of excess thinking time and whitematter that went to, amongst other things, daytime TV. Shirky's first point is that this effect is happening again right now as IT picks up more human labour leaving us spinning our cognitive wheels again, and there is a cognitive surplus going begging (or being 'wasted' on MMORPGs etc). His second, and more interesting point, is that the quantity of cognitive surplus is simply *immense*. Wikipedia represents 100megahours of human effort - daytime TV is currently absorbing a hundred times that every year in the US alone. How can you access that potential? How can you deploy it? Who, apart from sitcoms and Wikipedia, is competing with you to deploy it? Why aren't you measuring your country's efficiency in those terms?

And, to hark back to the stuff about scientists using cognitive enhancement drugs, once you've figured out how to access it, how are you going to maintain or boost the supply?

Scientists like to low-ball their estimates. The now-famous IPCC scenarios for the effects of climate change are already known to be woefully, unrealistically conservative (Freeman Dyson's recent comments notwithstanding). Arctic changes expected 20 years from now are happening now, and in North America the beginning of spring has already been pushed back by two weeks, which is enough to play havoc with the fertility cycle of many migratory birds (among other consequences). The worst-case scenarios used in public debate ignore some extremely worrisome factors, such as the possible release of oceanic methane from clathrates. If we're going to deal with this problem, we have to do it now, as in, within the term of your next government.

The science journal Nature asked its readers to take an online survey of cognitive enhancing drug use. 1400 responded and 20% reported using drugs for brain enhancement with methylphenidate (Ritalin) the most popular followed by modafinil (Provigil to reduce sleepiness).

For those who choose to use, methylphenidate was the most popular: 62% of users reported taking it. 44% reported taking modafinil, and 15% said they had taken beta blockers such as propanolol, revealing an overlap between drugs. 80 respondents specified other drugs that they were taking. The most common of these was adderall, an amphetamine similar to methylphenidate. But there were also reports of centrophenoxine, piractem, dexedrine and various alternative medicines such as ginkgo and omega-3 fatty acids.

The most popular reason for taking the drugs was to improve concentration. Improving focus for a specific task (admittedly difficult to distinguish from concentration) ranked a close second and counteracting jet lag ranked fourth, behind 'other' which received a few interesting reasons, such as “party”, “house cleaning” and “to actually see if there was any validity to the afore-mentioned article”.

The propranolol (sold as Inderal) is a beta blocker which suppresses flight-or-flight stress reactions. Some musicians use beta blockers for performances. Though their primary use is to lower high blood pressure. It is also used in lower doses against anxiety.

The willingness of scientific researchers to use currently available drugs as cognitive enhancers suggests that these drugs might really work to improve mental performance. It also shows that these people who do competitive intellectually difficult work look for ways to get an edge.

Ritalin for faster computer chip design, less buggy software development, and more optimized mechanical designs? Ritalin for brainstorming marketing strategies? Anyone tried it for intellectual work?

The flippant question is: got a policy framework to fit this in? It seems to me that this is not the next big thing; it's *the* big thing (so big that it is already treated lightly, which is the tone I extract from the above and from the Nature article).

Bear with me on this. Consider: science or applied discovery or transformative research or any of those things are definitely positively correlated to some degree with economic success. Consider also that it is entirely plausible that cognitive enhancement of researchers via drugs such as Ritalin may be positively correlated to some degree with science quality or pace of innovative output or somesuch. Given those two correlations, what position should you advocate and what incentives are you creating vis-a-vis better-brains-through-drugs when you ask for economic transformation?

The above is a pretty argument but a little sophomoric/sophomoronic. Nevertheless, I think the Futurewatch work is seeking heads-up of what will be socially and scientifically relevant in 15y or so (i.e. if it's 1992 right now, what is this 'web' thingy?). Cognitive enhancement *is* going to be a more relevant argument by then. Trite analogy: the communist bloc countries in the 70s and 80s sought drug-fuelled prestige from the Olympics; in this century, cognitive boosters can give your country a more direct and sustained advantage.

Sewer-gas-induced suspended animation is rapid and reversible

Heart rate and metabolism drop, while blood pressure and oxygen levels maintained

Low doses of the toxic gas responsible for the unpleasant odor of rotten eggs can safely and reversibly depress both metabolism and aspects of cardiovascular function in mice, producing a suspended-animation-like state. In the April 2008 issue of the journal Anesthesiology, Massachusetts General Hospital (MGH) reseachers report that effects seen in earlier studies of hydrogen sulfide do not depend on a reduction in body temperature and include a substantial decrease in heart rate without a drop in blood pressure.

“Hydrogen sulfide is the stinky gas that can kill workers who encounter it in sewers; but when adminstered to mice in small, controlled doses, within minutes it produces what appears to be totally reversible metabolic suppression,” says Warren Zapol, MD, chief of Anesthesia and Critical Care at MGH and senior author of the Anesthesiology study. “This is as close to instant suspended animation as you can get, and the preservation of cardiac contraction, blood pressure and organ perfusion is remarkable.”

Previous investigations into the effects of low-dose hydrogen sulfide showed that the gas could lower body temperature and metabolic rate and also improved survival of mice whose oxygen supply had been restricted. But since hypothermia itself cuts metabolic needs, it was unclear whether the reduced body temperature was responsible for the other observed effects. The current study was designed to investigate both that question and the effects of hydrogen sulfide inhalation on the cardiovascular system.

The researchers measured factors such as heart rate, blood pressure, body temperature, respiration and physical activity in normal mice exposed to low-dose (80 ppm) hydrogen sulfide for several hours. They analyzed cardiac function with electrocardiograms and echocardiography and measured blood gas levels. While some mice were studied at room temperature, others were kept in a warm environment – about 98º F – to prevent their body temperatures from dropping.

In all the mice, metabolic measurements such as consumption of oxygen and production of carbon dioxide dropped in as little as 10 minutes after they began inhaling hydrogen sulfide, remained low as long as the gas was administered, and returned to normal within 30 minutes of the resumption of a normal air supply. The animals’ heart rate dropped nearly 50 percent during hydrogen sulfide adminstration, but there was no significant change in blood pressure or the strength of the heart beat. While respiration rate also decreased, there were no changes in blood oxygen levels, suggesting that vital organs were not at risk of oxygen starvation.

The mice kept at room temperature had the same drop in body temperature seen in earlier studies, but those in the warm environment maintained normal body temperatures. The same metabolic and cardiovascular changes were seen in both groups, indicating that they did not depend on the reduced body temperature, and analyzing the timing of those changes showed that metabolic reduction actually began before body temperature dropped.

“Producing a reversible hypometabolic state could allow organ function to be preserved when oxygen supply is limited, such as after a traumatic injury,” says Gian Paolo Volpato, MD, MGH Anesthesiology research fellow and lead author of the study. “We don’t know yet if these results will be transferable to humans, so our next step will be to study the use of hydrogen sulfide in larger mammals.”

Zapol adds, “It could be that inhaled hydrogen sulfide will only be useful in small animals and we’ll need to use intravenous drugs that can deliver hydrogen sulfide to vital organs to prevent lung toxicity in larger animals.” Zapol is the Reginald Jenney Professor of Anaesthesia at Harvard Medical School.

 Well, you can't say it wouldn't be useful!

Famed geneticist creating life form that turns CO2 to fuel

Thu Feb 28, 3:57 PM ET

A scientist who mapped his genome and the genetic diversity of the oceans said Thursday he is creating a life form that feeds on climate-ruining carbon dioxide to produce fuel.

Geneticist Craig Venter disclosed his potentially world-changing "fourth-generation fuel" project at an elite Technology, Entertainment and Design conference in Monterey, California.

"We have modest goals of replacing the whole petrochemical industry and becoming a major source of energy," Venter told an audience that included global warming fighter Al Gore and Google co-founder Larry Page.

"We think we will have fourth-generation fuels in about 18 months, with CO2 as the fuel stock."

Simple organisms can be genetically re-engineered to produce vaccines or octane-based fuels as waste, according to Venter.

Biofuel alternatives to oil are third-generation. The next step is life forms that feed on CO2 and give off fuel such as methane gas as waste, according to Venter.

"We have 20 million genes which I call the design components of the future," Venter said. "We are limited here only by our imagination."

His team is using synthetic chromosomes to modify organisms that already exist, not making new life, he said. Organisms already exist that produce octane, but not in amounts needed to be a fuel supply.

"If they could produce things on the scale we need, this would be a methane planet," Venter said. "The scale is what is critical; which is why we need to genetically design them."

The genetics of octane-producing organisms can be tinkered with to increase the amount of CO2 they eat and octane they excrete, according to Venter.

The limiting part of the equation isn't designing an organism, it's the difficulty of extracting high concentrations of CO2 from the air to feed the organisms, the scientist said in answer to a question from Page.

Scientists put "suicide genes" into their living creations so that if they escape the lab, they can be triggered to kill themselves.

Venter said he is also working on organisms that make vaccines for the flu and other illnesses.

"We will see an exponential change in the pace of the sophistication of organisms and what they can do," Venter said.

"We are a ways away from designing people. Our goal is just to make sure they survive long enough to do that."

 Venter usually delivers, have you noticed?

 Interesting monetizing approach. A sort of cross between Digg and futures markets.

Armed robot rampage - February 28, 2008

Sheffield University professor and media darling Noel Sharkey took the spotlight at a policy conference yesterday, warning that wars and terrorist attacks may soon be conducted by robots that can think for themselves. The conference, sponsored by British defence think-tank Royal United Services Institute, was organized specifically to discuss the ethical and legal implications of using unmanned vehicles for defence and security.

 Knows how to get attention, doesn't he. We'll need Saffo's predicted 'Steve-Jobs-of-Robotics' to do a bit of work first - robots are expensive and you want to reuse them but terrorists are cheap and disposable - why would Osama bother?!

The University of Auckland has just announced that they have embedded Creative Commons licensing for all new submissions by PhD students into the university’s digital repository, ResearchSpace.

From the repository’s librarian Leonie Hayes:

“At the moment the showcase collection is PhD theses, there are nearly 800 in the PhD collection, most are open access. There are another 900 awaiting signoff from authors. When new graduates submit online they have a choice of adding a CC licence along with their consent for a digital copy.

We are also investigating application of Creative Commons licenses to our other digital collections.”

For the purposes of the repository, students are using a localized Creative Commons Attribution-Noncommercial-Share Alike license, legally ported to jurisdictional law by the CC team in New Zealand.

 Are the other universities doing this? Is there any reason why the research by the CRIs should not be under CC licences? And is there any decent, non-"we've-always-done-it" reason why NZ govt documents for public release are not CC (for 'Creative Commons' not 'Crown Copyright')?

 Really, it's coming. I'm telling you.

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium GenomeDaniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison, III, Hamilton O. Smith^*

We have synthesized a 582,970–base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.

Already "published" as press releases and heavy hints weeks ago. 

 As the commentary points out, "The 582,970-bp "synthetic" genome produced by Gibson et al. also unequivocally demonstrates that it is now possible to construct the genomes for all known human viruses, including strictly regulated pathogens (such as smallpox), from publicly available DNA sequence data, methods, and materials." But this is important anyway. Once you have a promising human probiotic, or cellulolytic ethanolic yeast, or therapeutic alkaloid-producing fungus you should boil it down to the smallest dot you can and make it from scratch.

 Plus, we reductionists now get to build up instead of whittle down!

 A sort of Digg-for-futurewatchers. Since it is based on the Wisdom Of Crowds principle, we have to hope that there is a big enough crowd (it doesn't have to be wise enough - the theory is that wisdom is inevitable). There's an accompanying blog at http://memebox.com/articles

Washington University unveils draft sequence of corn genome

Feb. 25, 2008 -- A team of scientists led by Washington University in St. Louis has begun to unlock the genetic secrets of corn, a crop vital to U.S. agriculture. The researchers have completed a working draft of the corn genome, an accomplishment that should accelerate efforts to develop better crop varieties to meet society's growing demands for food, livestock feed and fuel.

Corn, also known as maize, underlies myriads of products, from breakfast cereal, meat and milk to toothpaste, shoe polish and ethanol.

The genetic blueprint will be announced on Thursday, Feb. 28, by the project's leader, Richard K. Wilson, Ph.D., director of Washington University's Genome Sequencing Center, at the 50th Annual Maize Genetics Conference in Washington, D.C.

"This first draft of the genome sequence is exciting because it's the first comprehensive glimpse at the blueprint for the corn plant," Wilson says. "Scientists now will be able to accurately and efficiently probe the corn genome to find ways to improve breeding and subsequently increase crop yields and resistance to drought and disease."

The $29.5 million project was initiated in 2005 and is funded by the National Science Foundation (NSF), the U.S. Department of Agriculture and the U.S. Department of Energy. "Corn is one of the most economically important crops for our nation," says NSF director Arden L. Bement Jr. "Completing this draft sequence of the corn genome constitutes a significant scientific advance and will foster growth of the agricultural community and the economy as a whole."

The team working on the endeavor, including scientists at the University of Arizona in Tucson, Cold Spring Harbor Laboratory in New York and Iowa State University, has already made the sequencing information accessible to scientists worldwide by depositing it in GenBank, an online public DNA database. The genetic data is also available at maizesequence.org.

The draft covers about 95 percent of the corn genome, and scientists will spend the remaining year of the grant refining and finalizing the sequence. "Although it's still missing a few bits, the draft genome sequence is empowering," Wilson explains. "Virtually all the information is there, and while we may make some small modifications to the genetic sequence, we don't expect major changes."

The group sequenced a variety of corn known as B73, developed at Iowa State decades ago. It is noted for its high grain yields and has been used extensively in both commercial corn breeding and in research laboratories.

The genome will be a key tool for researchers working to improve varieties of corn and other cereal crops, including rice, wheat and barley. "There's a lot of great research on the horizon," says plant biologist Ralph S. Quatrano, Ph.D., the Spencer T. Olin Professor and chair of Washington University's Department of Biology. "The genome will help unravel the basic biology of corn. That information can be used to look for genes that make corn more nutritious or more efficient for ethanol production, for example."

Corn is only the second crop after rice to have its genome sequenced, and scientists will now be able to look for genetic similarities and differences between the crops, Quatrano adds.

"The maize genome sequence will be of great interest to maize geneticists and biologists around the world, but also will be an important resource for plant breeding and biotechnology companies," says project collaborator Rob Martienssen, Ph.D., of Cold Spring Harbor Laboratory. "The maize sequence will be an invaluable reference for research, especially in renewable energy and biofuels, similar in significance to the human genome sequence for biomedical research".

The genetic code of corn consists of 2 billion bases of DNA, the chemical units that are represented by the letters T, C, G and A, making it similar in size to the human genome, which is 2.9 billion letters long. By comparison, the rice genome is far smaller, containing about 430 million bases.

The challenge for Wilson and his colleagues was to string together the order of the letters, an immense and daunting task both because of the corn genome's size and its complex genetic arrangements. About 80 percent of the DNA segments are repeated, and corn also has 50,000 to 60,000 genes, roughly double the number of human genes. Mobile genes, or transposons, make up a significant portion of the genome, further complicating sequencing efforts.

"Sequencing the corn genome was like putting together a 1,000 piece jigsaw puzzle with lots of blue sky and blue water, with only a few small sailboats on the horizon," Wilson explains. "There were not a lot of landmarks to help us fit the pieces of the genome together."

[Editor's note: A press conference discussing the maize genome will be held at 12:30 p.m., Feb. 28 in the Hoover Room at the Marriott Wardman Park, 2660 Woodley Road, NW, Washington, D.C.]

The United States is the world's top corn grower, producing 44 percent of the global crop. In 2007, U.S. farmers produced a record 13.1 billion bushels of corn, an increase of nearly 25 percent over the previous year, according to the U.S. Department of Agriculture. The 2007 production value of corn was estimated at more than $3 billion. Favorable prices, a growing demand for ethanol and strong export sales have fueled an increase in farmland acreage devoted to corn production.

Washington University School of Medicine's 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children's hospitals. The School of Medicine is one of the leading medical research, teaching and patient care institutions in the nation, currently ranked fourth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children's hospitals, the School of Medicine is linked to BJC HealthCare.

 It's about time! We should know our most important crops

Electronic tattoo display runs on blood

The tattoo display: "Waterproof and powered by pizza."

Jim Mielke's wireless blood-fueled display is a true merging of technology and body art. At the recent Greener Gadgets Design Competition, the engineer demonstrated a subcutaneously implanted touch-screen that operates as a cell phone display, with the potential for 3G video calls that are visible just underneath the skin.

The basis of the 2x4-inch "Digital Tattoo Interface" is a Bluetooth device made of thin, flexible silicon and silicone. It´s inserted through a small incision as a tightly rolled tube, and then it unfurls beneath the skin to align between skin and muscle. Through the same incision, two small tubes on the device are attached to an artery and a vein to allow the blood to flow to a coin-sized blood fuel cell that converts glucose and oxygen to electricity. After blood flows in from the artery to the fuel cell, it flows out again through the vein.

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On both the top and bottom surfaces of the display is a matching matrix of field-producing pixels. The top surface also enables touch-screen control through the skin. Instead of ink, the display uses tiny microscopic spheres, somewhat similar to tattoo ink. A field-sensitive material in the spheres changes their color from clear to black, aligned with the matrix fields.

The tattoo display communicates wirelessly to other Bluetooth devices - both in the outside world and within the same body. Although the device is always on (as long as your blood´s flowing), the display can be turned off and on by pushing a small dot on the skin. When the phone rings, for example, an individual turns the display on, and "the tattoo comes to life as a digital video of the caller," Mielke explains. When the call ends, the tattoo disappears.

Could such an invasive device have harmful biological effects? Actually, the device could offer health benefits. That´s because it also continually monitors for many blood disorders, alerting the person of a health problem.

The tattoo display is still just a concept, with no word on plans for commercialization.

 Despite appearances this is not yet real. But I soooo want it to be! Got legislation to cover this? Gonna let them through airport security? Got the Privacy Act to cover it?

 Not so much a notable breakthrough but likely a framework for thinking about where scans might go. They are an odd mix of worthy, obvious, distracting and vague.

 Good list for the consumer; maybe too close to market for ministry. Offline web, wireless power and cellulolytic enzymes are my favourites

The Chinese Government's Plans for Nanotechnology

By Alexis Madrigal February 17, 2008 | 4:29:52 PMCategories: AAAS 2008, Nanotechnology  

BOSTON, MA - China aims to leapfrog the United States in technological development with substantial investment in nanotechnology, but whether those efforts will actually pay off is still unclear. That was the message from University of California at Santa Barbara researchers presenting their findings on the state of Chinese nanotechnology here at the AAAS annual meeting.

Richard Applebaum and Rachel Parker from the Center for Nanotechnology in Society at  UCSB conducted about sixty interviews with Chinese officials to piece together a picture of the current state of Chinese nanotechnology. Applebaum set the specific research effort within the context of China's stated overarching goal to "leapfrog" the West by using a combination of learning from the West (i.e. technology transfer) and increasing domestic research capacity ("indigenous innovation" or zizhu chuangxin).

Nanotechnology research is one of four Chinese "science Megaprojects" that have the central purpose of catching the country up to US research by 2020. Still, for all the big talk, the actual government investment is not overwhelming. The researchers estimated that the Chinese government only invested $400 million from 2002 to 2007, although that investment is expected to rise considerably.

They highlighted several international partnerships related to nanotechnology including the Tsinghua-Foxconn Nanotechnology Research Center and the Zheijang-California NanoSystems Institute, but didn't go into much detail about what types of projects are being developed in those centers.

Right now, most nanotech research is being pushed by the central and regional governments with little private capital contributing to the national output. There are a lot of questions about whether or not that is a sustainable model for developing a high-tech industry, Applebaum noted. (It should also be noted, though, that some would question whether the venture capital model is sustainable either.)

It also leads to strange applications of nanotechnology in high-profile venues. Parker said that the Olympic village parking lots being constructed in Beijing will have a nanopolymer coating that will absorb exhaust. It was just an off-hand mention, but I am officially intrigued by the idea of coating our parking lots with pollution absorbing material. I can't vouch for the true environmental-safety of that solution, but I'd love to know how they're doing it. The coating could be something like this  pollution absorbing concrete that uses titanium dioxide to degrade pollutants.

 More scare-stories from AAAS but an interestingly plausible one. China is not only going to become old before it becomes rich but it is going to become ultra-high-tech before it manages to distribute even post-WW2 technology through its domain. As usuaI with China these days, there are no precedents so it will be interesting. I suspect that, in a decade's time, it would be a ChAAS meeting that would be the one to attend

AAAS: Viral chatter

 Interesting not just because we might all be catching Simian Foamy Virus soon but mostly because it is a nice idea inspired from without the field of application. I don't think spies listening in to chatter is the best analogy, or at least that it shouldn't *stay* the best analogy - far better if it can move to being more like meteorology, where systematic harvesting of data like this is plugged into predictive models of quantified uncertainty and trends or upcoming specific events highlighted.

 And we will have to make decisions *today* to get the community ready for this. How many software licences will the scientist need to do this? What sort of mindset? What will be the price (not necessarily dollars) of admission for NZ scientists to this? What will we do with the hundreds of scientists mired in the massively outdated world of flat files and pdfs and GenBank when Generation Z is living in a world of rife clickthrough?

 Khosla backs himself

 Copy this initiative now! What possible gain is made for the public or the government by things like Crown Copyright and all that, at this point in our country's development? If there is one, you *must* articulate it. If, as I suspect, there kind of really isn't one (that's very good, when exposed to the open air) then make the change.

 Appealing to your patriotic side: are we really going to let the Aussies beat us at this?

AAAS: Wires and batteries made of viruses

 Energy storage technology is *the* field of interest at the moment and this is a surprising contribution by biology - the chemists and physicists are supposed to be looking after this for us

Oceans Eyed As New Energy Source

 Surely this is one of the things where gigantic-EEZ, maritime NZ has an advantage.

 

Mind you, one might've claimed the same thing about yachting, he said and quickly ran for cover...

'Recordable' proteins as next-generation memory storage materials

 Science by press release but you've got to admit that we are never so creative as when we are copying nature and nature opted for proteins to record memory (<-- NB this is my as-yet-unfalsified off-the-wall unsupported-by-evidence theory about cognitive memory, based on the assumption that protein plaques in the brain from CJD and suchlike are runaway artefacts of the normal process of information storage, totally unjustified, am just backing a random horse)

Cornell University researchers have succeeded in implanting electronic circuit probes into tobacco hornworms as early pupae. The hornworms pass through the chrysalis stage to mature into long-lived moths whose muscles can be controlled with the implanted electronics. The research was showcased at MEMS 2008, an international academic conference on Micro-Electrico-Mechanical Systems that took place from January 13-17 in Tucson, AZ.

The pupae insertion state was found to yield the best results. The resulting moth, a microsystem-controlled insect, has a circuit board protruding from the top of its midsection. Probes are inserted into the dorsoventral and dorsolongitudinal flight muscles. CT images show components of high absorbance indicating tissue growth around the probe.

The research also indicated the most favorable and least favorable times for insertion of control devices. The overall size of the circuit board is just 8x7mm, with a total weight of about 500 mg. The capacity of the battery is 16 mAh, and weighs 240 mg.

A driving voltage of 5 volts causes the tobacco hornworm blade muscles (two pairs) to move for flight and maneuvering.

The insect cyborgs are part of a program called HI-MEMS (Hybrid Insect MEMS), a DARPA program initiated by Program Manager Dr. Amit Lal. The ultimate goal of the HI-MEMS program is to provide insect cyborgs that can demonstrate controlled flight; the insects would be used in a variety of military and homeland security applications.

HI-MEMS program director Amit Lal credits science fiction writer Thomas Easton with the idea. Lal read Easton's 1990 novel Sparrowhawk, in which animals enlarged by genetic engineering (called Roachsters) were outfitted with implanted control systems.

Dr. Easton, a professor of science at Thomas College, sees a number of applications for HI-MEMS insects.

Moths are extraordinarily sensitive to sex attractants, so instead of giving bank robbers money treated with dye, they could use sex attractants instead. Then, a moth-based HI-MEMS could find the robber by following the scent."

"[Also,] with genetic engineering Darpa could replace the sex attractant receptor on the moth antennae with receptors for other things, like explosives, drugs or toxins," said Easton.

DARPA had better be careful with its insect army; in Easton's novel, hackers are able to gain control of genetically engineered animals by hacking the controller chips used in their implanted control structures.

If you are interested in one dark-side view of how this kind of invention could be used by corporations for advertising, see the madcap blurbflies from Jeff Noon's excellent 2000 sf novel Nymphomation.

Learn more about Hybrid Insect MEMS Sought By DARPA. Via Robot Watch.

 As if cockroaches weren't bad enough. Lots of applications. Who here in NZ does any of this kind of stuff? As Saffo says, robotics is about to take off just as soon as a 'Steve Jobs for robots' arrives. And, Asimov and Dick aside, successful robot deployment was never going to be about humanoid androids or replicants

Nature advance online publication 13 February 2008 | doi:10.1038/nature06557; Received 15 October 2007; Accepted 20 December 2007; Published online 13 February 2008

Gamete formation without meiosis in Arabidopsis

Maruthachalam Ravi¹, Mohan P. A. Marimuthu¹ & Imran Siddiqi¹

 Huge impact if it works - an understanding of the molecular basis of apomixis could fix hybrid vigour in several staples

Abstract PDF Supplementary Material Add to Personal Archive Add to Citation Manager Notify a Friend E-mail When Cited Related Article by Whitley, R. PubMed Citation

ABSTRACT

Background Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative.

Methods We evaluated RNA obtained from the liver and kidney transplants in two recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses.

Results High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points.

Conclusions Unbiased high-throughput sequencing is a powerful tool for the discovery of pathogens. The use of this method during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation.

 454 WGS as a way to identify a wholly novel pathogen in a wholly novel disease. Short-circuits much of the traditional way of discovering such things; don't mess around with typing or isolating, just sequence the bugger in one go. It's soon going to be not worth your time to do anything less, even with known pathogens. In fact, you have to wonder if we'll bother with markers of any kind (SNPs included!) if sequencing gets routine/cheap enough

Eric Kmiec, UD professor of biological sciences, undergraduate student Stephanie Callahan (center) and research associate Darlise DiMatteo conduct genetic research on spinal muscular atrophy in the lab at the Delaware Biotechnology Institute.

5:07 p.m., Feb. 11, 2008--Researchers at the University of Delaware have discovered a novel technique--that acts like a “spell-checker” for correcting a misspelling in the DNA code--to repair the defective gene that causes spinal muscular atrophy (SMA). This hereditary neuromuscular disease is the number-one genetic killer of children under two years old.

Babies born with Type 1 SMA, the most severe form of the disease, can't walk, crawl, sit unsupported, lift their heads, or breathe normally. Fifty percent die before their second birthday.

The research is published in the Jan. 14 online edition of Experimental Cell Research. The study was supported by $477,500 in National Tobacco Settlement funds to the state of Delaware. The research grant was awarded through the Delaware Health Fund.

“Think of it like a spell-check program--we're erasing the wrong letter in the DNA code and putting the right one in,” said Eric Kmiec, professor of biological sciences at UD.

Kmiec, who holds 14 patents for gene-editing technologies at the University, collaborated with research scientist Darlise DiMatteo and undergraduate Stephanie Callahan on the discovery in his laboratory at the Delaware Biotechnology Institute.

The technique has shown promising results in tests in mice and is now poised for development by OrphageniX Inc., based in Wilmington, Del. The start-up company was incorporated in 2005 to commercialize UD-patented technologies for repairing genes that cause rare, hereditary, “orphan” diseases, so named because they have not been “adopted” by the pharmaceutical industry for the development of treatments.

According to the Families of Spinal Muscular Atrophy, an international, nonprofit organization, the disease affects one in 6,000 babies born, and one in 40 people is a genetic carrier.

A genetic 'bandage'

Spinal muscular atrophy is caused by a mutation in the SMN1 gene, which affects the motor neurons, the nerve cells in the spinal cord that control the muscles of the rib cage and limbs, which are essential for breathing, swallowing, sitting and walking.

Each gene is made up of a length of DNA, a code composed of the four chemical units that make up the genetic alphabet: A for adenine, G for guanine, C for cytosine and T for thymine.

In spinal muscular atrophy, a defect occurs in the SMN1 gene. There's a letter out of place--a T (thymine) occurs where there should be a C (cytosine). As a result, the gene doesn't make a protein that the motor nerves in the spinal cord need to survive, which leads to the gradual atrophy, or wasting, of the muscles.

UD professor Eric Kmiec with his research team focused on spinal muscular atrophy, including senior research associate Hetal Parekh-Olmedo (left), undergraduate student Stephanie Callahan, and research associate Darlise DiMatteo (foreground).

To replace the function of the defective SMN1 gene, the UD research team used a gene in the human body that is nearly an exact copy (SMN2). Then they introduced a small fragment of this healthy gene's DNA--a genetic “bandage” referred to as an oligonucleotide--into a diseased cell, triggering the cell to heal itself.

Tests of the technique in mice with spinal muscular atrophy, conducted by Jackson Laboratory in Bar Harbor, Maine, showed “very promising results” with the development of healthy muscle in the animals, Kmiec said.

“Babies with SMA die early in life,” Kmiec noted. “But if we can deliver the healing agent to the appropriate cell, we can help address this horrible disease. We're not looking at a cure, but we hope this technique could lead to a series of treatments that could alleviate the symptoms and improve the quality of life of patients,” Kmiec said.

The technique, known as targeted gene alteration (TGA), is among a group of UD-patented technologies under development by OrphageniX, a pre-clinical development stage biotechnology company that has moved quickly out of the starting gate since its launch in February 2007.

“OrphageniX plans to develop a treatment for spinal muscular atrophy with help from expert consultants in the field,” Michael Herr, chief executive officer, said.

The development of a treatment for SMA would advance to clinical testing within a year from funding by either investors or commercial collaborators, Herr noted.

Patients with the less severe, Type III form of spinal muscular atrophy would be targeted for initial human trials. Although individuals with Type III SMA suffer from a range of muscle weakness and fatigue quickly, the disease generally is not life-threatening at this stage.

Herr said that OrphageniX is committed to helping people by commercializing scientific breakthroughs, but he noted that, “we must also provide an adequate return to investors for OrphageniX to succeed.”

Truly translational research

For his latest research to be truly “translational,” extending from the lab bench to the bedside, Kmiec said it has been critical to involve people like Darlise DiMatteo, who have a keen understanding of spinal muscular atrophy.

DiMatteo, who joined Kmiec's research team a year ago, formerly worked at Nemours Alfred I. duPont Hospital for Children, where she conducted research studies of muscular dystrophy and SMA for more than a decade. The world-renowned children's hospital continues to be an important partner on the project, Kmiec said.

“We've received significant assistance from Drs. Vicky Funanage and Wenlan Wang at A. I. duPont Hospital,” Kmiec noted. “They would be a natural choice for clinical trials in SMA.”

“I love coming to work knowing that this research could make a difference for families affected by this disease,” DiMatteo said. “It's intriguing--why does a deficit in this particular protein cause this disease? And why do humans have an SMN2 gene that's almost identical to SMN1 when animals don't have that kind of backup? The effort will have been worth it if we can help find the answers.”

The research also has had a profound effect on Stephanie Callahan, an undergraduate student at UD who helped carry out the laboratory experiments, working under DiMatteo's guidance.

Callahan had the opportunity to participate in the project through a summer internship in the IDeA Network of Biomedical Research Excellence (INBRE) program offered by the Delaware Biotechnology Institute when she was a student at Delaware Technical and Community College. Now she's finishing up her degree in biological sciences with a concentration in biotechnology and wants to pursue her master's degree at UD. After completing her education, she hopes to get a job doing research in industry, perhaps at a pharmaceutical company.

“It really opened my eyes to the possibilities and the potential applications of what you can do in the lab,” Callahan said. “It's been a great experience for me.”

Kmiec said the research so far has all the elements of a “real Delaware story”--connecting UD, A. I. duPont Hospital for Children, tobacco settlement funding awarded by the state, and a start-up company fueled by Delaware investors--and he's excited about the future.

“Publishing an article in a research journal is not the accomplishment--that is what some of us are paid to do, and my colleagues do this as well as I,” Kmiec said. “But the fact that the research program is translational and is working in that direction with outside validation and support is the real news. I hope our experience will help UD and other researchers like us realize their technology possibilities,” he added.

“What we've discovered--this gene spell-check--sounds very simple, where you erase one letter and put the right one in,” Kmiec noted, “but finding the pathway has taken a long time, since 1994. Now, with this latest development, we've taken a laser shot out of the primordial soup. It's a chance finally to make a difference for families with this disease.”

 Chimeraplasty appears under *another* name *again*. I still don't know if it is real or whether this is something pathological going on. Too good to be true or just too frequently resurgent to be anything other than a monstrous hydra?

Nine Cities, Nine Ideas

Ann Arbor, Mich., and Beijing, China, have precious little in common. But the modest college town and sprawling national capital do share one trait: They're part of a world-wide movement by cities to rein in their runaway energy use.

Ann Arbor is replacing the bulbs in its street lamps with light-emitting diodes that use much less power. Beijing is closing or relocating cement kilns, coal mines and chemical plants dating back to the era of Chairman Mao.

Elsewhere around the world, cities are embarking on all sorts of innovative programs to try to corral the amount of energy they consume. Chicago is planting rooftop gardens to cool down its municipal buildings. New York is working with a private company to harness the power of tidal currents in the city's East River. Amsterdam is using cold lake water to help air-condition homes.

 Not necessarily thought leaders (surely other cities are doing the same or more) but certainly some clever PR. This trend is *not* going to go away

 Open science is one of the two things I picked as hugely significant for future developments; the other is neo-neuroscience (= interventionist cognitive science). I think the NIH call to publish all papers as Open Access and the various experiments in arXiv-like publishing and content sharing, along with the ubiquity of blogs and wikis and what have you, will educate the up-and-coming generation of scientists so that they do it all in public.

Egham, UK, January 31, 2008 — Gartner, Inc. has highlighted 10 key predictions of events and developments that will affect IT and business in 2008 and beyond.

The predictions highlight areas where executives and IT professionals need to take action in 2008. The full impact of these trends may not appear this year, but executives need to act now so that they can exploit the trends for their competitive advantage.

"Selected from across our research areas as the most compelling and critical predictions, the trends and topics they address this year indicate a strong focus on individuals, the environment, and alternative ways of buying and selling IT services and technologies," said Daryl Plummer, managing vice president and Gartner Fellow. "These areas of focus imply a significant groundswell of change that may in turn change the entire industry."

These predictions are selected from more than 100 predictions that Gartner presents and reviews every year. These predictions focus on general technology areas rather than on specific industries or roles. This year's predictions include:

By 2011, Apple will double its U.S. and Western Europe unit market share in Computers. Apple's gains in computer market share reflect as much on the failures of the rest of the industry as on Apple's success. Apple is challenging its competitors with software integration that provides ease of use and flexibility; continuous and more frequent innovation in hardware and software; and an ecosystem that focuses on interoperability across multiple devices (such as iPod and iMac cross-selling).

By 2012, 50 per cent of traveling workers will leave their notebooks at home in favour of other devices. Even though notebooks continue to shrink in size and weight, traveling workers lament the weight and inconvenience of carrying them on their trips. Vendors are developing solutions to address these concerns: new classes of Internet-centric pocketable devices at the sub-$400 level; and server and Web-based applications that can be accessed from anywhere. There is also a new class of applications: portable personality that encapsulates a user's preferred work environment, enabling the user to recreate that environment across multiple locations or systems.

By 2012, 80 per cent of all commercial software will include elements of open-source technology. Many open-source technologies are mature, stable and well supported. They provide significant opportunities for vendors and users to lower their total cost of ownership and increase returns on investment. Ignoring this will put companies at a serious competitive disadvantage. Embedded open source strategies will become the minimal level of investment that most large software vendors will find necessary to maintain competitive advantages during the next five years.

By 2012, at least one-third of business application software spending will be as service subscription instead of as product license. With software as service (SaaS), the user organisation pays for software services in proportion to use. This is fundamentally different from the fixed-price perpetual license of the traditional on-premises technology. Endorsed and promoted by all leading business applications vendors (Oracle, SAP, Microsoft) and many Web technology leaders (Google, Amazon), the SaaS model of deployment and distribution of software services will enjoy steady growth in mainstream use during the next five years.

By 2011, early technology adopters will forgo capital expenditures and instead purchase 40 per cent of their IT infrastructure as a service. Increased high-speed bandwidth makes it practical to locate infrastructure at other sites and still receive the same response times. Enterprises believe that as service oriented architecture (SOA) becomes common "cloud computing" will take off, thus untying applications from specific infrastructure. This trend to accepting commodity infrastructure could end the traditional "lock-in" with a single supplier and lower the costs of switching suppliers. It means that IT buyers should strengthen their purchasing and sourcing departments to evaluate offerings. They will have to develop and use new criteria for evaluation and selection and phase out traditional criteria.

By 2009, more than one third of IT organizations will have one or more environmental criteria in their top six buying criteria for IT-related goods. Initially, the motivation will come from the wish to contain costs. Enterprise data centres are struggling to keep pace with the increasing power requirements of their infrastructures. And there is substantial potential to improve the environmental footprint, throughout the life cycle, of all IT products and services without any significant trade-offs in price or performance. In future, IT organisations will shift their focus from the power efficiency of products to asking service providers about their measures to improve energy efficiency.

By 2010, 75 per cent of organisations will use full life cycle energy and CO2 footprint as mandatory PC hardware buying criteria. Most technology providers have little or no knowledge of the full life cycle energy and CO2 footprint of their products. Some technology providers have started the process of life cycle assessments, or at least were asking key suppliers about carbon and energy use in 2007 and will continue in 2008. Most others using such information to differentiate their products will start in 2009 and by 2010 enterprises will be able to start using the information as a basis for purchasing decisions. Most others will stat some level of more detailed life cycle assessment in 2008.

By 2011, suppliers to large global enterprises will need to prove their green credentials via an audited process to retain preferred supplier status. Those organizations with strong brands are helping to forge the first wave of green sourcing policies and initiatives. These policies go well beyond minimizing direct carbon emissions or requiring suppliers to comply with local environmental regulations. For example, Timberland has launched a "Green Index" environmental rating for its shoes and boots. Home Depot is working on evaluation and audit criteria for assessing supplier submissions for its new EcoOptions product line.

By 2010, end-user preferences will decide as much as half of all software, hardware and services acquisitions made by IT. The rise of the Internet and the ubiquity of the browser interface have made computing approachable and individuals are now making decisions about technology for personal and business use. Because of this, IT organizations are addressing user concerns through planning for a global class of computing that incorporates user decisions in risk analysis and innovation of business strategy.

Through 2011, the number of 3-D printers in homes and businesses will grow 100-fold over 2006 levels. The technology lets users send a file of a 3-D design to a printer-like device that will carve the design out of a block of resin. A manufacturer can make scale models of new product designs without the expense of model makers. Or consumers can have models of the avatars they use online. Ultimately, manufacturers can consider making some components on demand without having an inventory of replacement parts. Printers priced less than $10,000 have been announced for 2008, opening up the personal and hobbyist markets.

 This informs science developments because the primary tool of even the molecular biologist these days is the computer. Apple is already proportionately over-represented in biotech labs and this will continue; the availability of new, more portable, more green infotech will enable scientists as much as anyone else, maybe more; open-source, cloud computing and SoaS are already making inroad into science, especially in commercial biotech (slowed only by institutional inertia/paranoia/security-awareness, all of which will be solved. 3-D printers? Cool!

Direct Sequencing Of DNA, RNA Using Novel Technique

 This has been coming for years. Kary Mullis (PCR inventor and Nobel laureate and eccentric) had an SEM in his house so he could play at this, though he never solved it.

The clearing of lands for biomass energy crops releases so much carbon dioxide that it takes many decades to cut the CO2 by as much as the land clearance originally released.

Together the two studies offer sweeping conclusions: It does not matter if it is rain forest or scrubland that is cleared, the greenhouse gas contribution is significant. More important, they discovered that, taken globally, the production of almost all biofuels resulted, directly or indirectly, intentionally or not, in new lands being cleared, either for food or fuel.

“When you take this into account, most of the biofuel that people are using or planning to use would probably increase greenhouse gasses substantially,” said Timothy Searchinger, lead author of one of the studies and a researcher in environment and economics at Princeton University. “Previously there’s been an accounting error: land use change has been left out of prior analysis.”

The Wall Street Journal quotes a figure of 93 years to get a payback for US grassland converted to corn ethanol.

But corn ethanol is far from the worst offender. Conversion of Indonesian peatlands to palm oil biodiesel takes 423 years to pay off.

The conversion of peatlands for palm oil plantations in Indonesia ran up the greatest carbon debt which would require 423 years to pay off. The production of soybeans in the Amazon, which would not "pay for itself" in renewable soy biodiesel for 319 years.

The shifting of US croplands into biomass energy causes lands in other parts of the world to shift into crop production. (this is called stating the obvious but with a scientific study to make the obvious harder to deny)

Searchinger's study focused on the global ripple effect of changing the use of farmland. U.S. farmers have been replacing soybean fields with cornfields to meet the rising demand for ethanol, lowering the world supply of soybeans and driving up their price.

As a result, farmers in Brazil are clearing rain forest to plant soybeans, he said.

His model estimated that devoting 12.8 million hectares of cornfields in the U.S. for ethanol production would bring 10.8 million hectares of additional land into cultivation throughout the world, including 2.8 million hectares in Brazil and 2.3 million hectares in China and India -- much of it forests and grasslands.

This demonstrates the foolishness of European Union rules to prevent import of biodiesel from high ecological value converted lands. Such bans just shifts the biomass energy production onto other lands while shifting food production from those other lands onto the lands that otherwise would have produced biomass energy crops. The only way to prevent habitat destruction from biomass energy is to use little land for biomass energy crops.

People want less ecological damage have a few alternatives staring at them: First, promote wider birth control use. Babies never conceived will never use land for biomass energy or for food to eat. Second, support energy sources that use small land footprints per amount of energy produced. Nuclear energy best fits the bill.

But if biofuels become large net producers of energy then they'll drastically increase in popularity regardless of their CO2 emissions effects.

A new analysis shows that the energy balance of biodiesel is a positive ratio of 3.5-to-1. For every unit of fossil energy needed to produce the fuel over its life cycle, the return is 3.5 units of energy, according to new research conducted at the University of Idaho in cooperation with the U.S. Department of Agriculture (USDA). The announcement of the increase—up from 3.2—was made today (6th February) at the National Biodiesel Conference & Expo in Orlando.

The yield of soybeans per acre keeps rising while energy inputs are not rising. So the ratio of energy out to energy in keeps rising.

The researchers found national soybean yield data from 1975 to 2006 shows that the yield has increased at the rate of 0.6 bushels per acre per year. Yet, the fertilizer application rate has essentially remained the same and the herbicide application rate has declined to one-fifth of its rate in 2000. Reduced herbicide applications have the added benefit of requiring less diesel for field spraying.

At the processing level, technology improvements at soybean crushing facilities led to 55 percent less energy needed than what was reported in the NREL study.

The best option I can see coming up for biomass energy is biodiesel algae. The algae approach might allow thousands of gallons of diesel to be produced per acre per year. But it is not clear when algae biodiesel will become cost effective. Maybe sooner than we think once oil production declines send oil prices into the stratosphere.

Electricity can be produced using the mechanics of human walking.

Philip Ball

The device creates as much power as the wearer has to expend to carry it.SCIENCE

A new device that straps to your leg can extract enough energy from your walking motion to power ten mobile phones — and the developers say that you'll barely notice the extra effort it requires.

Max Donelan of Simon Fraser University in Burnaby, Canada, and his colleagues say that their device should capture even more power, at a lower energy cost to the wearer, once it is improved beyond the current prototype.

It could eventually be used to power medical implants, eliminating the need for surgery to replace batteries. The device might also drive robotic prosthetic limbs by harnessing the movements of the wearer, and could power communications technology in parts of the world that lack electricity supplies.

Watt's new?

The knee brace is by no means the first device that scavenges energy from human movement. Wind-up flashlights and radios are now common, as are watches that are powered by everyday arm movements. Researchers have also made systems that generate electricity by compression of the soles of shoes, and 3 years ago a team at the University of Pennsylvania created a backpack that produces more than 7 watts of power as the load slides up and down on a frame¹.

Test subjects walking with the new device strapped on both legs produced about 5 watts of electricity². That's less than is produced by the backpack, but ten times more than is typically produced by shoe-mounted energy harvesters. Importantly, the cost in 'metabolic power' to the subjects was insignificant - also just about 5 watts.

The bending and unbending of the device is only used to create power during the second half of the step.SCIENCE

The knee device works so well because it can be programmed to engage in energy generation only during that part of the walking cycle when leg muscles are being used to slow down the swinging lower leg.

In other words the device can be set so that it doesn't impede a user swinging their lower leg forward during the first half of a step, but only to help slow the lower leg down during the second half of a step, when the foot comes to rest again. In this part of the step, the bending motion of the knee brace is translated into energy through a system of gears hooked up to a generator.

Applying the breaks

This is comparable to ‘regenerative braking’ used in some electric and hybrid motor cars to extract energy as the vehicle brakes. “Walking is a lot like stop-and-go driving,” Donelan says. “Within each stride, muscles are continually accelerating and decelerating the body. In hybrid-electric cars, energy normally dissipated as heat during braking drives a generator instead. We have applied this same principle to walking. That way, the device generates substantial electricity without increasing the effort required to walk.”

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The researchers are already working hard on an improved design. “We are about a year into the next generation of the device,” says Donelan. “We are making it lighter and shifting much of the remaining mass further up the leg so that it feels lighter still.” Weights lower down the leg are a greater burden as they have to be swung along during walking.

The tricky — and "fun", says Donelan — part is trying to develop a system that automatically senses the walking speed and style of the user on a particular terrain, and adapts itself to extract the maximum amount of power for the minimum user effort.

The South African and Kenyan mobile phone provides are allowing users to transfer talk-minutes from phone to phone. In an environment where most people have a mobile (and no landline, or even street name), this creates a new currency de novo. Sure, it's pegged to the rand right now, but in practice it can move based on market actions ("pay me ten rand or eight rand-minutes, cos I prefer minutes"). Superbly creative bypassing of the bank system, and a likely presage of the abolition of physical credit cards or EFTPOS (why bother, when you have a phone?). Hurry up and allow this innovation in our mobile system please! 

International magazine announces New Zealand “tearless onion” breakthrough

George Raine, Chronicle Staff Writer

Tuesday, February 5, 2008

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HELSINKI (Reuters) - Scientists in Finland said they had replaced a 65-year-old patient's upper jaw with a bone transplant cultivated from stem cells isolated from his own fatty tissue and grown inside his abdomen.

Researchers said on Friday the breakthrough opened up new ways to treat severe tissue damage and made the prospect of custom-made living spares parts for humans a step closer to reality.

"There have been a couple of similar-sounding procedures before, but these didn't use the patient's own stem cells that were first cultured and expanded in laboratory and differentiated into bone tissue," said Riitta Suuronen of the Regea Institute of Regenerative Medicine, part of the University of Tampere.

She told a news conference the patient was recovering more quickly than he would have if he had received a bone graft from his leg.

"From the outside nobody would be able to tell he has been through such a procedure," she said.

She added, the team used no materials from animals -- preventing the risk of transmitting viruses than can be hidden in an animal's DNA, and followed European Union guidelines.

Stem cells are the body's master cells and they can be found throughout the blood and tissues. Researchers have recently found that fat contains stem cells which can be directed to form a variety of different tissues.

Using a patient's own stem cells provides a tailor-made transplant that the body should not reject.

Suuronen and her colleagues -- the project was run jointly with the Helsinki University Central Hospital -- isolated stem cells from the patient's fat and grew them for two weeks in a specially formulated nutritious soup that included the patient's own blood serum.

In this case they identified and pulled out cells called mesenchymal stem cells -- immature cells than can give rise to bone, muscle or blood vessels.

When they had enough cells to work with, they attached them to a scaffold made out of a calcium phosphate biomaterial and then put it inside the patient's abdomen to grow for nine months. The cells turned into a variety of tissues and even produced blood vessels, the researchers said.

The block was later transplanted into the patient's head and connected to the skull bone using screws and microsurgery to connect arteries and veins to the vessels of the neck.

The patient's upper jaw had previously been removed due to a benign tumor and he was unable to eat or speak without the use of a removable prosthesis.

Suuronen said her team had submitted a report on the procedure to a medical journal to be reviewed.

(Reporting by Sami Torma, Editing by Maggie Fox and Michael Kahn and Matthew Jones)

A Futurist Panel At The World Economic Forum Suggests Print Newspapers Will Cease By 2014 So Should We Start Packing Our Bags?

Philip M. Stone January 25, 2008

A World Economic Forum (WEF) panel featuring such futurists as Paul Saffo of Stanford and Peter Schwartz, chairman of Global Business Network, suggested Thursday that print newspapers will disappear by 2014. But ever since the Internet became a powerhouse we’ve heard similar predictions on the end of print, so, no need to pay attention to this prediction either. Right?

Right!

Mind you, it could well depend upon semantics. At last year’s WEF there was that famous quote by New York Times Company Chairman Arthur Sulzberger given to the Israeli Haaretz newspaper, “I really don’t know whether we’ll be printing the Times in five years, and you know what? I don’t care either.” That caused a bit of a hue and cry back at headquarters and a month later Sulzberger had to explain himself to staff.

“We are continuing to invest in our newspapers, for we believe that they will be around for a very long time. This point of view is not about nostalgia or a love of newsprint. Instead, it is rooted in fundamental business realities: Our powerful and trusted print brands continue to draw educated and affluent audiences.

"Traditional print newspaper audiences are still significantly larger than their Web counterparts. Print continues to command high levels of reader engagement. And, of course, we still make most of our money from print advertising and circulation revenue. And yes, I remember what I said here last year and what I was supposed to have said last month at Davos about not having a printed product in five years time.

"So let me clear the air on this issue. It is my heartfelt view that newspapers will be around--in print--for a long time. But I also believe that we must be prepared for that judgment to be wrong. My five-year timeframe is about being ready to support our news, advertising and other critical operations on digital revenue alone ...whenever that time comes."

Haaretz had also written in its interview, “Sulzberger says the New York Times is on a journey that will conclude the day the company decides to stop printing the paper. That will mark the end of the transition. It's a long journey, and there will be bumps on the road, says the man at the driving wheel, but he doesn't see a black void ahead.”

So based on all of that could it be the futurists are right that at some point in the future print newspapers will cease to be, and the only real crystal ball question is “When”?

Rebekah Wade, editor of Murdoch’s tabloid Sun newspaper with the largest daily circulation in the UK, believes it is going to take at least 15 years for Internet revenues to become meaningful to a print newspaper’s bottom line. She told a House of Lords Committee on Media Ownership and the News that The Sun's revenue from the internet would only become significant in “14 to 15 years time”.

While newspapers may be reporting huge increases in their Internet traffic and revenues she reminded the committee that the recent starting base was zero and that print revenues were significantly far more important than were the Internet’s.
"We have a set of projections and sets of targets that we want to achieve, and so far we are achieving them. Long-term I can't be detailed and say what percentage will come from the internet but it will become significant in 14 to 15 years time. Right now the (print) newspaper makes the money."

But she did agree that the Internet brought new readers to the newspaper – mainly younger readers. "Out of the 300,000 daily unique (Sun Internet) users 70% will be under 35. It's very different from the newspaper, online we are bringing young readers to the Sun world. This is our strategy," she said.

The debate of “when” rather than “if” has taken on added interest this week because of a piece in the Washington Post headlined, “Does The News Matter To Anyone Anymore” . It was written by former Baltimore Sun journalist David Simon who is now executive editor of the HBO series “The Wire” which in its final episode shows the struggles facing newspapers today. His Post article really bit for it gave pretty good chapter and verse how a great newspaper like the Baltimore Sun has transformed from the great newspaper it once was to what it is today, and there are few veteran journalists out there reading that article who couldn’t sub the name of their own newspaper in that same story in place of the Sun’s. That seems to have opened up a hornet’s nest of defensive reaction.

One such response,  by Alex Alben for the Seattle Times,  was fascinating for reminding us of the “writing on the wall”  prediction “on the future of news” given at a Columbia University forum in 1996 by Mike Slade, CEO of Starwave Corporation. Remember this was the time when the Internet was just beginning to make itself felt and a good five years before anyone heard of Craigslist. Slade’s view even then was that the newspaper print model was in trouble:

 “• Well over half of the content in a given daily edition is commodity content, such as feeds from The Associated Press and syndicated comics and columns;

“• The other half is really the product of (give or take) 50 to 100 people with journalism degrees;

“• A relatively small percentage of a given metro area subscribes to a daily paper;

“• Newspapers rely on classified ads, which would one day be supplanted by free online classified ads.”

His advice: Build a defensible business model, but the industry wasn’t listening and is now paying the cost.

What newspapers still have going for them is that people do very much want news in this modern digital world. The platforms may be varied, but they want news and newspapers are trying to find their niche in that multi-faceted world. The problem is that with the continuing staff cutbacks newspapers are inhibiting what most analysts believe is the one thing going for them – their dominance in being able to cover their own local communities.

With that in mind, one should not lose sight of what the Chicago Tribune is doing with its hyper-local web sites that now cover 21 communities in which readers themselves upload their community news. Who better to know what is happening locally then those who are living it?

The message there is really quite clear – either newspapers dominate that local and hyper-local reporting, or someone else, once again, will eat their cake and those dire predictions of ceasing to exist could be closer to the truth than any of us would care to believe.

BUSINESS WORLD By HOLMAN W. JENKINS, JR.

Future Farmer
January 30, 2008; Page A16

History records that previous commodity booms were not followed by mass starvation, resource wars and the end of civilization. John Atkin is out to make sure it doesn't happen again.

An agricultural zoologist by training, he serves as chief operating officer for crop protection at Switzerland's Syngenta, a competitor to the U.S. giant Monsanto in the controversial business of agricultural technology.

Of the recent surge in prices for all manner of foodstuffs, he says don't blame biofuels. Coffee and frozen orange juice are up, and they don't go into your gas tank or compete for land with ethanol-related crops. Iron ore, copper and most nonfarm commodities are up too. And whatever the errors of Alan Greenspan and Ben Bernanke, the biggest factor may be a simple failure of optimism about the global economy. Every CEO's mental map now includes India and China, yet somehow the whole spectrum of natural resources producers failed to invest sufficiently to meet the demand of several hundred million new consumers.

Mr. Atkin cites a United Nations forecast that, by 2030, food production will have to have increase 50%, partly to feed a bigger world population and partly to supply the richer, more varied diets demanded by the newly affluent of the developing world.

"Agriculture can respond to this," he says. "Absolutely it can respond to this."

He also says: "Organic farming is not the solution." Technology is.

Only Brazil offers sizable acreage of uncultivated lands, in its scrubby central and western provinces. Transportation costs were once prohibitive, but with high crop prices, enterprising farmers are bringing virgin lands under the tractor. Who's financing these sodbusters? "We're financing them," says Mr. Atkin, slightly astonished by his own answer. Seed and agrochemical suppliers have been letting their receivables go unpaid 200 or 300 days, serving effectively as banks.

Also making a contribution will be Russia and Ukraine, where modern techniques will dramatically improve productivity. But the heaviest lifting will be done by technology. Syngenta, based in Basel, is carving out a different approach than Monsanto, involving chemistry as much as gene technology, and working particularly closely with farmers to adapt its formulas to local conditions.

Take its forthcoming Invinsa, marketed in a joint venture with developer Rohm and Haas. It's a spray that inhibits a plant's normal reaction to modest drought conditions. Plants overreact to dry weather -- they stop growing and turn yellow as a defensive measure, thanks to the natural plant hormone ethylene. By blocking ethylene, Invinsa allows plants to remain robust and ready to respond when moisture returns. (The same stuff keeps supermarket apples bright and crunchy.)

On biofuels, Mr. Atkin doesn't doubt that cellulosic ethanol, made from agricultural waste and weeds, will one day make a cost-effective and climate-friendly contribution to transportation fuels. In the meantime, however, Washington is keen to shovel protectionism and subsidies at corn ethanol, which is neither cost-effective nor climate friendly, so Syngenta is working up a genetically modified corn that already contains a key enzyme additive, cutting a step from the ethanol manufacturing process.

But a headache looms: The company may have to endure the costly rigmarole of registering the trait in the world's major markets, given the risk of trace amounts of the genetically modified corn finding their way into crop shipments for human consumption. Haunting the industry is 2000's "StarLink" debacle. Tiny amounts of a corn approved only for animal feed and ethanol turned up in tacos, corndogs and other packaged foods, leading to costly recalls. Subsequent testing confirmed what experts knew all along -- that the corn posed virtually zero risk to human beings.

Mr. Atkin admits to "frustration" (a word that pops out several times) with respect to his fellow Europeans' finicky attitude toward gene technology, the U.S.'s steep tariffs on ethanol imports, and the rich world's general disregard for the "minor miracle" of cheap, abundant, healthy food.

"Freer trade and an open door to technology" -- that's what's industry needs from government to meet the world's food demand. Alas, he sees France moving in the wrong direction, even under the supposedly modern Nicolas Sarkozy, with a ban on testing of genetically modified plants. The U.S., he adds, is the "gold standard" in welcoming innovation and evaluating products strictly on the basis of science. We could do better, however, on trade. One of Syngenta's promising products is a hardy sugar beet that could turn countries like India into exporters of motor fuel.

Syngenta was born in 1999, ironically, from the unwanted agrochemical divisions of drug makers AstraZeneca and Novartis. Markets were flat or shrinking at the time for crop protection products. Gerber, Heinz, Frito-Lay and others were swearing off genetically modified ingredients. But the world has woken up in the past 12 months. Now if Syngenta could just get its prices up. In ordinary times, Mr. Atkin says, two-thirds of the payoff from new technology ends up in the pockets of farmers. In the current boom, that ratio has only shifted further in the farmer's favor. Your customers getting rich is not the worst problem to have. Bottom line: It's a good time to be an ag-science company, and even a better time to be a farmer.

Artists and intellectuals despondent over the prospects for originality can take heart from a phenomenon identified about twenty years ago by Don Swanson, a library scientist at the University of Chicago. He called it “undiscovered public knowledge.” Swanson showed that standing problems in medical research may be significantly addressed, perhaps even solved, simply by systematically surveying the scientific literature. Left to its own devices, research tends to become more specialized and abstracted from the real-world problems that motivated it and to which it remains relevant. This suggests that such a problem may be tackled effectively not by commissioning more research but by assuming that most or all of the solution can already be found in various scientific journals, waiting to be assembled by someone willing to read across specialties. Swanson himself did this in the case of Raynaud's syndrome, a disease that causes the fingers of young women to become numb. His finding is especially striking—perhaps even scandalous—because it happened in the ever-expanding biomedical sciences.

 Link to the discovery of new metabolic pathway

Scientists have built the first synthetic genome by stringing together 147 pages of letters representing the building blocks of DNA.

The researchers used yeast to stitch together four long strands of DNA into the genome of a bacterium called Mycoplasma genitalium. They said it's more than an order of magnitude longer than any previous synthetic DNA creation. Leading synthetic biologists said with the new work, published Thursday in the journal Science, the first synthetic life could be just months away -- if it hasn't been created already.

"We consider this the second in our three-step process to create the first synthetic organism," said J. Craig Venter, president of the J. Craig Venter Institute where scientists performed the study, on Thursday during a teleconference. "What remains now that we have this complete synthetic chromosome … is to boot this up in a cell."

With the new ability to sequence a genome, scientists can begin to custom-design organisms, essentially creating biological robots that can produce from scratch chemicals humans can use. Biofuels like ethanol, for example.

"The J. Craig Venter Institute will be able to take a file stored on a computer and using synthetic chemistry, turn that information into life," said Chris Voigt, a University of California at San Francisco synthetic biologist. "I would be shocked if it doesn't come out in six months. I think they've done it."

The technique is basically a reverse of the Human Genome Project, which translated DNA into the letters A, C, T and G, which represent the body's building blocks: the nucleotides adenine, thymine, guanine and cytosine. Synthetic biologists' ambitious goal is to arrange those letters to create never-before-seen organisms that will do their bidding.

The first phase of Venter's three-step process, which he published last year, involved transplanting and "booting up" the genome of one species of bacterium into another. The remaining step is to combine the first two steps, then insert the new synthetic genome into a standard bacterium. Scientists said they expect the announcement of man-made life this year.

The ability to synthesize longer DNA strands for less money parallels the history of genetic sequencing, where the price of sequencing a human genome has dropped from hundreds of millions of dollars to about $10,000. Just a few years ago, synthesizing a piece of DNA with 5,000 rungs in its helix, known as base-pairs, was impossible. Venter's new synthetic genome is 582,000 base-pairs.

"The largest piece that had been published in the scientific literature was 32 kilobases," Venter said. "This is on the order of 20 times the size."

"I would think that you could get to a million base pairs," said Jim Collins, a professor of biomedical engineering at Boston University. "I don't think there's anything that's hindering the use of these approaches to go for much bigger genomes."

The key to the new technique is the yeast's natural ability to staple long strands of DNA together.

"What's really interesting about yeast is that … (it takes) multiple incomplete synthetic parts and assembles them," said Daniel Gibson, a synthetic biologist at the Venter institute and senior author of the paper.

Hamilton Smith, a synthetic biologist who led the Venter Institute research, said that the team's new technique should work for other genomes, although the full potential of the technique is unknown. But scientists were enthusiastic about the possibilities.

"Once this becomes routine, it allows us to build whatever genome we want," Voigt said. "You can design a genome to incorporate a particular chemical process to change what the cells are eating and what the cells are making. You can make robotic cells."

One goal of synthetic biology is to create a so-called minimal genome that would consist of the smallest amount of genes necessary to keep the organism alive. Such a bacterial "chassis" would provide an ideal platform for mounting modules like biofuel production to create tiny biological robots.

Other researchers, like Tom Knight of MIT, Drew Endy of Stanford, and a host of synthetic biology startup companies are all after this prize, which could lead to a replacement for fossil fuels. Voigt sits on the scientific advisory board of a biofuels startup, Amyris.

But synthetic biologists are also planning to scale up from the simplest organisms to the most complex: human beings. The first bacterial genome was sequenced in 1995 and was followed by the landmark sequencing of the human genome in 2001. Based on that trajectory, Voigt estimated that a synthetic human genome -- which could be used in human cloning research -- could be created by 2014.

But before researchers can do that level of synthetic biology, scientists will need to automate their methods. Beyond this work, Voigt said, scientists will need programming tools, in the same way computer scientists use higher level programming languages like Fortran, C++ and Java, to control computer function.

"(Otherwise it's like) writing Vista in binary," he said. "It's just not going to happen."

PAUL SAFFO
Technology Forecaster

The best forecasters will be computers

When I began my career as a forecaster over two decades ago, it was a given that the core of futures research lay beyond the reach of traditional quantitative forecasting and it's mathematical tools.  This meant that futures researchers would not enjoy the full labor-saving benefits of number-crunching computers, but at least it guaranteed job security.  Economists and financial analysts might one day wake up to discover that their computer tools were stealing their jobs, but futurists would not see machines muscling their way into the world of qualitative forecasting anytime soon.

I was mistaken.  I now believe that in the not too distant future, the best forecasters will not be people, but machines: ever more capable "prediction engines" probing ever deeper into stochastic spaces.  Indicators of this trend are everywhere from the rise of quantitative analysis in the financial sector, to the emergence of computer-based horizon scanning systems in use by governments around the world, and of course the relentless advance of computer systems along the upward-sweeping curve of Moore's Law.

We already have human-computer hybrids at work in the discovery/forecasting space, from Amazon's Mechanical Turk, to the myriad online prediction markets.  In time, we will recognize that these systems are an intermediate step towards prediction engines in much the same way that human "computers" who once performed the mathematical calculations on complex projects were replaced by general-purpose electronic digital computers.

The eventual appearance of prediction engines will also be enabled by the steady uploading of reality into cyberspace, from the growth of web-based social activities to the steady accretion of sensor data sucked up by an exponentially growing number of devices observing and increasingly, manipulating the physical world.  The result is an unimaginably vast corpus of raw material, grist for the prediction engines as they sift and sort and peer ahead.  These prediction engines won't ever exhibit perfect foresight, but as they and the underlying data they work on co-evolve, it is a sure bet that they will do far better then mere humans.

Mmmm … Bacteria

By Elsa Youngsteadt
ScienceNOW Daily News
15 January 2008

The human gut hosts 1000 species of microorganisms--more than a kilogram of cells in all. Recent studies indicate that this thriving ecosystem plays an important role in human health and may even contribute to obesity (ScienceNOW, 20 December 2006). Last year, Jeremy Nicholson, a biochemist at Imperial College London, and a team of researchers from Imperial College and the Nestlé Research Center in Lausanne, Switzerland, showed that replacing mouse gut microbes with human microbes caused widespread metabolic changes in the mice (ScienceNOW, 23 May 2007). Nevertheless, scientists remained skeptical that probiotics could have a similar effect, because probiotic foods add only a few billion foreign microbes to a native population of tens of trillions.

In the new study, Nicholson's group returned to the mice harboring human gut microbes. The researchers supplemented the animals' diets with a solution containing one of two species of Lactobacillus bacteria, which are present in yogurt and baby formula. Control mice were given saline solution as a supplement.

After 2 weeks, the team measured the metabolic profiles of the mice, analyzing feces, urine, plasma, intestinal contents, and liver tissue. The results, published in the 15 January issue of Molecular Systems Biology, show that although the composition of gut microbes changed only slightly in the three groups of mice, the animals' metabolic profiles--including various markers for blood cholesterol and amino acid levels in the liver--were profoundly different.

Of particular note, says Nicholson, was the effect of probiotics on bile acids, which help the small intestine absorb fat. Probiotics diminished the function of the acids, Nicholson notes, which may make it harder for the animals to absorb fat--and thus should keep them slim. As for how a relatively small number of foreign microbes could have such a dramatic effect, Nicholson believes it results from communication with the native bugs. "Gut bacteria talk to each other," he says, so despite their relatively modest numbers, "probiotics have a huge effect on what those other bugs do."

Although he cautions that the gut is simpler in the experimental mice than in humans, Glenn Gibson, a microbiologist at Reading University in the U.K., calls the work "very thorough" and says that it foretells an exciting and potentially revolutionary future in which microbial interventions can correct metabolic abnormalities. "We can't change human genetics," he notes, "but if we can alter metabolism with minor changes in gut bacteria, that's very exciting."

The Physical World as a Virtual Reality

Abstract: This paper explores the idea that the universe is a virtual reality created by information processing, and relates this strange idea to the findings of modern physics about the physical world. The virtual reality concept is familiar to us from online worlds, but our world as a virtual reality is usually a subject for science fiction rather than science. Yet logically the world could be an information simulation running on a multi-dimensional space-time screen. Indeed, if the essence of the universe is information, matter, charge, energy and movement could be aspects of information, and the many conservation laws could be a single law of information conservation. If the universe were a virtual reality, its creation at the big bang would no longer be paradoxical, as every virtual system must be booted up. It is suggested that whether the world is an objective reality or a virtual reality is a matter for science to resolve. Modern information science can suggest how core physical properties like space, time, light, matter and movement could derive from information processing. Such an approach could reconcile relativity and quantum theories, with the former being how information processing creates space-time, and the latter how it creates energy and matter.

Visualizing Future Stories: A Day in the Life of a Designer, 2030

December 03, 2007

Security in Ten Years

This is a conversation between myself and Marcus Ranum. It will appear in Information Security Magazine this month.

Bruce Schneier: Predictions are easy and difficult. Roy Amara of the Institute for the Future once said: "We tend to overestimate the effect of a technology in the short run and underestimate the effect in the long run."

Moore's Law is easy: In 10 years, computers will be 100 times more powerful. My desktop will fit into my cell phone, we'll have gigabit wireless connectivity everywhere, and personal networks will connect our computing devices and the remote services we subscribe to. Other aspects of the future are much more difficult to predict. I don't think anyone can predict what the emergent properties of 100x computing power will bring: new uses for computing, new paradigms of communication. A 100x world will be different, in ways that will be surprising.

But throughout history and into the future, the one constant is human nature. There hasn't been a new crime invented in millennia. Fraud, theft, impersonation and counterfeiting are perennial problems that have been around since the beginning of society. During the last 10 years, these crimes have migrated into cyberspace, and over the next 10, they will migrate into whatever computing, communications and commerce platforms we're using.

The nature of the attacks will be different: the targets, tactics and results. Security is both a trade-off and an arms race, a balance between attacker and defender, and changes in technology upset that balance. Technology might make one particular tactic more effective, or one particular security technology cheaper and more ubiquitous. Or a new emergent application might become a favored target.

I don't see anything by 2017 that will fundamentally alter this. Do you?

Boosting your brainpower: Ethical aspects of cognitive enhancements

• People have long been interested in improving their brainpower. Developments in medicine and pharmacy could provide new ways of doing that but because they raise ethical issues that have not been widely discussed, there is a need for public debate about them. In Part One, this paper sets out some definitions and a framework for debate.
• Drugs and medical interventions designed as therapy for people with diagnosed problems are likely to be sought in future by healthy people to “improve” on nature. It is important to distinguish, however, between what is possible now or will be in the near future and more abstract speculation about longer-term developments. In Part Two, the document examines the evidence (or lack of it) for different methods of enhancement, including nutritional supplements, pharmaceuticals and surgery.
• People may not only want to choose enhancement for themselves but also for their children. The possibilities and limitations of genetic manipulation and selection as a means of enhancing future people are also covered in Part Two.
• Individuals have always been able to try and improve their own or their children’s intellectual abilities through study and effort. The possibility of shortcutting that process and lessening the effort required by using nutrition, drugs or medical techniques is more controversial. Part Three considers why this might be.
• It looks at the speculation about how the new technologies might bring about either positive or negative social and cultural changes, affecting not only individuals but the fabric of society. Arguments that have been put forward by those for and against such a change are briefly summarised.
• One of the main arguments concerns interconnectedness. For the purposes of discussion, the paper looks at cognitive functioning as if it could be isolated from other parts of a person’s life. In reality the potential risks or benefits of cognitive enhancement for other aspects of individuals’ personality, such as emotional stability and creativity, cannot be isolated. People are also interconnected in a social sense, so that choices made by some are likely to impact on others and possibly on society at large. This is highlighted throughout the paper and discussed in detail in Part Three where some suggestions are considered about how a balance might be attained between personal liberty and responsibility to the community.
• Why we may have quite different moral views about different methods, even though they all have the same goal, is also discussed in Part Three.
• Almost anything we try may have some unforeseen side-effects or carry some risks. In order to decide whether change should be regulated, the scope and limits of what individuals should be able to choose for themselves or for other people also need to be discussed. Part Four sets out the arguments for and against limiting choice and considers how regulation, if needed, might be implemented.
• The main questions arising from the paper are summarised in Part Five. The BMA does not have policy or recommendations to put forward on these issues but would welcome informed public debate about how, as a society, we should respond to these developments.

Free version licence

WordWeb may be freely used only by people who meet the conditions below.

Global greenhouse gas emissions are currently around 5 tonnes per person per year, and need to be reduced by about 80% have a good chance of avoiding catastrophic warming. Most computer users are responsible for far more emissions than is sustainable. For example one medium distance return flight can be equivalent to over 1 tonne of emissions¹: more than an average person should be emitting in an entire year. A typical SUV causes about twice as much warming per mile as a typical normal European car: 10,000 miles of travel in an SUV is responsible for about 5 tonnes of emissions. Offsetting emissions is no substitute for direct cuts.

You may use the program free of charge indefinitely only if

• You take at most 4 flights (2 return flights) in any 12 month period
• AND you do not own or regularly drive an SUV (sports utility vehicle).

If you do not qualify you must uninstall the program after the 30-day trial period or purchase WordWeb Pro. The licence is designed to provide a small incentive for people with massively unsustainable emissions to cut down.

Whenever a user no longer meets the above requirements, and they have installed the product for more than 30 days, they must uninstall the product or purchase WordWeb Pro; otherwise it is software theft.

There are two exceptions to the above: not-for-profit educational establishments may install WordWeb for the use of their students (regardless of whether their students meet the "sustainable user" requirement), and the registered disabled who require an SUV for transport may use the program freely if they take at most four flights per year.

Please note that even if you meet the above requirements you are probably still unsustainable: turn down the heating (or reduce the amount of air conditioning), use energy efficient lighting, insulate your house and travel by public transport whenever possible.

A tiny new generator that produces electricity from small variations in temperature could turn people into power packs for medical implants and clear the way for complex wireless monitoring systems.

Game company sued over virtual land squabble

• 18:03 18 May 2006
• NewScientist.com news service
• Will Knight

A US gamer has filed a "first-of-its-kind" lawsuit in an acrimonious dispute over the sale of virtual land within the online role-playing game Second Life

FDA Asked to Better Regulate Nanotechnology

By Rick Weiss

Washington Post Staff Writer
Wednesday, May 17, 2006; Page A14

Citing research suggesting that some invisibly small engineered nanoparticles might pose health risks, a coalition of consumer and environmental groups petitioned the Food and Drug Administration yesterday to beef up its regulation of nanoparticle-containing sunscreens and cosmetics and recall some products.

The legal filing was synchronized with the release of a report by the environmental group Friends of the Earth that highlighted the growing number of personal care products with nanoingredients, defined as smaller than 100-millionths of a millimeter.

Exploring the Academic Invisible Web

Lewandowski, Dirk and Mayr, Philipp (2006) Exploring the Academic Invisible Web.

Abstract

Purpose: To provide a critical review of Bergman’s 2001 study on the Deep Web. In addition, we bring a new concept into the discussion, the Academic Invisible Web (AIW). We define the Academic Invisible Web as consisting of all databases and collections relevant to academia but not searchable by the general-purpose internet search engines. Indexing this part of the Invisible Web is central to scientific search engines. We provide an overview of approaches followed thus far. Design/methodology/approach: Discussion of measures and calculations, estimation based on infor-metric laws. Literature review on approaches for uncovering information from the Invisible Web. Findings: Bergman’s size estimation of the Invisible Web is highly questionable. We demonstrate some major errors in the conceptual design of the Bergman paper. A new (raw) size estimation is given. Research limitations/implications: The precision of our estimation is limited due to small sample size and lack of reliable data. Practical implications: We can show that no single library alone will be able to index the Academic Invisible Web. We suggest collaboration to accomplish this task. Originality/value: Provides library managers and those interested in developing academic search en-gines with data on the size and attributes of the Academic

The Community Patent Project

The patent system needs our help. The United States Patent Office is actively seeking ways to bring greater expertise to bear on the review of patent applications and ensure that only worthwhile inventions receive the patent monopoly. Currently, underpaid and overwhelmed examiners struggle under the backlog of applications. Under pressure to expedite review, patents for unmerited inventions are approved.

Sponsored by IBM, the Community Patent Project seeks to create a peer review system for patents that exploits network technology to enable innovation experts to inform the patent examination procedure. In every field of scientific endeavor, peer review is a critical quality control mechanism to improve innovation. Throughout the public sector both peer review and citizen consultation are either legally mandated or practiced as a way to inform policymaking.

The Community Patent Project aims to design and pilot an online system for peer review of patents. The Community Patent system will support a network of experts to advise the Patent Office on prior art as well as to assist with patentability determinations. By using social software, such as social reputation, collaborative filtering and information visualization tools, we can apply the “wisdom of the crowd” – or, more accurately the wisdom of the experts – to complex social and scientific problems. This could make it easier to protect the inventor’s investment while safeguarding the marketplace of ideas.

For more information, please read the background paper: “Peer to Patent: Building a Community Patent Review Process” (Beth Noveck, 2005) available on this website. The Peer to Patent article offers a draft proposal for design of the software and the system. The paper will serve as input to the Community Patent Workshops where the proposal will be refined into a specification and prototype.

Algae produce biofuel

17 May, 2006

Source: Aquaflow Bionomic Corporation

Biofuel produced by algae growing on Marlborough sewage ponds may provide a new alternative energy source, while helping clean up the environment at the same time.

“We believe this is the world’s first commercial production of bio-diesel from algae outside the laboratory,” Barrie Leay of Aquaflow Bionomic Corporation says.

The exact technology being used by Aquaflow is a closely guarded secret, but it does involve processing the algae pulp before extracting lipid oil which is then turned into bio-diesel, the company says.

The process also provides a solution to some of the problems excess algae can cause.

“Although algae are good at taking most of the nutrients and chemicals out of sewage, too much algae can taint the water and make it smell,” Barrie adds.

Creating clean water from a waste product and removing a problem at the same time is a form of environmental remediation, the company points out.

The eventual aim is to blend the bio-diesel with conventional diesel and use it to run vehicles.

Increasing production and testing it out in a range of diesel engines is the next step for Aquaflow, which expects to produce at least a million litres of bio-diesel per year.

Citation Advantage of Open Access Articles

Gunther Eysenbach¹

1 Centre for Global eHealth Innovation, University Health Network; and Department of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada

Open access (OA) to the research literature has the potential to accelerate recognition and dissemination of research findings, but its actual effects are controversial. This was a longitudinal bibliometric analysis of a cohort of OA and non-OA articles published between June 8, 2004, and December 20, 2004, in the same journal (PNAS: Proceedings of the National Academy of Sciences). Article characteristics were extracted, and citation data were compared between the two groups at three different points in time: at “quasi-baseline” (December 2004, 0–6 mo after publication), in April 2005 (4–10 mo after publication), and in October 2005 (10–16 mo after publication). Potentially confounding variables, including number of authors, authors' lifetime publication count and impact, submission track, country of corresponding author, funding organization, and discipline, were adjusted for in logistic and linear multiple regression models. A total of 1,492 original research articles were analyzed: 212 (14.2% of all articles) were OA articles paid by the author, and 1,280 (85.8%) were non-OA articles. In April 2005 (mean 206 d after publication), 627 (49.0%) of the non-OA articles versus 78 (36.8%) of the OA articles were not cited (relative risk = 1.3 [95% Confidence Interval: 1.1–1.6]; p = 0.001). 6 mo later (mean 288 d after publication), non-OA articles were still more likely to be uncited (non-OA: 172 [13.6%], OA: 11 [5.2%]; relative risk = 2.6 [1.4–4.7]; p < 0.001). The average number of citations of OA articles was higher compared to non-OA articles (April 2005: 1.5 [SD = 2.5] versus 1.2 [SD = 2.0]; Z = 3.123; p = 0.002; October 2005: 6.4 [SD = 10.4] versus 4.5 [SD = 4.9]; Z = 4.058; p < 0.001). In a logistic regression model, controlling for potential confounders, OA articles compared to non-OA articles remained twice as likely to be cited (odds ratio = 2.1 [1.5–2.9]) in the first 4–10 mo after publication (April 2005), with the odds ratio increasing to 2.9 (1.5–5.5) 10–16 mo after publication (October 2005). Articles published as an immediate OA article on the journal site have higher impact than self-archived or otherwise openly accessible OA articles. We found strong evidence that, even in a journal that is widely available in research libraries, OA articles are more immediately recognized and cited by peers than non-OA articles published in the same journal. OA is likely to benefit science by accelerating dissemination and uptake of research findings.

Finding solutions to the biggest problems facing humanity and identifying the key opportunities of the 21st century.

The innovation that is the 21st Century School has been made possible through the unique foresight of James Martin. His commitment to this project makes him one of the most significant drivers of academic enterprise today.

The scale of this potential is possible because of the extent of the ambition that the School sets for itself: to foster new thinking that will tackle the pressing issues facing the world today. But, typically of the man whose great generosity has made it possible, the School also sets out to achieve its aims in an imaginative and innovative way, stimulating research within and across many disciplines.

Of course, at Oxford we already carry out a considerable amount of work that might be considered to fall within the orbit of the new School. But this new initiative will provide a focus around which such distinct projects can cluster, interact and grow. At the same time, it will establish a core of James Martin Fellows who will ensure that the vision behind this creation becomes a reality.

The James Martin 21st Century School is committed to encouraging those involved in this research to work in an ever more integrated way, bringing together leading scholars and practitioners to focus on the same theme but from different disciplinary perspectives.

It is a truly visionary enterprise – a unique resource.

Dr John Hood
Vice-Chancellor

Handling everything from the experiment to the OA results

Simon J. Coles and 14 co-authors, An E-Science Environment for Service Crystallography-from Submission to Dissemination, Journal of chemical information and modeling, May 22, 2006. Only this abstract is free online, at least so far:

Abstract: The U.K. National Crystallography Service (NCS) has developed a prototype e-science infrastructure for the provision of a small molecule crystallography service from sample receipt to results dissemination. This paper outlines the two strands of this service, which (a) enable a user to contribute in the conduction of an experiment and (b) provide an effective route for the archival and dissemination of the arising results. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure, which seamlessly provides instantaneous feedback and the ability to remotely monitor and guide diffraction experiments and stage the diffraction data to a securely accessible location. Publication of all the data and results generated during the course of the experiment, from processed data to analyzed structures, is then enabled by means of an open access data repository. The repository publishes its content through established digital libraries' protocols, which enable harvester and aggregator services to make the data searchable and accessible.

Mutant mice challenge rules of genetic inheritance

DNA's cousin, RNA, may also pass information down the generations.

Helen Pearson

Mice without the DNA for a white-tipped tale can still inherit the feature - thanks to RNA.

In a discovery that rips up the rulebook of genetics, researchers in France have shown that RNA, rather than its more famous cousin DNA, might be able to ferry information from one generation of mice to the next.

DNA has long been credited with the job of passing traits from parent to child. Sperm and egg deliver that DNA to the embryo, where it ultimately decides much of our looks and personality.

The new study in Nature¹ thrusts RNA, DNA's sidekick, into the limelight. It suggests that sperm and eggs of mammals, perhaps including humans, can carry a cargo of RNA molecules into the embryo - and that these can change that generation and subsequent ones.

"It's a very exciting possibility," says Emma Whitelaw who studies patterns of inheritance at Queensland Institute of Medical Research in Brisbane, Australia. "DNA is certainly not all you inherit from your parents."

Tip to tail

Minoo Rassoulzadegan and his colleagues were studying a strain of mice with a mutation in a gene called Kit that produces white fur patches on the tails and feet of grey or brown mice.

The team found something odd when they bred together two mice, each carrying one normal copy of the Kit gene and one mutated copy. Most of the mice that inherited two copies of the normal gene inexplicably still had a white tail tip. They appeared to ignore the DNA instructions written in their normal Kit gene.

The team found hints that RNA might be responsible for this strange phenomenon. RNA is conventionally thought to act as a go-between from DNA to proteins. But the mutant Kit gene manufactures lots of odd-sized RNA molecules, and the mouse sperm accumulate this RNA. When the team extracted RNA from mutant cells and injected it into fertilised eggs with normal Kit genes, it caused white patches.

The burning question now is whether this phenomenon may be happening all the time in other organisms, including people, but and has been completely overlooked. "We are convinced it's a more general phenomenon," says team member Francois Cuzin at Inserm in Nice, France.

This method of inheritance could serve a useful purpose. A plant, for example, could adapt to drought during its lifetime by quenching activity of a gene and passing that on through inherited RNA, rather than picking up a mutation in the DNA. Should this characteristic prove useless a few generations down the line when conditions change, it could prove easier to undo.

Corn and cress

Researchers have known of a similar phenomenon in plants, called paramutation, for nearly 90 years. In maize, for example, a perfectly normal pigmentation gene can act as if it is mutated, simply because one of the plant's parents carried a mutated version.

"It was thought to be relatively obscure," says Vicki Chandler, who studies paramutation at the University of Arizona, Tucson. But Chandler says that she has unpublished evidence that paramutation in plants may also be caused by inherited RNA.

There have been other tantalising hints that RNA could be inherited. Last year, for example, a surprise study showed that cress plants sometimes rewrite their DNA back into the sequence of their grandparents². At the time, the authors suggested that a hoard of RNA might be passed down, alongside DNA, and somehow used as a template to rewrite the DNA code.

The new study is the most convincing evidence so far that this phenomenon is happening in mammals - and perhaps in people. Researchers have found RNA accumulated in the heads of human sperm. A 1997 study showed that children's risk of diabetes is partly determined by whether or not their father carried a particular genetic region, regardless of whether that region was actually inherited³.

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References Rassoulzadegan M., et al. Nature, doi:10.1038/nature04674 (2006). Lolle S. J., et al. Nature, 434. 505 - 509 (2005). | Article | PubMed | ISI | ChemPort | Bennett S. T., et al. Nature Genetics, 17. 350 - 352 (1997). | Article |

Biotech firm raises furor with rice plan Truth about Trade & Technology, IA - 18 May 2006 San Francisco - In its quest to genetically engineer rice with human genes to produce a treatment for childhood diarrhea, tiny Ventria Bioscience has made an ...

Biotech upsets just about everybody with its diarrhea treatment Capital Press (subscription), Oregon - 19 May 2006 ... SAN FRANCISCO (AP) — In its quest to genetically engineer rice with human genes to produce a treatment for childhood diarrhea, tiny Ventria Bioscience has ...

Biotech upsets just about everybody with its diarrhea treatment Notebooks (press release), CA - 20 May 2006 Environmental groups, corporate food interests and thousands of farmers across the country have succeeded in chasing Ventria Bioscience's rice farms out of two ...

Biotech firm bucks GM trend, stirring controversy New Scientist (subscription), UK - 19 May 2006 But while some companies have switched to non-staple crops like tobacco and safflower, Ventria Bioscience, based in Sacramento, California, US, is ploughing ...

Firm in line for incentives, steams some rice farmers Topeka Capital Journal (subscription), KS - 17 May 2006 Though complaints from rice growers helped drive Ventria Bioscience rice farms out of California and Missouri, Joint Economic Development Organization members ...

Anti-Diarrheal Rice Makers Flushed Out of California, Straining to ... Medgadget.com, CA - 22 May 2006 Ventria Bioscience has managed to splice human genes coding for proteins in breast milk, tears and saliva into rice as a way to mitigate the effects of diarrhea ...

Biopharm Thrilla in Manila Truth about Trade & Technology, IA - 5 hours ago ... Just last month, California-based Ventria Bioscience reported favorable clinical results with two human proteins biopharmed in rice and used to treat pediatric ...

CRI	Biotech Firm Raises Furor With Rice Plan CRI, China - 14 May 2006 Lundberg and other California rice farmers are concerned over Sacramento biotech company Ventria Biosciences application to grow commercial quanities of rice ...

SOYLENT GREEN IS PEOPLE!! ProgressiveU.org, CA - 15 May 2006 ... Ventria, with 16 employees, practices "biopharming," the most contentious segment of agricultural biotechnology because its adherents essentially operate open ...

Firm looks at Topeka as site of processing plant Topeka Capital Journal (subscription), KS - 9 May 2006 ... Organization, a city-county body that administers proceeds from a half-cent, countywide sales tax, voted to offer the incentives to Ventria Biosciences, a start ...

11155936 2006-0104952 2006-0022990 C/GENOMIC BARRIER TO VIRAL DISEASE Document Type: Utility; Patent Application-First Publication Inventors:Abramson Fredric D (US) Assignee: Unassigned Or Assigned To Individual Assignee Code: 68000 Attorney, Agent or Firm: Bell, Boyd & Lloyd LLC, P.O. Box 1135, Chicago , IL, 60690-1135, US
Publication Application Number Kind Date Number Date -------------- -- -------- -------------- -------- US 20060104952 A1 20060518 US 2005124312 20050506 Continuation of: Pending US 2004912246 20040806 Priority Applic: US 2005124312 20050506 US 2004912246 20040806
Abstract: The present disclosure describes methods for the formation of a genomic barrier to viral infection as a means preventing or mediating viral disease. The formation of a genomic barrier would complement a person's immune system response based on the ability of a specific person to create a genomic environment which inhibits cellular exploitation by invading virions, which is normally dependent on the person's genotype and gene expression patterns (Expressitype). However, by modulating gene expression patterns using various agents, including foodstuffs, extracts and/or pharmaceutical supplements, individuals with essentially the same genotypes (relative to the invading virus) may be treated by the methods described to produce such a barrier. By using microarrays and other related technologies such Expressitypes and compounds which re-regulate gene expression to establish genomic barriers can be identified and carried out, respectively, with the methods as described.
Exemplary Claim:
D R A W I N G 1. A method of re-regulating the expression of one or more genes of a host to prevent or mediate viral infection comprising: i) generating a gene expression pattern for a host; ii) contacting the host with a battery of one or more agents; and iii) determining the resulting gene expression pattern of the host of step (ii), wherein determining comprises relating the pattern of gene expression resulting from agent re-regulation with an inability of the virus to establish infection.

Bacterial DNA and IVF contamination risk on New Scientist

Medical Research News

Published: Wednesday, 30-Nov-2005

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Some children conceived by a common method of IVF could be carrying chunks of bacterial DNA in their chromosomes, according to a study in mice. The researchers who conducted the work say that such accidental genetic modification would be very rare, but they argue that fertility doctors should take more precautions to exclude it. Intracytoplasmic sperm injection, or ICSI, is used to help would-be fathers with very low sperm counts or sperm that cannot swim normally. Rather than mixing sperm and eggs in a culture dish as in conventional IVF, technicians take individual sperm and inject them into a woman's eggs. ICSI has been growing in popularity since its debut in 1991, and now accounts for around half of the IVF procedures in many countries, including the UK and the US. Over the past five years, researchers have experimented with using ICSI to make genetically modified animals by mixing DNA with sperm before injecting the cells into eggs. For large DNA sequences, which would be difficult to transfer by other techniques, it turns out to be an efficient method. So Pedro Nuno Moreira and his team at INIA, the Spanish agricultural research agency in Madrid, decided to investigate the possibility that children's DNA could be accidentally modified if a sperm sample was contaminated with bacteria. They mixed samples of mouse sperm with Escherichia coli containing a gene that codes for a fluorescent protein, and then used the sperm in ICSI. For fresh sperm "washed" by spinning in a centrifuge, to separate them from the other components of semen, 12 per cent of newly fertilised embryos contained the fluorescence gene, although it was not found in embryos that implanted in female mice. For samples of sperm that had been frozen but not washed in this way, 19 per cent of newly fertilised embryos and 6 per cent of those that implanted contained the gene. ICSI experts stress that Moreira used high concentrations of bacteria, which would typically be spotted under the microscope by IVF technicians. "I don't think there is any need to alarm patients or to change procedures for the moment," says Maryse Bonduelle of the Flemish Free University of Brussels (VUB) in Belgium, who is studying the health of several hundred children conceived by ICSI who are now around 10 years old. But Moreira points out that sperm samples are frequently contaminated with skin bacteria carried by the donor. He argues that IVF clinics conform to different standards, and many should take more precautions to eliminate the possibility of accidental genetic modification, such as treating sperm with antibiotics. "It's better to be sure that no children will inherit these problems," he says. One worry is that bacterial DNA could disrupt genes that suppress cancer. Bonduelle thinks this unlikely, adding that the children in her study seem to be healthy. But she concedes that the consequences of accidental genetic modification might emerge later in life. "It is one more reason to continue the follow-up over a long time," says Bonduelle. The Human Fertilisation and Embryology Authority, which regulates IVF in the UK, says it will review Moreira's study to see if any guidelines need to be changed.

A metabolic network in the evolutionary context: Multiscale structure and modularity

( clustering | evolution | modules )

Victor Spirin *, Mikhail S. Gelfand , Andrey A. Mironov , and Leonid A. Mirny *¶

^*Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139; Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetnu Pereulok 19, Moscow 127994, Russia; State Scientific Center GosNIIGenetika, 1-j Dorozhny Proezd 1, Moscow 117545, Russia; and Department of Bioengineering and Bioinformatics, Moscow State University, Vorobjevy Gory 1-73, Moscow 119992, Russia

Edited by David J. Lipman, National Institutes of Health, Bethesda, MD, and approved April 18, 2006 (received for review November 28, 2005)

The enormous complexity of biological networks has led to the suggestion that networks are built of modules that perform particular functions and are "reused" in evolution in a manner similar to reusable domains in protein structures or modules of electronic circuits. Analysis of known biological networks has revealed several modules, many of which have transparent biological functions. However, it remains to be shown that identified structural modules constitute evolutionary building blocks, independent and easily interchangeable units. An alternative possibility is that evolutionary modules do not match structural modules. To investigate the structure of evolutionary modules and their relationship to functional ones, we integrated a metabolic network with evolutionary associations between genes inferred from comparative genomics. The resulting metabolic-genomic network places metabolic pathways into evolutionary and genomic context, thereby revealing previously unknown components and modules. We analyzed the integrated metabolic-genomic network on three levels: macro-, meso-, and microscale. The macroscale level demonstrates strong associations between neighboring enzymes and between enzymes that are distant on the network but belong to the same linear pathway. At the mesoscale level, we identified evolutionary metabolic modules and compared them with traditional metabolic pathways. Although, in some cases, there is almost exact correspondence, some pathways are split into independent modules. On the microscale level, we observed high association of enzyme subunits and weak association of isoenzymes independently catalyzing the same reaction. This study shows that evolutionary modules, rather than pathways, may be thought of as regulatory and functional units in bacterial genomes.

[Impacts on any plans to tinker at the gene level. Equally true of prokaryotes and eukaryotes?]

Science 2 June 2006: Vol. 312. no. 5778, pp. 1355 - 1359 DOI: 10.1126/science.1124234

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Research Articles

Metagenomic Analysis of the Human Distal Gut Microbiome

Steven R. Gill,^1* Mihai Pop,¹ Robert T. DeBoy,¹ Paul B. Eckburg,^2,3,4 Peter J. Turnbaugh,⁵ Buck S. Samuel,⁵ Jeffrey I. Gordon,⁵ David A. Relman,^2,3,4 Claire M. Fraser-Liggett,^1,6 Karen E. Nelson¹

The human intestinal microbiota is composed of 10¹³ to 10¹⁴ microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

What You Need to Know about Peak Oil

Author:	Robert Rapier
Date:	17 May 2006
Summary:	Examines the Peak Oil debate from both sides and attempts to provide the information you need to better understand this complex, but very important issue.

Carbon nanotubes pinned down at last

• 12:06 30 May 2006
• NewScientist.com news service
• Kurt Kleiner

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• Chris Papadopoulos, University of Victoria

 

A new technique that places carbon nanotubes exactly where they are needed could help overcome one of the biggest obstacles blocking the development of nanotube-based electronic devices.

The method uses a specially constructed molecule that attaches one end to a carbon nanotube and the other end to a strip of metal oxide that has been placed on piece of silicon. The nanotubes are just a few nanometres in diameter, and knowing exactly where a tube is means researchers can use it to make a transistor.

"We can use this approach to make lots of devices," says team member James B Hannon, at IBM's T J Watson Research Center in Yorktown Heights, New York, US.

Researchers have previously created nanotube-based transistors, which could eventually be used to make smaller, faster computers. But there was no efficient way of exactly positioning nanotubes. Some researchers have manipulated tubes one at a time with atomic force microscopes. Others have laid down thousands at random, and then created contacts and repeatedly tested them until they found a working circuit.

Nanotube solution

To line up the nanotubes more reliably, the IBM researchers created a molecule that bonds to nanotubes at one end and metal oxides at the other, and mixed this molecule into a solution containing nanotubes. This left each tube attached to a molecule.

They then took a piece of silicon and dipped it into the nanotube solution – the silicon had previously had aluminium oxide stripes laid onto it using electron beam lithography. The free end of the molecule stuck to the aluminium oxide, holding the nanotubes in place.

The next step was to heat the silicon to 600°C, which removed the sticky molecules and left the nanotubes in place, held there by Van der Waals forces (weak intermolecular attraction). Finally, the team used lithography to attach palladium leads to the nanotubes, completing the transistor.

"What needs to be examined further is whether it can be used for large-scale integration. It's a step in that direction," says Chris Papadopoulos, an electrical and computer engineer at the University of Victoria in British Columbia, Canada.

He says that as the researchers try to pack more devices closer together, nanotubes might start crossing each other, ruining many of the transistors.

And the technique is still far from perfect. From a total of 49 measurements made by the researchers, 28 working transistors were detected. But Hannon believes that refinements will eventually allow the technique to produce hundreds or thousands of working devices in precise locations.

Journal reference: Nano Letters (vol 6, p 906)

OK Computer

Chemical & Engineering News published a brief news story today on Ashworth et al., which appeared in the June 1st issue of Nature. In that paper, the authors showed that computational protein design could be used to alter the specificity of the homing endonuclease I-MsoI. The redesigned enzyme was highly active and it cleaved the new recognition sequence about 10,000 times more effectively (in vitro) than the wild-type enzyme.

Earlier this year, David Liu's laboratory demonstrated that it was possible to use directed evolution to modify the specificity of another homing endonuclease (I-SceI), but Ashworth et al. is the first paper in which computational protein design was successfully used to modify the specificity of a homing endonuclease.

The authors say that "the method should be generalizable to any protein–DNA interface redesign problem: for example, the reprogramming of transcription factor binding specificity" and they believe that "[t]he use and refinement of the computational modelling and design strategies described here should ... [enable them to design] novel proteins [that are] able to recognize and cleave any desired DNA site with high specificity for targeted genomics applications."

Joshua

Joshua Finkelstein (Associate Editor, Nature)

Published online before print May 30, 2006
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0508246103

Applied Biological Sciences
Multiple and time-scheduled in situ DNA delivery mediated by -cyclodextrin embedded in a polyelectrolyte multilayer

( gene delivery | layer-by-layer films | transfection )

N. Jessel *, M. Oulad-Abdelghani , F. Meyer *, P. Lavalle *, Y. Haîkel *, P. Schaaf , and J.-C. Voegel *

^*Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 595, Faculté de Médecine, 11 Rue Humann, 67085 Strasbourg Cedex, France and Faculté de Chirurgie Dentaire de l'Université Louis Pasteur (ULP), 67000 Strasbourg Cedex, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut Clinique de la Souris (ICS), Centre National de la Recherche Scientifique (CNRS)/INSERM/ULP, Collège de France, BP10142, 67404 Strasbourg, France; and Institut Charles Sadron (CNRS/ULP), 6 Rue Boussingault, 67083 Strasbourg Cedex, France

Edited by Pierre Chambon, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France, and approved March 17, 2006 (received for review September 21, 2005)

The basic premise of gene therapy is that genes can be used to produce in situ therapeutic proteins. The controlled delivery of DNA complexes from biomaterials offers the potential to enhance gene transfer by maintaining an elevated concentration of DNA within the cellular microenvironment. Immobilization of the DNA to the substrate to which cells adhere maintains the DNA in the cell microenvironment for subsequent cellular internalization. Here, layer-by-layer (LBL) films made from poly(L-glutamic acid) (PLGA) and poly(L-lysine) (PLL) containing DNA were built in the presence of charged cyclodextrins. The biological activities of these polyelectrolyte films were tested by means of induced production of a specific protein in the nucleus or in the cytoplasm by cells in contact with the films. This type of coating offers the possibility for either simultaneous or sequential interfacial delivery of different DNA molecules aimed at cell transfection. These results open the route to numerous potential applications in patch vaccination, for example.

---

Author contributions: N.J. and M.O.-A. designed research; N.J. and M.O.-A. performed research; F.M. and P.L. contributed new reagents/analytic tools; and N.J., Y.H., P.S., and J.-C.V. wrote the paper.

Conflict of interest statement: No conflicts declared.

To whom correspondence should be addressed.

N. Jessel, E-mail: nadia.jessel@medecine.u-strasbg.fr

www.pnas.org/cgi/doi/10.1073/pnas.0508246103

Nature's peer review trial

Peer review is the bedrock of scientific publication (for Nature's position on peer review, see our Guide to Authors). It is widely considered essential for improving submitted papers and enhancing the credentials of scientists as well as those of the journals in which they choose to publish.

But, like any process, peer review requires occasional scrutiny and assessement. Has the Internet bought new opportunities for journals to manage peer review more imaginatively or by different means? Are there any systematic flaws in the process? Should the process be transparent or confidential? Is the journal even necessary, or could scientists manage the peer review process themselves?

Nature's peer review process has been maintained, unchanged, for decades. We, the editors, believe that the process functions well, by and large. But, in the spirit of being open to considering alternative approaches, we are taking two initiatives: a web debate and a trial of a particular type of open peer review.

The trial will not displace Nature's traditional confidential peer review process, but will complement it. From 5 June 2006, authors may opt to have their submitted manuscripts posted publicly for comment.

Any scientist may then post comments, provided they identify themselves. Once the usual confidential peer review process is complete, the public 'open peer review' process will be closed. Editors will then read all comments on the manuscript and invite authors to respond. At the end of the process, as part of the trial, editors will assess the value of the public comments.

At the close of the trial, we will assess the value of public comments overall as well as the practicalities of their inclusion on a longer-term basis. We will publish an account of the trial and our conclusions.

For further details about the trial for authors and reviewers, please go to the question and answer page provided. Further general questions not answered by this list can be directed to the editors. Questions from authors and referees about particular manuscript submissions should be sent to the editor who is handling the manuscript.

Philip Campbell PhD / Editor-in-Chief, Nature

Published online: 4 June 2006; | doi:10.1038/ng1810

A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep

Published online before print June 12, 2006
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0601096103
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Engineering
Novel nanocomposites from spider silk-silica fusion (chimeric) proteins

( biomaterials | nanostructures | silaffin | biomineralization | ceramics )

Cheryl Wong Po Foo *, Siddharth V. Patwardhan , David J. Belton , Brandon Kitchel *, Daphne Anastasiades *, Jia Huang *, Rajesh R. Naik , Carole C. Perry , and David L. Kaplan *¶

^*Departments of Biomedical Engineering, Chemistry, and Chemical and Biological Engineering, Bioengineering and Biotechnology Center, Tufts University, Medford, MA 02155; Biomolecular and Materials Interface Research Group, School of Biomedical and Natural Sciences, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom; and Materials and Manufacturing Directorate, Air Force Research Laboratory, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7702

Edited by Charles R. Cantor, Sequenom, Inc., San Diego, CA, and approved May 8, 2006 (received for review February 10, 2006)

Silica skeletal architectures in diatoms are characterized by remarkable morphological and nanostructural details. Silk proteins from spiders and silkworms form strong and intricate self-assembling fibrous biomaterials in nature. We combined the features of silk with biosilica through the design, synthesis, and characterization of a novel family of chimeric proteins for subsequent use in model materials forming reactions. The domains from the major ampullate spidroin 1 (MaSp1) protein of Nephila clavipes spider dragline silk provide control over structural and morphological details because it can be self-assembled through diverse processing methods including film casting and fiber electrospinning. Biosilica nanostructures in diatoms are formed in aqueous ambient conditions at neutral pH and low temperatures. The R5 peptide derived from the silaffin protein of Cylindrotheca fusiformis induces and regulates silica precipitation in the chimeric protein designs under similar ambient conditions. Whereas mineralization reactions performed in the presence of R5 peptide alone form silica particles with a size distribution of 0.5-10 µm in diameter, reactions performed in the presence of the new fusion proteins generate nanocomposite materials containing silica particles with a narrower size distribution of 0.5-2 µm in diameter. Furthermore, we demonstrate that composite morphology and structure could be regulated by controlling processing conditions to produce films and fibers. These results suggest that the chimeric protein provides new options for processing and control over silica particle sizes, important benefits for biomedical and specialty materials, particularly in light of the all aqueous processing and the nanocomposite features of these new materials.

Science 23 June 2006: Vol. 312. no. 5781, pp. 1795 - 1798 DOI: 10.1126/science.1127404

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Reports

Metagenomic Analysis of Coastal RNA Virus Communities

Alexander I. Culley,¹ Andrew S. Lang,² Curtis A. Suttle^3*

RNA viruses infect marine organisms from bacteria to whales, but RNA virus communities in the sea remain essentially unknown. Reverse-transcribed whole-genome shotgun sequencing was used to characterize the diversity of uncultivated marine RNA virus assemblages. A diverse assemblage of RNA viruses, including a broad group of marine picorna-like viruses, and distant relatives of viruses infecting arthropods and higher plants were found. Communities were dominated by distinct genotypes with small genome sizes, and we completely assembled the genomes of several hitherto undiscovered viruses. Our results show that the oceans are a reservoir of previously unknown RNA viruses.

Technological advance could help infertile people to have children.

Stem cells from a mouse embryo have been coaxed into producing both eggs and sperm in the same dish. The eggs and sperm are the most mature yet grown in the lab, and the advance brings researchers closer to their ultimate aim: producing human eggs and sperm from adult body cells so that infertile men and women can have their own children.

1. Geoengineering our way out of trouble (21stC, Fall 1996)

    save this

   "In the past decade a handful of scientists and engineers have offered some big, bold, and highly controversial schemes to avert impending global environmental problems. These... range from ortho-tech to Star Trek, from massive reforestation efforts geare

   to geoengineering climate environment ... on june 27

2. BBC NEWS | Science/Nature | Guns and sunshades to rescue climate

    save this

   "[T]he most radical of all geoengineering concepts involves nothing less than moving the Earth itself, cooling the planet by shifting its orbit further from the Sun."

   to geoengineering climate environment ... saved by 11 other people ... on june 27

3. How to Cool a Planet (Maybe) - New York Times

    save this

   "[S]ome of the world's most prominent scientists say the [geoengineering] proposals deserve a serious look because of growing concerns about global warming."

   to climate environment geoengineering ... saved by 2 other people ... on june 27

4. Geoengineering: A Climate Change Manhattan Project (Stanford Environmental Law Journal January, 1998)

    save this

   "In the wake of Kyoto, the time has now come to expand our policy horizons to include geoengineering, the direct manipulation of the Earth's climatic feedback system, as a serious alternative to ineffective and contentious regulation."

   to environment climate geoengineering ... on june 27

Post-Normal Science

Our theoretical framework is the so-called "Post-Normal Science" (PNS).
The concept and theory of "post-normal science" was developed by Funtowicz and Ravetz in a series of studies in the 1990s (see Bibliography).
Simplifying matters, one may say that this is a philosophical proposal of adjusting the role of science when serving for policy-making by, in a sense, democratising it. In particular, the theory addresses the situation of "hard decisions based upon soft facts", above all urgent environmental decisions of great complexity. The decisions have to be made on the basis of partial and uncertain information; but then appears the question about the relevance and importance of various types of information.
Funtowicz' and Ravetz' answer is to open up the process of producing expert advise to public inspection (extended peer review) and public participation.

More information: What_is_PNS.pdf

In the 1970s, before the PC era, there were computer hobbyists. A group of them formed the Homebrew Computer Club in a Menlo Park garage in 1975 to trade integrated circuits and swap tips on assembling rudimentary computers, like the Altair 8800, a rig with no inputs or outputs and memory measured in kilobytes.

Among the Club's members were Apple founders Steve Wozniak and Steve Jobs.

As the tools of biotechnology become accessible (and affordable) to a wider public for the first time, hobbyists are recapturing that collaborative ethos and applying it to tinkering with the building blocks of life.

Eugene Thacker is a professor of literature, culture and communications at Georgia Tech and a member of the Biotech Hobbyist collective. Just as the computer hobbyists sought unconventional applications for computer circuitry, the new collective is looking for "non-prescribed uses" of biotechnology, Thacker said.

The group has published a set of informal DIY articles, mimicking the form of the newsletters and magazines of the computer hobbyists -- many of which are archived online. Thacker walks readers through the steps of performing a basic computation using a DNA "computer" in his article "Personal Biocomputing" (PDF). The tools for the project include a $100 high school-science education kit and some used lab equipment.

Other how-to articles guide readers through cultivating skin cells and "Tree Cloning" -- making uniform copies of plant tissue.

Thacker calls the spirit of his article "playful," but adds that it's entirely possible that hobbyists could be part of the future of important biotechnology.

"The people in the Homebrew Computing Club didn't all aim to be Bill Gates," Thacker said. "Nobody knew what was going to happen. There was an interest in the technology as it first became accessible to people who didn't work in big corporations."

The Collective is the inspiration of Natalie Jeremijenko, who began the Collective in 1997. An artist and professor of Visual Arts at the University of California at San Diego, Jeremijenko says the virtue of the hobbyist's "hands-on, DIY mentality" lies in its power to engage a wider audience in the issues surrounding biotechnology.

"Messing with the stuff of the future allows you to have an opinion and to participate in the political process that determines our technological future," she said. "It's a little theoretical; it's also fun."

She conjures Benjamin Franklin as the patron saint of the hobbyist. Rather than appealing to God or to experts, Franklin appealed to the "sense-making of the everyman," she said.

With the tools of the biotech amateur now available for purchase -- used laboratory equipment has its own section on eBay -- some have asked why "garage biotech" has not spread even further.

The main factor limiting an amateur biotech community is the immaturity of the technology, according to Drew Endy, a biological engineering professor at MIT. "Even though it's cheap it's extraordinarily difficult," he said. "The technology isn't reliable enough."

And there's another reason.

"People are very comfortable manipulating silicon," said Endy. "A lot of people, to be blunt about it, are not comfortable with taking responsibility for the manipulation of genetics."

Kim Coghill, a spokeswoman for the Biotechnology Industry Organization, was wary of a potential Bill Gates of biotech starting out as an amateur. "I hope he's not doing (something) in his basement without the guidance of the FDA," she said.

All the members of the collective are familiar with the case of Steve Kurtz, a professor and artist who has had to defend himself against accusations of "bio-terrorism" after local police happened upon his amateur home lab in May 2004.

He says his case has had a moderate "chilling effect."

"Amateurs need experts," Kurtz said. "We come to them with ideas and ask them for help. Scientists are (now) a lot more hesitant to get involved."

Kurtz adds that Tepnel, the company selling a biokit used to conduct a homebrew test for genetically modified organisms designed by Critical Art Ensemble, now refuses to sell to the general public.

While inconvenient, none of these obstacles will stop amateur engagement in the long-term, says Kurtz.

"They're not doing it because it's trendy -- people like the Biotech Hobbyist Collective," he said. "They authentically believe in what they're doing."

Evidence-Based Decision Making Will Help Transform Society

I am optimistic (and hopeful) that one of the key tenets of scientific investigation, "evidenced-based decision making" will be extended to all aspects of modern society. Good experimental design works toward creating conditions that provide the most useful information on a given topic while attempting to eliminate, or at least limit, spurious, irrelevant artifacts from being generated that could falsely influence data interpretation. Data or information is collected until a threshold is exceeded permitting either conclusions to be drawn or at least development of a hypothesis that with further testing can be validated or falsified. 

Not all questions can be simply answered by just looking at the evidence because we are still at a very early stage in understanding the universe around us. For example, in attempting to understand how life began on our planet we can only guess based on certain assumptions whether it originated de novo here or arrived from another planet or a distant galaxy. We do know that a few hundred kilograms of material is exchanged annually between the Earth and Mars, and that new planets are discovered at an unprecedented pace.  When we discover microbial life on Mars we will double the number of planets with known life while increasing the possibility of finding life elsewhere in the universe.

For most scientists the evidence for evolution, regardless of its origins, has been overwhelming.  The fossil record was sufficient evidence for most, but now with genome sequencing information from all branches of life, including from some of our closest relatives like Neanderthals, chimps and rhesus monkeys, the results should be clear cut for anyone whose thinking is not overly clouded by a "belief" system.

In contrast we have newspapers, radio and television news stations owned by individuals or governments presenting subjective, selective subsets of information. As well, there are political campaigns and statements by those wishing to gain or retain power that can only be dismissed as partisan."

We need to push harder for an education system that teaches evidence-based decision making while we hold our public leaders to a higher standard and less partisan behavior as we attempt to tackle some of the historically most difficult challenges facing the future of humanity.