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DayVectors

sep 2009 / last mod nov 2015 / greg goebel

* 22 entries including: parasites, smart grids, HAARP, NASA human spaceflight options, possible HIV vaccine, P-8 Poseidon sub-hunter, hydrogen fuel for cars examined, carbon capture examined, antibiotics maybe not toxins after all, scrubbing systems against global warming, Qaddafi survives and prospers, and the origins of photosynthesis.

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[WED 30 SEP 09] NEWS COMMENTARY FOR SEPTEMBER 2009
[TUE 29 SEP 09] HIV VACCINE?
[MON 28 SEP 09] NEW OPTIONS FOR HUMAN SPACEFLIGHT (1)
[FRI 25 SEP 09] THE PARASITES (20)
[THU 24 SEP 09] GIMMICKS & GADGETS
[WED 23 SEP 09] P-8 POSEIDON IN PREPARATION
[TUE 22 SEP 09] HYDROGEN ALTERNATIVE?
[MON 21 SEP 09] THE HAARP CONSPIRACY (2)
[FRI 18 SEP 09] THE PARASITES (19)
[THU 17 SEP 09] SPACE NEWS
[WED 16 SEP 09] CARBON CAPTURE?
[TUE 15 SEP 09] THE ANTIBIOTICS PUZZLE
[MON 14 SEP 09] THE HAARP CONSPIRACY (1)
[FRI 11 SEP 09] THE PARASITES (18)
[THU 10 SEP 09] SCIENCE NOTES
[WED 09 SEP 09] SCRUBBING GLOBAL WARMING
[TUE 08 SEP 09] QADDAFI THE SURVIVOR
[MON 07 SEP 09] SMART GRID (2)
[FRI 04 SEP 09] THE PARASITES (17)
[THU 03 SEP 09] GIMMICKS & GADGETS
[WED 02 SEP 09] THE NEW GREEN WORLD
[TUE 01 SEP 09] ANOTHER MONTH

[WED 30 SEP 09] NEWS COMMENTARY FOR SEPTEMBER 2009

* NEWS COMMENTARY FOR SEPTEMBER 2009: Although the Obama Administration has been spending much of its time spinning its wheels since it entered office, on 9 September the president gave an eloquent address to a joint session of Congress on a national health-care plan that seemed like it had a fair chance of breaking the unending political logjam on the issue. The speech outlined a moderate plan, with Americans all required to carry health insurance, and subsidies provided to the poor on a sloped scale. Insurance companies would not be able to deny coverage for pre-existing conditions.

Obama insisted that he would not approve any plan that would raise the deficit, and detailed a number of measures to get health care in line -- one interesting one being a independent panel to monitor government-funded health programs like Medicare. The president also said that he would like a public-funded health insurance scheme, but since that idea has been poison to the health insurance companies and to the Right, Obama hinted that compromise was possible. Observers have suggested it might be a good idea to keep the public option in the wings for, say, five years, to be exercised if the health insurance companies don't deliver.

The White House proposal on health care was evidently middle of the road, and given some cooperation with Republican lawmakers, had a good chance of flying. There are hopes that it might even help tone down the national political debate, which so far has involved the Left proclaiming Obama walks on water, while the Right claims he's an emergent Stalin. The president deserves his fair share of constructive criticism -- but it's not coming from his friends, and the ranting from his enemies is merely tiresome.

Some of it goes beyond ranting: a Facebook user recently conducted a poll asking other users if the president "should be killed". The poll was quickly yanked by Facebook and the user found out that the Secret Service does not regard such buffoonery as particularly amusing: "Question authority and the authorities will question YOU." It was, to no surprise, the work of an empty-headed kid, who the authorities declined to name; he wasn't arrested, but his Facebook account was yanked.

* In mid-month, a US intelligence assessment that concluded Iranian work on long-range missiles was progressing much more slowly than predicted led the Obama Administration to cancel plans to set up a long-range anti-ballistic missile (ABM) battery in Poland, and an associated control radar in the Czech Republic. The judgement was that less expensive assets could do the job.

The "SM-3" variant of the Standard naval surface-to-missile (SAM) -- the latest incarnation of a family of missiles whose roots go back to the late 1940s -- has been proven effective against the class of threats expected from Iran, and represents a much more flexible solution. AEGIS-class cruisers and destroyers can be sent to regions where a defense seems needed, and work is under way to develop a ground launcher system for the SM-3 that could be deployed quickly to regions warships can't cover.

Some sources seem to hint that a radar system for SM-3 ground launchers may still be set up in the Czech Republic. Incidentally, thanks to North Korean missile sabre-rattling, the Obama Administration still supports the long-range ABM sites at Fort Greeley in Alaska and Vandenberg Air Force Base in California.

SM-3 SAM launch

The step back on ABM deployment in Poland seems perfectly sensible given the details, but it's been an occasion for grand political posturing. The Russian government had always opposed a US ABM system in Eastern Europe, not because it was a threat to Russia -- if the Russians ever decided to launch a nuclear strike, the ABM system could barely dent the swarms of missiles -- but because it represented a high-profile US military presence in what the Kremlin regarded as Russia's back yard. The loud objections were clearly mostly theatrics meant for domestic consumption; it was not surprising, then, that Moscow crowed the Americans had "caved in" because of Russian opposition.

That was silliness, to be sure, but on the other side of the coin, the decision also accompanied something of a cooling off in US relations with Eastern Europe. The Poles were not happy with Washington over the cancellation of the plans to set up the ABM battery in Poland, with the timing of the announcement of the decision unfortunately coinciding with the 70th anniversary of the Nazi-Soviet invasion of Poland in 1939. The reaction of the Poles was also more emotional than pragmatic, but politics has an inescapable emotional component. The Obama Administration has had other fumbles recently in its dealings with Eastern Europe, and administration officials admit that things could be improved in that regard.

* According to WIRED Online, sketchy reports indicate that in mid-September, American commandos performed a helicopter raid on the town of Barawe in Somalia, killing a senior al-Qaeda official named Saleh Ali Saleh Nabhan. The victim was believed to have been a prime mover in the 2002 terror attacks in Mombasa, Kenya. The incident highlighted the mysterious covert war of American forces against Islamists in the Horn of Africa. Since of course such operations are being conducted with White House authorization, the incident suggests that Barack Obama's public repudiation of the heavy-handed tactics of his predecessor did not mean a complete rejection of black operations and dirty tricks. Indeed, it would be foolishly naive to think that it did.

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[TUE 29 SEP 09] HIV VACCINE?

* HIV VACCINE? The human immunodeficiency virus (HIV) is noted for its ability to mutate rapidly, which has made development of a vaccine very difficult, with some researchers wondering if it's impossible. A recent paper in AAAS SCIENCE suggests that may be overly pessimistic.

The paper was published by a research team led by Laura Walker of the Scripps Research Institute in San Diego and Sanjay Phogat of the International AIDS Vaccine Initiative (IAVI) in New York, who worked together as part of a project named "Protocol G". The focus of the paper was on what are known as "broadly neutralizing antibodies (bNAbs)", proteins that can recognize a wide range of HIV strains and mark them for destruction by the immune system. Medical researchers have been looking for bNAbs that would be effective against HIV for some time, but up to now none have been found that had a broad enough range.

The Protocol G effort, however, was able to find two very promising bNAbs by screening blood serum from a total of 1,800 volunteers from seven African countries -- Cote d'Ivoire, Kenya, Nigeria, Rwanda, South Africa, Uganda, and Zambia -- as well as America, Australia, Britain, and Thailand. The research effort focused on the component of HIV called the "spike", which consists of two sugar-protein molecules known as "gp120" and "gp41" that target a protein named "CD4" found on certain human immune system cells. The spike gives the virus entry to these host cells.

Working with two US biotech firms -- Monogram Biosciences of San Francisco and Theraclone Sciences of Seattle -- the researchers identified the most effective antibodies from the serum samples and engineered cells that could produce them. The antibodies produced by these cells were then tested to see if they could block HIV from recognizing CD4, effectively locking out the virus. Two antibodies, named "PG9" and "PG16" that were both from the same donor, seemed to do the trick.

The next step is to figure out how PG9 and PG16 interact with the HIV spike, the goal being to design a biomolecule that can be used as a vaccine, provoking the immune system into producing bNAbs that would cripple HIV. However, nobody is celebrating yet. Protocol G is continuing their search for new bNAbs on the premise that if one doesn't work, maybe another will.

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[MON 28 SEP 09] NEW OPTIONS FOR HUMAN SPACEFLIGHT (1)

* NEW OPTIONS FOR HUMAN SPACEFLIGHT (1): After taking office, President Obama established a committee to determine options for US policy in space exploration, specifically human space exploration. The chairman was Norman Augustine, once boss of Lockheed, who had led a similar exercise two decades previously. On 8 September 2009, the committee submitted its report to the president, and it makes for interesting reading.

At the outset, the report identified the problem that led to the formation of the committee in the first place: a mismatch between projects and funding, specifically that the current US space program "is perpetuating the perilous practice of pursuing goals that do not match allocated resources." However, the report then immediately pointed out that the USA now has options that were not available when President John F. Kennedy committed America to landing on the Moon in 1961:

In terms of specific issues, the report focused on five questions:

Currently, the plan is to retire the space shuttle at the end of Fiscal 2010. The Obama Administration has relaxed the "hard" retirement date, but there's no funding for shuttle operations beyond that time. However, although there was no question that the shuttle had to be phased out, the committee noted that the shuttle launch schedule is extremely, possibly dangerously, aggressive, and that shuttle operations should be funded into the middle of 2011. In addition, under current plans, the retirement of the shuttle will leave the USA without a human space launch capability in place for at least seven years. The suggestion is that shuttle flights could continue, at a low and cautious rate, well beyond 2011.

As far as the ISS goes, there has been some thought to deorbiting it as early as 2015. The committee was not enthusiastic about that idea at all, pointing out that the station is now effectively complete, and that only five years of operational life would seem absurd in the face of the quarter century of work it took to get the ISS assembled in space in the first place. Hastily abandoning the ISS would certainly damage American credibility with space partners, making international collaborations more troublesome in the future. The committee felt the ISS was an asset that needed to be put to work, both as a space lab and a space exploration testbed, as well as an exercise in working out the inevitable difficulties in international space partnerships.

With regards to futures, the existing plan is defined by the "Constellation Program", devised by NASA under the direction of the Bush II Administration. The Constellation program envisions new human landings on the Moon as a stepping stone to a human mission to Mars and defines the following elements:

The Constellation Program seemed financially realistic when it was initiated, but its funding was dependent on retiring the shuttle in 2010 and deorbiting the ISS in 2016. Since that time, active work on the Ares I / Orion has been delayed; the original in-service target date was 2012, but it is now 2015, and the committee believed that it would very likely slip to 2017. As far as Ares V and Altair go, they remain trapped in early development work.

Ares I & Ares V

The committee felt the technical issues with the Ares I / Orion were manageable, and that development schedules for elaborate space systems were likely to slip in any case. However, the delays have thrown the original Constellation planning assumptions into confusion. The committee did raise concerns about the Orion design, pointing out that while it seemed perfectly capable relative to its mission requirements, it was also expensive, and that a smaller capsule with accommodations for four astronauts would be cheaper. Of course, redesigning the Orion capsule would mean more program delays.

The question remains open as to whether the government should be developing the new human launch system. Ares I was designed with safety and reliability in mind, using well-established hardware and a launch escape system -- the lack of an effective escape system being one of the biggest flaws in the shuttle design. Given the advance in the commercial space business over the past few decades, commercial companies may be able to deliver a system that is just as satisfactory more quickly at lower cost, and the committee recommended that a competition be set up towards that end. [TO BE CONTINUED]

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[FRI 25 SEP 09] THE PARASITES (20)

* THE PARASITES (20): Although parasites can acquire impressive tricks in manipulating the behavior of their hosts, it might seem that humans are too cognizant to be played as puppets by a mindless hitchhiker. However, although it is certainly true that no parasites can perform horror-movie "zombie mind control" on us, they still have brute-force means of influencing our behavior.

The guinea worm spends its juvenile phase in a copepod, a small aquatic crustacean, but humans are its adult host. Humans drink contaminated water and swallow a copepod; the copepod is digested but the young guinea worm goes free, to travel into the intestine and burrow into the abdominal cavity. The worm then wanders through connective tissue until it finds a mate. The male, which is 5 centimeters (2 inches) long, mates with a female, which is 60 centimeters (2 feet) long. The male, having served his purpose, dies. The pregnant female slithers along under the host's skin to reach a leg. By the time she reaches a leg, her eggs have hatched and she carries a clutch of juveniles inside her. Once in position, some of the juveniles force themselves out of the mother.

The juveniles have to escape from the human host into water, and so they have acquired trickery to encourage humans to go to water. An adult guinea worm has tactics to suppress the host immune system, but the juveniles deliberately provoke it, causing the skin to swell and blister. The host splashes water on the inflammation or sticks a leg into a pond, and the juveniles then escape into the water in hopes of finding a copepod. The mother guinea worm responds to the presence of water as well, heaving up the tiny juveniles through her mouth, of all places, with hundreds of thousands of young ejected with each contraction. The contractions force the mother out through the sore as well. At the end she has left the human host, but she is spent and dies.

This strategy works best where supplies of water are scarce since hosts will concentrate at a limited number of waterholes, which helps ensure that the guinea worm will be able to continue in its life cycle. As a result, guinea worm infection or "dracunculiasis" is strongly prevalent in deserts, where humans crowd around oases.

* The guinea worm relies on a certain degree of chance in jumping from host to host. Once the juveniles get into the water, they have to find a copepod, and once they find a copepod, it has to be ingested by a human. Other parasites, particularly those transmitted by biting insects, leave less to chance. Such parasitic infections include malaria and filariasis, spread by mosquitoes; sleeping sickness, by tsetse flies; kala-azar, by sand flies; and river blindness, by black flies. Bacteria and viruses also hitch rides on biting insects, causing bubonic plague, dengue fever, yellow fever, and other diseases.

Once a parasite gains entry to a host through the wound made by the biting insect, the intruder lives in the skin or in the bloodstream, where it has a good chance of infecting the next insect that bites the host. However, the parasite may influence both of its hosts to improve its chances of successfully completing its full life-cycle.

Asian tiger mosquito

The life of a biting insect like a mosquito is not as simple as it might seem. Our skin is tough and it's hard to penetrate. If a mosquito is less than deft about it, it's liable to be slapped into a smear. If the skin simply seems too tough, the mosquito will give it up and try to a more vulnerable patch on the victim. Even once it penetrates the skin, the blood begins to clot, making the drinking ever harder. The mosquito will inject chemicals to prevent clotting and increase blood flow.

The Plasmodium parasite that causes malaria will try to make life easier for an uninfected mosquito by interfering with the platelets in its host, making them do a poorer job of clotting and giving a mosquito a better shot at a blood meal. Once it gets into the mosquito, Plasmodium then moves to the mosquito's gut, where it mates and reproduces, generating about ten thousand ookinetes. The ookinetes become sporozites, which then find their way to the mosquito's salivary gland. Until they reach the salivary gland, they cannot infect a human, and so during the developmental phase they suppress the mosquito's appetite: no sense in letting the mosquito trying to bite anyone and take the chance of getting smashed before the sporozites are in position.

Once Plasmodium is ready, however, it makes the mosquito very hungry, so it will be driven to find victims. In addition, the sporozites neutralize the anticoagulant chemicals produced by the mosquito's salivary glands, meaning that the mosquito has to work harder to get blood, giving Plasmodium more opportunity to infect a human host. [TO BE CONTINUED]

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[THU 24 SEP 09] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: BBC WORLD Online had an interesting article on fire-fighting robots that have been recently introduced in the UK, developed by the British QinetiQ defense research organization with backing by UK Network Rail, the UK Highways Agency, and Transport for London. Four different robots have been demonstrated:

The major rationale in the development of these robots was handling fires involving explosion threats, most significantly acetylene tanks, that are a threat to human firefighters. The robots have already been used a number of times in real-world situations, with QinetiQ responding to firefighter emergency calls. Before the robots were available, the fire area had to be cordoned off for a day or so; with the robots, such situations can be resolved in a few hours.

UK fire-fighting robots

* Prominent Harvard chemist George Whitesides runs a research group that has a wide portfolio, one facet being development of advanced low-cost technologies appropriate for use in the developing world. Adam Siegel, a Harvard graduate student in the lab, has led work to build indicator displays based on paper and "thermochromic" ink -- the kind of ink used in mood rings and disposable thermometers that changes color with temperature. As Siegel put it: "At first, paper may not sound like exciting, state of the art stuff, but in fact it is a very interesting material. The goal here is to get people to think outside of the silicon box -- that is, to think that simple, everyday materials like paper can be used in very technologically sophisticated ways."

Siegel built a readout display by attaching metal heating elements to one side of a sheet of paper and laying down thermochromic ink to the other. Running a current through the heating elements causes the ink on the other side of change color. Siegel believes they could be useful as indicators for a simple cheap sensor system to show if water is safe to drink.

* As reported by the WIRED Autopia blog, researchers at the Fraunhofer Institute in Germany have come up with a scheme where cars could be commanded to start honking to warn citizens of a disaster. In 2010, all cars sold in Europe will be fitted with the "eCall" system that will use GPS and wireless technology to alert emergency responders that an accident has occurred, allowing them to get on the scene faster. The German researchers would like to add a receiver capability; they estimate that if 14% of the cars on the road were able to start honking on demand, they would be able to effectively alert everyone simultaneously. This is one of those ideas where the reaction is: "Yes, BUT ... " It's definitely worth thinking over, but the possible pitfalls will need some careful examination.

* In classic gimmick news, the WIRED Online blogs report that 2009 is the 50th anniversary of the three-point seat belt. This is one of the inventions we now all take for granted, it being found in every car, but there was a time when car seat belts were only across the waist, or if they had upper-body restraint it was with a clumsy arrangement of twin belts.

The simple, elegant, and highly effective three-point belt was developed by an engineer at Volvo of Sweden named Nils Bohlin. Bohlin had worked on ejection seats for aircraft at SAAB and had a better handle on safety restraints than most automotive engineers. Volvo was very tuned to car safety and was enthusiastic about Bohlin's clever design, introducing it into production in 1959. In an act of remarkable far-sightedness, the company also covered the gimmick under an "open" patent, meaning anyone could use it and nobody could claim rights to it. Bohlin's invention is believed to have saved hundreds of thousands of lives and averted countless injuries -- if he'd never done anything else, it would have made his entire career.

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[WED 23 SEP 09] P-8 POSEIDON IN PREPARATION

* P-8 POSEIDON IN PREPARATION: During much of the Cold War, the mainstay of ocean defense of the West was the Lockheed P-3C Orion, a four-turboprop maritime patrol aircraft. The Orion was built in large quantities and not only used by the US Navy (USN) but by many American allies. By the end of the 20th century, however, the Orion was beginning to show its age, and the USN began to cast about for a replacement.

As discussed by an article in AVIATION WEEK ("New On The Ramp" by David A. Fulghum, 13 April 2009), after a frustrating search, in 2004 the USN finally awarded a contract to Boeing for the "P-8A Poseidon Multimission Maritime Aircraft", with plans to obtain up to 108 machines. India, in that nation's first significant buy of US miltech, is also obtaining a slightly modified variant, the "P-8I", and the market among nations that have been long-time users of the Orion is likely to be good as well.

Boeing P-8A Poseidon

The P-8A is a militarized derivative of the long-serving Boeing 737 twin-fan jetliner, based on the fuselage of the 737-800 variant fitted to the wing of the 737-900ER. It is clearly a weapon system, however, with a weapons bay in the fuselage for homing torpedoes and depth charges; four underwing pylons for Harpoon antiship missiles and other guided munitions; and a rotary dispenser for up to 126 sonar buoys ("sonobuoys") or stores designed to a sonobuoy form factor. The aircraft is equipped for mid-air refueling.

The primary combat avionics sensor is the Raytheon AN/APY-10 radar system, installed in the nose. The AN/APY-10 is a multimode search radar, with a synthetic aperture radar (SAR) capability for detection, imaging, classification, and identification of large or stationary vessels or for ground surveillance. The radar also features an inverse SAR (ISAR) capability to characterize small or fast moving vessels; has wide-area and high-resolution "spotlight" modes; and possesses passive signals intelligence (SIGINT) capabilities, allowing it to detect, characterize, and locate a wide range of radio or radar "emitters". In addition, the P-8A carries a Wescam electro-optical / infrared camera turret for visual inspection of targets.

Other avionics include a Global Positioning System receiver / inertial navigation system unit; a suite of communications gear for voice and datalink using direct transmission or satcom relay; and a self-defense suite, including a radar warning system, a heat-seeking missile dazzler, and towed decoys to divert radar-guided missiles. Crew includes pilot and copilot, plus five or six mission crew.

* Three prototypes are in the pipeline, with the first having taken its initial flight on 25 April 2009. Trials will last into 2011, with introduction to service in 2013. Orion crews are eager to get their hands on the Poseidon, not least because it's a nicer ride: the Orion tends to fly rough, while the P-8A has the smooth quiet flight of a jetliner, an important consideration when flying long and exhausting patrols. They're also looking forward to the aircraft's "Mission Computing & Display System (MCDS)", which allows the "tactical coordinators (TACCOs)" to display overlaid data from the aircraft's sensors and remote datalinked systems on the twin 61 centimeter (24 inch) displays of each TACCO workstation.

The MCDS provides an annotated view of the battlespace, integrating inputs from up to 64 sonobuoys along with radar and video. The system includes a reference library to provide useful information on identified targets, as well as a stores menu to allow the TACCOs to select stores for deployment or launch. The TACCOs also will be able to communicate with other platforms over secure comlinks, including access to and control over unmanned aerial vehicles.

The P-8A is designed with upgrades in mind. Software will be updated every two to three years; to support new hardware, the aircraft provides 50% more power and cooling capability than needed at the outset and can handle almost 11 tonnes (12 tons) more payload. A new radar, the "Littoral Surveillance Radar System (LSRS)" is in the pipeline, while new "smart" munitions and small expendable UAVs, possibly dispensed from the sonobuoy launcher, are being considered as options. The expendable UAVs would be dropped to perform close-up inspections of targets, reducing the transit time and fuel burn required for the aircraft itself to descend and then return to cruise altitude.

* The USN has also been searching for a replacement for their airborne electronic intelligence (ELINT) platform, the EP-3E Aries, much like the P-3C except for payload. This requirement has proven even more difficult to deal with, and in fact at the present time no competition has been initiated to obtain the Aries replacement. The need is obviously there, however, and so Boeing has come up with notional designs for the "EP-X", based like the P-8A on the Boeing 737.

Given that no specification has been issued by the Navy, however, for the time being the configuration of the EP-X is variable. A notional configuration involves 14 operator stations and an advanced active-array radar system. Ideas are being floated for modular payloads that could be swapped out to tailor the EP-X to different missions. Nobody is quite sure if a competition will be initiated, however.

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[TUE 22 SEP 09] HYDROGEN ALTERNATIVE?

* HYDROGEN ALTERNATIVE? The notion of using hydrogen as a fuel for powering vehicles has been around for a long time. Its advocates say that we have an effectively unlimited source of hydrogen in the planet's water, and that fuel cells "burning" hydrogen will produce little but water -- no more pollutants, no more CO2. Critics are very skeptical, pointing to the challenges of producing, distributing, and storing the hydrogen, as well as dealing with its highly inflammable nature.

As reported in an article from AAAS SCIENCE ("Hydrogen Cars: Fad Or The Future?" by Robert F. Service, 5 June 2009), US Energy Secretary Steven Chu, a Nobel prize-winning physicist, has generally sided with the doubters, instructing the Department of Energy (DOE) to scale back on development of hydrogen fuel cells. As Chu put it: "Is is likely in the next 10 or 15 or even 20 years that we will convert to a hydrogen-car economy? The answer, we felt, was no."

Hydrogen's defenders believe that Chu made the wrong call. The advocates point out that there's not going to be a true revolution in transport over the next 20 years anyway, because it will take decades to replace all the existing vehicles once a game-changing technology is introduced. For the time being, the only noteworthy change in vehicle technology we are facing is increasing use of plug-in hybrids, and they're more an incremental change than a revolutionary innovation. If it's going to take decades to remake the way Americans drive, so the advocates reason, why take one option off the table just because it won't be available in the near future? The advocates include some members of Congress who are promising to resist Chu's decision.

* The DOE hydrogen fuel cell program was initiated by the Bush II Administration in 2003, with the Federal government providing a total of $1.5 billion USD of funding for the technology. Car companies pumped in billions of their own funds as well and are now demonstrating second-generation fuel-cell cars, with hundreds of them on the road. Toyota, GM, and Honda say they will continue research regardless of what the US government does. The advocates say that there's been a lot of progress since 2003 and that this is not the time to pull the plug.

Even the advocates admit that much more progress is required. The fuel cell systems demand precious-metal catalysts and remain about twice as expensive as targeted. Storing adequate fuel remains troublesome: current high-pressure tank systems have capacity for a range of about 320 kilometers (200 miles), but DOE believes that 480 kilometers (300 miles), a reasonable range, is attainable by 2015. Durability is not up to desired standard either -- current designs need servicing about every 2,000 hours of operation, with DOE shooting for 5,000 -- and worst of all there is effectively no hydrogen distribution infrastructure.

The advocates point out, however, that plug-in hybrids are essentially a bandaid solution, not a real change in the status quo, and that pure electric vehicles (EVs) also have range, cost, and infrastructure challenges. A 2007 analysis of new vehicle technologies by engineers at the Massachusetts Institute of Technology showed that a fuel-cell car with a range of 400 kilometers (350 miles) would come at a premium of $3,600 USD relative to an ordinary internal-combustion car, while a plug-in hybrid with an electric-only range of a mere 16 kilometers (10 miles) would have a $3,000 USD premium, and an EV with a range of 320 kilometers (200 miles) would have a $10,200 USD premium. As one hydrogen advocate puts it: "None of these technologies are free."

But what about infrastructure? There's well less than a hundred hydrogen refueling stations in North America and no distribution system to speak of, with estimates of the cost of development of a hydrogen infrastructure system running to about $200 billion USD for the government, business, and citizens. We already have a power grid that can service EVs -- but it takes hours to charge up an EV, which makes long-distance travel problematic, and estimates of the cost of the home circuitry for the charging system run in the range of $1,000 USD to $2,000 USD. Critics of hydrogen particularly like to zero in on the means used to generate the hydrogen, saying that there's nothing "clean" about it if it means just shunting emissions to the production end -- but the advocates, who see renewable energy as the ultimate "green" future, say that issue plagues alternatives like EVs as well.

And what about hydrogen storage? No technology has yet met DOE targets, but automotive engineers working on fuel-cell vehicles are not all that intimidated. The new Daimler B-class fuel-cell vehicles have a range of 400 kilometers (250 miles) using a tank that stores hydrogen at a pressure of 700 bars, and GM's new Sequel machines are doing better than that. A Daimler engineer shrugs: "Storage technology is not the issue."

Many hydrogen advocates felt that things were going well and were taken off-guard by the DOE's announcement. Chu insists the department is not abandoning work on fuel cells, just scaling it back. Still, the advocates know that the lead time for conversion to a hydrogen economy is measured in decades, and worry that by removing the push toward it now, it is likely to just recede far off into the future.

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[MON 21 SEP 09] THE HAARP CONSPIRACY (2)

* THE HAARP CONSPIRACY (2): The HAARP project's difficulties with the lunatic fringe began in the next year, 1993, when an Anchorage teacher's union representative named Nick Begich got wind of the project through the conspiracy theory network. Begich was fond of lecturing about secret government projects, and to him HAARP just seemed much too suspicious. Hadn't Bernard Eastlund obtained patents on using the technology to control weather? Begich wrote a tract on HAARP and issued dire warnings in lectures. The rumors began to snowball, claiming HAARP was not merely capable of altering weather, but of causing earthquakes or setting the sky on fire, and even -- of course -- performing mind control. Denials by the military were simply proclaimed a cover-up.

The anti-HAARP agitation amounted to little more than noise and didn't really cause the project much trouble, with a pilot array of 48 antennas in place by 1999. However, the cost of the project was tripling, and the military sponsors were beginning to worry about payoff of their investment. The researchers pushing HAARP set up a committee to ensure that the project had a solid justification on a relatively near-term basis, with Tony Tether becoming chairperson. The conclusion of the committee was that ELF waves could be used to "clean up" near-Earth space if, say, the North Koreans set off a nuke in orbit. The explosion would leave radioactive particles circling the Earth that would fry satellites; ELF transmissions, however, could drive the particles to fall back into the atmosphere. To test out the idea meant a bigger array and even more money, but in 2001 Tether became boss of DARPA and threw his weight behind the effort. By 2007, the full 180-antenna HAARP array was in operation.

* The military has on occasions escorted visitors into the HAARP complex, where they are usually awed by its scale and elaboration. The 180 antenna masts, each with four aerials arranged like the rotors of a helicopter at the top, are spaced precisely, with everything held tightly in place by a web of kevlar tethers. There's a wire mesh about 4.6 meters (15 feet) above the ground beneath the tops of the antennas. By varying the phase of the signals to the antennas, the beam can be focused from 5 degrees to 60 degrees of sky, and steered as well. The beam can produce up to 3.6 megawatts of power, being driven by six huge diesel generator.

Researchers have been having great fun with HAARP, producing significant research papers in quantity. The conspiracy theorists have been conducting "research" on the facility of their own, it seems competing to come up with ever wilder plots behind the facility, blaming it for everything from Hurricane Katrina to the 2008 earthquake in China. Scientists associated with the project are "dumbfounded" by the accusations. Smaller-scale ionospheric heating experiments were earlier performed in Norway and Alaska without any negative effects. While HAARP radiates much more power than any of these other experiments, its effects on the ionosphere are smaller than those due to normal day-night heating variations. The idea that it can modify weather seems particularly absurd, since the RF energy doesn't have much effect on the un-ionized atoms and molecules of the lower atmosphere, where weather is created and occurs. Said one researcher: "If climate modifications were even conceivable using this technology, you can bet there would be a lot more funding available for it."

Funding is becoming an issue again since the project's high-profile patrons have moved on. Tony Tether left his job at DARPA, and Ted Stevens got voted out of his Senate seat in 2008. His replacement was Mark Begich, ex-mayor of Anchorage and Nick Begich's little brother. Senator Begich is known as a moderate Democrat and has no tangible association with the lunatic fringe except in the form of his brother, but that association is a bit worrying to HAARP proponents.

The conspiracy theorists would like to see HAARP funding dry up completely. If it doesn't, they will almost certainly claim that proves the facility is too important to the government conspiracy to be allowed to die. However, if HAARP is indeed part of a conspiracy, it is a highly visible one -- which suggests that its true role might be as a diversion, to simply distract the conspiracy theorists, while the real secret work goes on undisturbed. Maybe the paranoids are just not paranoid enough. [END OF SERIES]

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[FRI 18 SEP 09] THE PARASITES (19)

* THE PARASITES (19): The ability of parasites to manipulate the behavior of a host can be surprisingly precise. For example, there's a species of fungus that parasitizes house flies, with spores that land on a fly's body to then spread tendrils over the host, sucking up nutrients from its blood. The fly's abdomen grows but the fly goes on about its business, seeking out trash and cowflops to get a meal. However, in a few days the parasitized fly reaches the end of the road. The fly then is compelled to seek out a high place to alight, possibly a branch or a doorsill. It lands, clamps itself in place with its proboscis, extends its front legs to raise its abdomen, and locks its wings in an upright position. With the fly in the proper position, the fungus sends tendrils out from the host's body, with the tips of tendrils containing packages of spores that are then ejected to the wind, in hopes of getting lucky and landing on another unfortunate fly.

What makes the fungus particularly intriguing is that the fly not only goes through this terminal dance, but that it only does it before sunset. Timing is everything: the air needs to be a bit cool and dewy so the spores will stick, and in the evenings healthy flies tend to head down towards the ground, where they will make easy targets for the spores. Exactly how the fungus keeps track of the time of day is not clear.

* The problem of making the jump from host to host also applies to parasites that cycle through multiple host species, and parasites have acquired the ability to manipulate hosts in such cases as well. Off the coast of the US state of Delaware, there lives a fluke that uses mud snails as its juvenile host and crabs as its adult host. The problem is that the snails don't leave the water and the crabs don't go into it. To solve the problem, the flukes influence the snails to wander onshore or onto sandbars at low tide, where the flukes exit the snail in hopes of finding a crab host.

Another fluke named Dicrocoelium dendriticum or the "lancet fluke" -- common in Europe and Asia, not unknown in America and Australia -- uses cows and other grazers its adult host. The fluke has an unusual life cycle in that it involves three different host species, not just two. The flukes begin the cycle by reproducing in cows, which distribute fluke eggs in their manure, with snails ingesting the manure with the eggs to become infected. The eggs hatch in the intestine of a snail, with the newborn drilling through the gut to settle in the snail's digestive gland.

In the digestive gland, the newborn grow into the mobile juvenile cercariae, which the snail ejects by encapsulating them in balls of slime and spitting them out. That's all right for the parasites, however, since ants find the slimeballs tasty and eat them. The flukes wander about inside the ant's body, to gradually accumulate in the abdomen, where they form cysts. However, a few remain in the ant's head to ensure the ant is properly considerate to its unwanted guests, forcing the ant to climb to the top of a blade of grass and then clamp onto the tip of the blade with its mandibles.

There, the ant stands a good chance of being eaten by a grazer chewing on the grass. Once that happens, the flukes discard their old host and head for the cow's liver, to mature and create a new generation of flukes. Once again, the parasites are careful in timing their "commands" to their host, ensuring that the ant only goes up the blade of grass in the evening. If the host hasn't been eaten by the time the sun comes up, the parasites release their control, allowing the ant to go back down to the ground and continue its existence. Come the next evening, the ant is compelled to go back up a blade of grass again -- to wait to be eaten by a cow. [TO BE CONTINUED]

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[THU 17 SEP 09] SPACE NEWS

* SPACE NEWS: Space launches for August included:

-- 11 AUG 09 / ASIASAT 5 -- A Proton Breeze M booster was launched from Baikonur to put the "AsiaSat 5" geostationary comsat into orbit for Asia Satellite Telecommunications LTD of Hong Kong. The spacecraft was built by Space Systems / Loral; it was an SS/L 1300 series comsat, with a launch mass of 3,765 kilograms (8,290 pounds), a payload of 26 C-band / 14 Ku-band transponders, and a design lifetime of 15 years. It was placed in the geostationary slot at 100.5 degrees east longitude to provide communications services to the East Asia region.

-- 17 AUG 09 / GPS 2R-21 -- A Delta 2 7925 booster was launched from Cape Canaveral to put the "GPS 2R-21" navigation satellite into orbit; it was also referred to as "USA 206" and "Navstar 64". This was the eighth and last of the "Block 2R-M" GPS satellites and had a further alternate designation of "GPS 2R-M8". It was to be followed by the improved "Block 2F" GPS spacecraft. This was the last launch of a Delta 2 booster for the Air Force, though further civil launches were scheduled.

-- 21 AUG 09 / JCSAT 12, OPTUS D3 -- An Ariane 5 ECA booster was launched from Kourou to put the Japanese "JCSAT 12" and Australian "Optus D3" geostationary comsats into orbit. JCSAT 12 was built by Lockheed Martin for Sky Perfect JSAT Corporation of Tokyo, and was based on the A2100 comsat platform. It had a launch mass of 4,035 kilograms (8,900 pounds), a payload of 30 Ku-band / 12 C-band transponders, and a design life of 15 years. It was placed in geostationary orbit as a backup spare.

OPTUS D3 was built by Orbital Sciences for Optus Telecom of Australia and was based on the Orbital Star 2 comsat platform. The satellite had a launch mass of 2,450 kilograms (5,400 pounds), a payload of 24 Ku-band transponders, and a design life of 15 years. It was placed in the geostationary slot at 156 degrees east longitude to provide direct broadcast and other communications services to Australia and New Zealand.

Ariane V lofts Optus D3 & JCSAT 12

-- 25 AUG 09 / STSAT 2 (FAILURE) -- A "Korean Satellite Launch Vehicle 1 (KSLV)" AKA "Naro 1" was launched from the Naro space facility at the southern end of South Korea to put the "Science & Technology Satellite 2 (STSAT 2)" into orbit. This was the first launch of a South Korean booster. The KSLV 1 was based on a first stage with a Russian-built liquid fuel engine, while the second stage had a Korean-built solid-fuel engine. The 100 kilogram (220 pound) satellite carried a microwave radiometer to obtain thermal data on the Earth, as well as a laser retroreflector to permit tracking. The vehicle did not reach orbit.

-- 28 AUG 09 / SHUTTLE DISCOVERY (STS-128) -- The NASA space shuttle Discovery was launched from Cape Canaveral on "STS-128", an International Space Station (ISS) support mission. This was the 128th shuttle flight and the 37th flight of Discovery. There were seven crew, including:

Discovery carried the Leonardo MultiPurpose Logistics Module (MPLM) and an exposed carrier rack, hauling a load of cargo including a new sleeping compartment and the new COLBERT treadmill, named after comedian Stephen Colbert. The astronauts performed spacewalks to swap out external experiments on the ESA Columbus module and replaced an ammonia tank used on the ISS cooling system.

Discovery returned to Earth on 11 September, landing at Edwards Air Force Base in California. Mission duration was 13 days 20 hours 54 minutes. Kopra had spent 58 continuous days in space.

-- 31 AUG 09 / PALAPA D1 (FAILURE) -- A Long March 3B booster was launched from Xichang to put the "Palapa D1" geostationary comsat into orbit for Indosat of Indonesia. The satellite was not put into its proper orbit due to a booster upper stage malfunction.

* OTHER SPACE NEWS: This last month a panel assembled by the White House to examine current US space plans submitted its report to President Obama. It promises to be significant, with early leaks suggesting that it dismisses the plans for sending astronauts back to the Moon and then on to Mars proposed by the previous administration as financially absurd. No big surprise there; the funding for such efforts was never specified.

Anyway, the report will be discussed here once the details become apparent. For the moment, one of the interesting options, discussed here last year, is to perform a crewed visit to a near-Earth asteroid. Lockheed Martin has followed up this idea by outlining a mission plan, using two Orion crewed spacecraft mated together to provide resources for a multi-week trip to the asteroid and back. A lander would not be needed; the spacecraft could simply fly "formation" with the asteroid, with astronauts shuttling back and forth on a tether. Lockheed Martin also suggests the same spacecraft configuration could be used for servicing missions to the outer Earth-Sun libration point, beyond the Moon's orbit, where the Webb Space Telescope will be sited. NASA has been very cool on a crewed asteroid mission, fearing it would distract from "return to the Moon" plans, but given current circumstances it's starting to seem much more attractive.

crewed mission to an asteroid

Incidentally, an article in AVIATION WEEK commented that Lockheed Martin officials have expressed concerns over the push to develop commercial crewed space capsules, such as the SpaceX Dragon-X, pointing out that right now the Orion program is straining budgets: "If we can't afford one program, how can we afford two?" They similar warn against "cutting corners" and warn that NASA could "pay the penalty" down the road. Superficially, that makes some sense, but it also sounds suspiciously like a classic exercise in spreading FUD ("fear uncertainty doubt") about a competitor. We've heard that tune before.

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[WED 16 SEP 09] CARBON CAPTURE?

* CARBON CAPTURE? The notion of capturing carbon emissions from coalfired power plants to head off global warming has been discussed here in the past. An article in THE ECONOMIST ("Trouble In Store", 5 March 2009) took a hard and skeptical look at the subject.

Although oil is starting to run short, there's plenty of coal still left in the ground, enough to provide fuel for several more generations. It's a cheap energy source, providing half or more of the energy for America, Australia, China, Germany, and India. The big problem with coal, of course, is that burning it dumps carbon dioxide into the atmosphere, aggravating global warming. In fact, it's the dirtiest of all the hydrocarbon fuels, producing twice as much CO2 for unit of energy delivered as natural gas.

Policy-makers claim that the problem can be solved with CCS, with the CO2 emissions from powerplants stored underground. US President Barack Obama has endorsed the idea, as has British Prime Minister Gordon Brown. The difficulty is that there is not a single large coal-fired powerplant in the world with CCS, and there doesn't seem to be any rush to build one. Utilities are not under pressure to do so, or at least not any pressure great enough to overcome the risk and expense of doing so.

CCS does sound nice on paper. The idea is to draw off the CO2 emitted by powerplants, compress it, and store it deep in the earth. Most of the technology needed is already in use by the oil and chemical industries, though not in combination. Oil, gas, and salt water seem to stay put in certain rock formations indefinitely, suggesting that carbon dioxide should as well. With CCS, so politicians would like to believe, we can all have our cake and eat it too, burning cheap coal without contributing to global warming.

Technologies are in fact available to draw off C02 from an exhaust stream, using scrubbing technology. Oil firms also have plenty of experience is pumping CO2 into underground petroleum deposits to increase pressure and bring up more oil. Exxon Mobil has a huge carbon-capture facility at La Barge, Wyoming; the USA has a network of 5,800 kilometers (3,600 miles) of pipelines to carry CO2 from capture facilities to the petroleum fields where it's needed. Of course, traditionally the oil firms haven't worried about whether the CO2 leaks out again, but in recent years a few of them have started keeping tabs on whether the CO2 stays underground or not. The oldest such project, codenamed "Sleipnir", off the coast of Norway in the North Sea, has been running for 13 years with no sign of leaks.

There has actually been a little small-scale work with CCS for coal-fired powerplants. In 2008 Vattenfall, a Swedish utility, opened the first power plant to incorporate CCS at Schwarze Pumpe, in Germany. It's only a pilot project, less than a twentieth of the size of most modern coal-fired plants, but so far it's working fine. Several other firms hope to start pilot plants on a similar scale this year.

The core problem with CCS is the expense. As it works now, the process consumes energy, roughly a quarter the output of power station, and the infrastructure to support CCS is not trivial or cheap. It gets worse if long pipelines have to be built to haul CO2 from a powerplant to a storage facility. Nobody's sure how much a CCS plant would cost -- at least a billion dollars, maybe two billion. Estimates of the incremental cost of sequestering a tonne of emissions with CCS run in the range of roughly $50 USD to $100 USD; contrast this with the value of $10 USD assigned by the European Union for carbon trading. Of course, once in use the price of CCS is likely to drop, maybe by half, but the startup sticker shock remains -- and given that these estimates are of technologies that nobody's actually put to practical work yet, few feel very confident in them.

And then there's the risk of CO2 "spills" that could potentially cause widespread suffocation. That means an insurance overhead, driving up the cost of CCS even further. Worst of all, some Green organizations, for example the environmental group Greenpeace, suggests that CCS just won't work. To be sure, once CO2 is locked up in carbonate minerals it's not going anywhere, but as long as it remains a gas it can leak. Greenpeace points out that a leakage rate of only 1% a year would release almost two-thirds of the supposedly sequestered CO2 in a century, rendering the scheme ineffectual.

In 2008, the EU mandated that its members draw up rules for CCS. At a minimum, the governments are supposed to lay down criteria for selecting storage sites and to set standards for monitoring, financial guarantees, safety and so on. The exercise is supposed to be done in 2010, but it doesn't seem to be moving along rapidly; in the absence of rules and realistic financial models, the utilities are reluctant to follow the lead.

Some governments are offering big handouts. Barack Obama's stimulus bill set aside $3.4 billion USD for CCS. The EU, Australia, Britain, Norway, and others have also been talking up incentives. However, actual plans to implement CCS seem to keep receding over the horizon. Al Gore, America's Jeremiah of global warming, flatly doesn't see CCS as practical in the short term or even the medium term. Greenpeace doesn't believe it will ever be workable on a reasonable financial basis, pointing out that in the meantime, renewables like wind and solar just keep getting cheaper and more competitive.

Whether we like it or not, we are obviously heading towards a New Era of Energy, and the squabbling over which turns to take on the road is, as it could be guaranteed to be, loud and noisy. Of course everyone wants the perfect solution; obviously that's not how the real world works, we will end up with an imperfect solution -- but which one?

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[TUE 15 SEP 09] THE ANTIBIOTICS PUZZLE

* THE ANTIBIOTICS PUZZLE: One of the more famous stories in modern science is how Scots biologist Alexander Fleming was conducting research on Staphylococcus bacteria when he noted that some of his staph cultures had been contaminated by fungi, which killed the bacteria. This accidental insight led to the discovery of penicillin, the first "antibiotic" (bacteria-targeting) drug, and Fleming's win of the Nobel Prize in 1945.

The discovery of penicillin is often held up as an example of how humans have been able to leverage off nature by copying molecules that organisms evolved to defend themselves from bacteria. However, as reported by an article in AAAS SCIENCE ("Antibiotics In Nature: Beyond Bacteriological Warfare" by Christine Mlot, 26 June 2009) that leads to the interesting question of whether these molecules actually served such a lethal function in their original organisms -- or whether we had simply stumbled onto a very useful side effect. The reality is that the molecules we use as antibiotics may actually perform functions such as chemical communications, or may even be important metabolic components. Possibly they are not particularly toxic to organisms except in high concentrations -- like many drugs humans use, benign except when administered in an overdose.

* One of the pioneers in this line of research has been Julian Davies of the University of British Columbia in Canada. When he was at the Harvard Medical School in the 1960s, he became interested in antibiotics -- initially focusing on streptomycin, one of the large number of antibiotics produced by the soil bacteria known as "actinomycetes". He determined that streptomycin attacked bacterial pathogens like Mycobacterium tuberculosis by jamming their protein synthesis and so inhibiting their growth.

By the 1980s, after about two decades of investigating antibiotics, Davies had begun to wonder exactly what function antibiotic molecules actually served in the soils and in other microbial environments. In 1990, he wrote a provocative review that suggested that antibiotics did not evolve to combat pathogens -- instead proposing that they were very ancient, that they might be "molecular fossils" that even predated the synthesis of proteins, being originally used as fundamental metabolic elements, and had been retained because they proved useful later for other functions.

Davies continued his research and obtained other insights. One was that an individual actinomycete genome can code for many more antibiotic and antibiotic-like biomolecules than anyone had realized, sometimes more than 25. It seems hard to swallow that an organism would maintain such a large arsenal of bioweapons -- they wouldn't all be useful, and so they would tend to lost over time, with the microorganism retaining only a core set of the most effective of the lot. Over the range of comparable organisms there was a vast corresponding range of antibiotic-like molecules, which only puzzled Davies more: "There are millions and millions of small molecules out there. I couldn't believe they were all weapons."

Davies also noted that the microbes producing molecules useful as antibiotics lived in soils, while the drugs obtained from them were being used against pathogens infecting mammals. Why would soil bacteria target these pathogens? As Davies put it, "they would never see each other" in nature.

* There are clear-cut cases where microbes actually do generate molecules to defeat other microbes, for example in the "rhizosphere", the nutrient-rich zone around plant roots. Research has shown that wheat plants provide a nurturing environment around the roots for Pseudomonas bacteria, with the bacteria in turn generating toxins to defeat fungi dangerous to the wheat. Other research has shown that bacterial symbionts living in insects similarly produce toxins to kill fungi that can infect the insects.

However, most other studies have shown that in their natural environments, microbes rarely produce antibiotics in high enough concentrations to do any other organisms harm. Taking this observation as a cue, in 2002 Davies published a paper in collaboration with Michael Surrette of the University of Calgary in Canada that described the effects of administering microbially produced antibiotics, such as erythomycin and rifampcin, to other microbes. They used as a target organism the Salmonella typhimurium bacteria, with colonies genetically engineered to bioluminesce like fireflies if a particular gene promoter was activated. They ended up with a lights show, with any one antibiotic affecting up to 200 promoter genes, and with different antibiotics affecting different sets of promoter genes. In other words, the antibiotics were actually commanding the bacterial genome to conduct a wide variety of actions, from transport of molecules to DNA repair.

As one microbiologist put it: "These compounds are signals, and a sort of language that microorganisms have that allows them to interact with each other." This insight may help explain why only about 1% of the microbes found in nature can be grown in pure cultures in a laboratory: the microbes may be dependent on compounds produced by other members of a community that isn't present in the lab.

* In the meantime, Dianne Newman, a professor of geoscience at the California Institute of Technology in Pasadena, was investigating how microorganisms have helped shape the Earth's geochemistry, with Newman focusing on microorganisms that use iron or other mineral compounds instead of oxygen in their metabolism. Her group noticed the Shewanella bacteria, which uses iron in its metabolism, employed compounds known as "quinones" in its metabolic system -- and then realized that the quinones looked a good deal like the antibiotic molecules made by Pseudomonas bacteria known as "phenazines".

Maybe the phenazines weren't really weapons; maybe they were actually elements in the Pseudomonas metabolic system. Further research showed that Pseudomonas aeruginosa, which can cause lung infections in humans, tends to produce phenazines when the bacteria forms a biofilm; once the film forms, not all the bacteria have access to oxygen, and so they alter their metabolism to live without it. Newman's group has found that phenazines have control over a number of Pseudomonas genes, and sees them as central to the metabolism of the bacteria, instead of handy bioweapons the bacteria acquired along the line.

Other research has shown that antibiotics can have a surprising range of influence over the behavior of microorganisms that did not produce the antibiotics in the first place. It is now becoming obvious that humans have been using antibiotics as a simple brute-force hammer when they are actually much subtler tools. A proper understanding of exactly what these molecules do may yield much improved drug therapies. Thanks to the work of Davies and others, the idea of antibiotics being natural weapons is falling by the wayside. It is now apparent that antibiotics made by microbes have a wide range of functions and are more likely to be an element in microbial crosstalk instead of crossfire. We just got lucky to find out that they could be used as poisons as well.

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[MON 14 SEP 09] THE HAARP CONSPIRACY (1)

* THE HAARP CONSPIRACY (1): As reported by an article in WIRED magazine ("Sky Lab" by Noah Schachtman, August 2009), near the town of Gakona, about 300 kilometers (185 miles) south of Fairbanks in the state of Alaska, the US Air Force operates a unique facility, named the "High Frequency Active Auroral Research Program (HAARP)". HAARP consists 180 21 meter (69 foot) antennas arranged on a grid over the 9 hectare (30 acre) site. The array dumps high frequency radio energy into the ionosphere, which extends from 80 to 400 kilometers (50 to 250 miles) above the Earth, with the energy heating ionized molecules there. HAARP is a scientific marvel, a treasure for ionospheric research -- but somewhere along the way it seriously captured the imagination of the conspiracy theory network, which has interpreted it as government "black" program for mind control or some other sinister purpose.

HAARP array

The origins of HAARP and its association with the lunatic fringe make for an elaborate story. Atmospheric scientists had been probing the ionosphere for decades by transmitting radio waves into it, but they were hard pressed to find any other tools for investigation -- it was too high for balloons and too low for satellites. So little was known that the ionosphere was sometimes jokingly called the "ignorosphere". In the 1980s, a plasma and space physicist at the University of Maryland named Konstant "Dennis" Papadopoulos, now in his early seventies, decided to do something about it. He was familiar with lobbying the US Federal government, and got in touch with other researchers in his community to push for an ionospheric research center.

In the meantime, a physicist named Bernard Eastlund working for oil giant Atlantic Richfield (ARCO) had ideas for using gas vented from the company's oil fields to build an ionospheric heater that could, for example, fry Soviet missiles or direct hurricanes and other bad weather against adversaries. He had even obtained patents for these concepts. Eastlund pushed his ideas up to the Pentagon, where they ended up in the military's Defense Advanced Research Projects Agency (DARPA). A senior DARPA official named Tony Tether awarded a research contract to ARCO, with ARCO hiring Papadopoulos as a consultant.

Papadopoulos thought Eastlund's ideas about frying missiles and influencing weather were preposterous, but there was considerable interest in the ionospheric research community for setting up an ionospheric heater in Alaska, where the ionosphere intersects with the Earth's magnetic field. In 1988, Papadopoulos and company were able to talk to Alaska Senator Ted Stevens and convince him that an ionospheric research facility in his state would prove a benefit for Alaskans. Stevens was agreeable -- he was noted for his enthusiasm in directing Federal pork dollars to Alaska, most prominently in the case of the notorious and expensive "bridge to nowhere" from Ketchikan -- and was able to earmark money for startup work.

Having DARPA interest was all very well and good, but the researchers really needed to get the armed services involved to get rolling. In a series of meetings with the US Navy and Air Force in 1988:1989, Papadopoulos and his colleagues pitched their facility. What they envisioned was a giant "phased array" antenna that could direct a controlled beam of high-frequency radio waves into the sky, with the beam exciting electrons in the ionosphere, altering the target area's electrical properties and causing it to emit "extremely low frequency (ELF)" radio waves.

It was the ability to generate ELF waves that was the hook for the armed services, since ELF will penetrate deep into the ground or water, allowing it to be used to probe for buried bunkers or communicate with submarines undersea. The Navy already had an ELF system for communicating with submarines, but it required a massive antenna system that sprawled all over the landscape -- making it both expensive and a magnet for criticism by environmentalists. Using the sky itself as an ELF transmitter seemed cheaper and much less controversial, but figuring out how that might be done required a high-class ionospheric research facility. Research funds started to flow from the Federal government. In 1992, the Navy awarded a $21.6 million USD contract to ARCO for detailed studies of HAARP, as it had become known. [TO BE CONTINUED]

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[FRI 11 SEP 09] THE PARASITES (18)

* THE PARASITES (18): The tricks the Sacculina parasitic barnacle plays to manipulate the behavior of its crab host are impressive, in a repellent way, and suggest the parasite's high degree of optimization for its lifestyle. It's actually not so difficult for a parasite to manipulate its host's behavior, it's just a question of generating the proper behavior-modifying biochemicals -- either by stimulating the host to generate them itself, or by the parasite producing analogs of those chemicals. Many other parasites perform similar behavior control.

The parasitic wasp Cotesia congregata not only produces a load of viruses to temporarily disable the immune system of its hornworm host, it also manipulates the hornworm's behavior. The caterpillar grows to about twice the size it would have otherwise, and changes its digestion of leaves from the usual production of fats, which the caterpillar needs for long-term survival, to the production of sugars, which the wasp larvae use to grow rapidly. The wasp also spays male caterpillars to ensure that the host is working for the parasites and not for itself. As it turns out, disabling the reproductive system of a host is a common tactic among parasites, being a simple way to divert host resources to the parasites without killing the host.

Parasites can influence the behavior of plant hosts as well. The fungus Puccinia monoica infests mustard plants living on the slopes of the Colorado Rockies and sterilizes them, preventing them from forming their normal little yellow flowers. However, the fungus sexually reproduces itself, and it hijacks the flower in an elaborate way to get that job done. The parasite drives the plant to form clusters of leaves that end up being a reasonable impersonation of the plant's little yellow flowers, with the "fakes" producing a sweet, sticky secretion. Bees try to "pollinate" the false flowers, to end up being plastered with fungal sperm and female sex organs, which the bees carry to other infected mustard plants.

* Eventually, parasites have to move on from a host to the next part of their parasitic life-cycle, and not surprisingly parasites often manipulate the behavior of the host to assist in the process. Normally hornworms will moult about five times, then crawl down from the plant they have been eating to bury themselves in a cocoon in the ground, where they eventually transform into a moth. Once infested by Cotesia larvae, however, a hornworm will only moult once or twice, and it will never leave the plant: if the hornworm forms a cocoon, the wasp larvae will be trapped, and so they make sure the host never gets the signal to do so. Very late in the infestation, the wasps also shut down the host's appetite, apparently to make sure it doesn't eat any of the wasp cocoons littering its body.

Another species of parasitic wasp that targets the cabbage worm caterpillar even enlists the host to guard the larvae. When the larvae of these wasps have matured in the host, they paralyze the host and push out of its abdomen, to spin cocoons on the leaf the caterpillar is standing on. However, once the wasp larvae have left the host, it recovers from paralysis -- to weave a silk mesh over the top of the wasp cocoons and then curl up on top of them, biting and spitting noxious fluids at any intruder. The caterpillar, grossly maimed though it is, lives just long enough for the mature wasps to leave their cocoons and fly off.

* Unlike parasitic wasps, some parasites need to get to water once they leave a host, and some have acquired schemes to encourage the host to help out. Some forms of parasitic nematode worms are present as free-living adults in streams, where they mate and lay eggs. When the eggs hatch, the newborns drill into mayfly larvae that also live in the stream, the worms curling up inside the hosts. The mayflies eventually mature into their delicate flying adult form and depart the stream, carrying off their nematode freeloaders with them.

The mayflies only mature to breed, finding partners alongside the stream. Having mated, the males simply die. The females find a rock sticking out of the stream and lay their eggs; if the female is carrying a nematode, it burrows out of the host at that time. Either way, the mayfly then dies. That seems simple enough, except for nematodes that have infected a male; the males aren't choosy about where they die, and so the nematode is likely to be left high, dry, and doomed. To make sure that doesn't happen, the nematode transforms the male into a quasi-female, complete with distinctively female features, that attempts to lay eggs that he doesn't really have. All he gives birth to is a nematode. [TO BE CONTINUED]

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[THU 10 SEP 09] SCIENCE NOTES

* SCIENCE NOTES: An article in AAAS SCIENCE discussed a study of the pea aphid, Acyrthosiphon pisum, and a symbiotic bacterium that lives in the aphid's gut named Buchnera aphidicola. The pea aphid, as its name implies, is a common pest of legume plants, sucking on their sap. The sap is sugary and low in protein, but the Buchnera symbiont is considerate enough to provide about nine essential amino acids for its host. That's not any big deal in itself, it's a common sort of arrangement between hosts and their digestive-system symbionts, but genetic analysis of the aphid and the bacterium revealed something interesting: the synthesis of the amino acids was in almost all cases a joint venture, with processes in both organisms required to turn out the finished amino acids. For example, the bacterium lacks the enzyme needed for the last step in synthesizing the amino acid leucine; the enzyme is coded in the aphid genome instead.

There was some suspicion that there had been some "lateral gene transfer" between the aphid and the bacterium -- lateral gene transfer being a hot science topic these days -- and in fact about 11 transplanted genes were discovered. However, to the surprise of the researchers, the genes weren't necessarily from Buchnera. Two of these genes seemed to be important in providing materials for the bacterium's cell wall and were active in the aphid cells reserved to host the bacteria, but they seem to have been imported from an entirely different species of bacteria.

The genetic analysis of the aphid showed that it had over 34,604 genes, a fairly large number -- twice that of the well-known Drosophila fruitfly -- with the high gene count due to large numbers of gene duplications. The aphid also had some genes never seen before in other species, associated with salivary proteins that apparently keep sap flowing in after the aphid has penetrated a plant. These unique genes may provide useful targets for selective pest control against the aphid.

* One of the running themes in modern work on micromechanical systems (MEMS) -- microscale machines generally built with silicon using fabrication techniques derived from those used to manufacture integrated circuitry -- has been the development of "lab-on-a-chip" systems to perform chemical analysis. SCIENTIFIC AMERICAN reports that a team under chemist Robert Linhart at the Renssaeler Polytechnic Institute (RPI) in New York State has developed a lab-on-a-chip system to simulate a cellular organelle, the Golgi apparatus.

The Golgi apparatus looks like a set of sacks piled up like pancakes. It is known to alter proteins to improve their stability and effectiveness, and also is important in the synthesis of complicated sugars, but it is the least understood of the cell's subsystems. It's a hard target, since it changes shape easily and often, making it troublesome to observe and to trace the flow of chemical reactions through it. The RPI researchers decided to develop a MEMS device that could perform the same reactions but in a more easily observed fashion.

The RPI device is a millimeter on a side and features a set of nine tiny chambers, each containing specific enzymes, linked by channels connected by a central "bus". A sample to be run through the device is mixed with magnetic particles, with electric and magnetic fields controlling the movement of the sample through the chambers. The current device is strictly a proof-of-concept demonstrator and uses only one enzyme, but the RPI researchers have been happy with its performance and are planning to move on to improved MEMS devices that are increasingly closer analogs to the Golgi apparatus. They are also interested in simulators for other cellular systems. They believe that their technology could have practical applications, for example in the synthesis of complicated, high-value biomolecules.

* BBC WORLD Online reports that a biological census performed of the polar regions during the last International Polar Year exercise, which ended in 2009, shows that at least 235 marine species are common to the Arctic and Antarctic, despite the fact that the regions are on opposite sides of the world.

Ron O'Dor, a senior scientist involved in the global marine census effort that included these findings, says there's no puzzle involved with species such as whales and birds that migrate between the poles seasonally. More surprising were mud worms, sea cucumbers and "swimming snails" AKA "sea butterflies" that were common to both regions. On consideration, however, there doesn't appear to be much mystery involved with them, either, since the polar regions are linked by cold deep sea currents. Says O'Dor: "There is continuity in the ocean as the result of the major current systems, which we call the 'conveyor belt'. A lot of these animals have egg and larval stages that can get transferred in this water."

sea butterfly

The species are being genetically "barcoded" as part of a global "Census of Marine Life (CoML)", to be released in 2010. The genetic analysis should help define subspecies and relationships of different populations of similar organisms living in the polar regions and elsewhere.

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[WED 09 SEP 09] SCRUBBING GLOBAL WARMING

* SCRUBBING GLOBAL WARMING: One of the more interesting schemes for dealing with global warming is to set up networks of carbon dioxide scrubber systems to soak up the CO2. An article in THE ECONOMIST ("Scrubbing The Skies", 7 March 2009), examined the idea to see if it could actually work.

CO2 is a trace gas, and above concentrations of about 1.5% people start getting sick; higher concentrations will kill even though there is plenty of oxygen left in the air to breathe. Systems to scrub CO2 out of the air have long been in use in submarines and spacecraft, so there's nothing magical about the technology. The question is whether it can be scaled up enough to actually put a dent in global warming.

A scrubber simply consists of a material that absorbs CO2. Absorption is proportional to the surface area presented by such a "sorbent" material, and one of the best ways to maximize surface area is to spray a liquid sorbent as a fine mist. Researchers at the Xerox Palo Alto Research Center (PARC) in California have considered a large-scale scrubber system consisting of towers several meters high, filled with a sorbent mist. The mist liquefies at the bottom and is collected into a chamber, with the CO2 removed by chemical reactions or an electric current. The CO2 is then sequestered. A group under David Keith at the University of Calgary in Alberta, Canada, has implemented a prototype of such a spray scrubber tower.

A team at Columbia University in New York City under Klaus Lackner, a pioneer in the field, has designed an alternative atmospheric scrubber that uses a solid sorbent, with the scrubber featuring thin sheets coated with chemicals to trap CO2 from the air that circulates over them. Liquid chemicals then soak up the CO2 from the sheets, with the liquid heated to draw out the CO2 for sequestration. The group has developed a handheld prototype; a scaled-up version the size of a standard shipping container could pick up a tonne of CO2 a day.

Such scrubber systems require energy, and of course it is no good to soak up CO2 if more CO2 is released by the powerplant that drives the scrubber system. Not to worry -- worst-case estimates show that the coal-fired power required to soak up a tonne of CO2 will only release 5%, 50 kilograms, of the gas, and any use of renewable energy in the process will greatly reduce even that small quantity.

Ah, but then there's the sticky problem of cost. The sorbent material tends towards the expensive and it can't be indefinitely recycled. Right now the cost of atmospheric capture is estimated at $200 USD per tonne, while the cost of a tonne of CO2 in emissions-trading schemes is less than $10 USD. That's preposterous economics on the face of it, but Lackner believes that the industry could be primed by selling small air-capture systems to facilities that have a use for CO2. It's actually the 19th most important commodity chemical in the USA, and in some places it has to be trucked in at considerable expense. Of course, once air scrubbers are in widespread service, the cost will drop, possibly by a factor of five, and environmentalists believe that the price of CO2 in emissions trading is likely to rise by a similar factor, making carbon capture more economically attractive than trading.

Current atmospheric scrubbing schemes envision simply storing the CO2, but the CO2 could be combined with hydrogen obtained by electrolyzing water to produce hydrocarbon fuels. This process requires energy of course -- it can be thought of as converting electrical power into fuels -- and though it is technologically sexy, it is economically impractical at the present time.

And yet, who knows what may happen tomorrow? In 1909, the German chemist Fritz Haber developed a process to combine nitrogen from the air to produce ammonia. It had been possible to do so before, but it was strictly an inefficient lab procedure. The Haber process, in contrast, could be scaled up to an industrial level, and now all ammonia is produced in such a fashion, the process being particularly important for the production of fertilizers. Much the same was true of aluminum, which was more expensive than gold before Charles Hall figured out an electrochemical process for refining it. Today we buy rolls of aluminum foil at the supermarket. It isn't wise to bank on radical breakthroughs, but past experience suggests that what may seem preposterous today may be perfectly ordinary tomorrow. It's certainly worth further investigation.

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[TUE 08 SEP 09] QADDAFI THE SURVIVOR

* QADDAFI THE SURVIVOR: The 20 August 2009 issue of THE ECONOMIST took a close look at Libya leader Muammar Qaddafi, who has just celebrated the 40th anniversary of the coup that toppled King Idriss, making Qaddafi now the most enduring of all of Africa's "Big Men". Qaddafi has survived multiple wars with neighbors, assassination attempts, and international sanctions, not to mention persistent jibes as "the Libyan Lunatic". He's the current president of the African Union, which he would like to become a more powerful coalition under his guidance.

Muammar Qaddafi

Indeed, Qaddafi is flying high at the moment. Libya currently sits as a rotating member of the United Nations Security Council -- a scenario that would make Ronald Reagan spin in his grave, the American president once having called Qaddafi a "mad dog". Reagan would spin even more rapidly if he knew Qaddafi is now planning his first trip to America this September to address the UN General Assembly. Qaddafi recently made a low-profile visit to a G8 summit meeting, and has been visited the leaders of the UK, France, and Russia, as well as the US secretary of state, at the time Condi Rice.

Oddly, most of the attention focused on Qaddafi is not so much because he has been a good boy, but because he has stopped being such a bad one. Ronald Reagan saw him, as discussed here some years back, as one of the world's worst troublemakers. Reagan certainly had reason, given Libya's links with terrorism and violent insurgent movements like various Palestinian organizations and the IRA. In 1986, in response to a Libyan-arranged bombing of a Berlin nightclub where US servicemen liked to hang out, Reagan ordered a massive air raid against Libya codenamed EL DORADO CANYON. In retaliation, Libyan agents then arranged the bombing of Pam Am Flight 103 over Lockerbie, Scotland, in 1988, and UTA Flight 772 over the Sahara in 1989, causing hundreds of deaths.

Qaddafi's rehabilitation began in 2001, when Libya, partly influenced by its own fight against jihadists, decided to join the American "Global War On Terror"; Libya later gave up its programs to develop weapons of mass destruction, even going so far as to finger suppliers. Libya also negotiated compensation agreements for victims of its terrorist activities. All was forgiven; now Tripoli, Libya's capitol, sports a new airport and shiny new hotels for foreign visitors and investors. The regime has reasons to feel pleased with itself, not merely for its reformation, but because of such accomplishments as establishing near-universal literacy among schoolchildren, raising the life expectancy of Libyans by 20 years, and cutting infant mortality by a factor of ten.

Alas, while Libya exports as much oil per head as Saudi Arabia -- $46 billion USD's worth in 2008 for 6 million Libyans -- visitors are greeted with trash-littered streets in Tripoli instead of the gleaming 21st-century thoroughfares encountered in the Gulf States. Libyans may praise their leader and his revolution, but not with much real conviction. To be sure, things aren't as bad as they were in the 1980s, when Qaddafi tinkered with disastrous social experiments and had dissidents hunted down; the people do enjoy free education and health care, along with subsidized transport and housing. However, there are no trade unions or any other social organizations with potential for power except for those dominated by the government. The government has a chokehold on the economy, resulting in high unemployment and low salaries, while the treasury builds up foreign reserves and the central ruling clique enjoys luxuries.

Qaddafi is, always was, a visionary. What he has never been is much of a manager, and his sense of the practical is inconsistent. For over a generation, Libya has been mismanaged by a clumsy government bureaucracy -- under a leader who has demonstrated that though representative government doesn't always work perfectly, it's far preferable to rule by the whimsical "Big Men" who have become such an unfortunate trademark of African governance. For now Qaddafi remains in charge, and who will follow him remains unclear. Two of his seven sons, Saif and Mutassim, are regarded as strong possibilities -- though Saif, the eldest and noted for his interest in human rights issues, appears to be losing influence to his more obscure younger brother Mutassim, who has a quiet but powerful role in the state security services. Both are believed to have encouraged their father to mellow out since the turn of the century, which is all for the good -- but Libya still has a long ways to go before it becomes the healthy and prosperous state that it could and should be.

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[MON 07 SEP 09] SMART GRID (2)

* SMART GRID (2): The unpredictability of renewable energy leads to the bottom-up component of the smart grid. The power grid has very little storage capacity; using traditional thinking, any shortfall in renewable energy would require conventional powerplants to step in and take up the load. However, modern networked communications and distributed digital intelligence allows the situation to be turned around. As envisioned, the bottom-up component of the smart grid would allow customers to tailor their power use to availability, drawing power when it is available and conserving when it runs short. This component of the smart grid system makes sense whether the new power distribution system is in place or not.

Minneapolis-based Excel Energy is now implementing such a smart grid system as a pilot project in Boulder, Colorado. 25,000 Boulder homes and businesses are being fitted with "smart" electrical power meters that communicate with a central server over the power lines themselves, tracking the power usage by the end users. The end users can then log in to a website to determine their pattern of power usage versus power availability and adjust their use of power accordingly -- for example, drying clothes in the evening instead of the morning.

smart power meter

Ultimately household and business systems that draw power from the grid will have automated smarts to control when electrical systems should go idle and when they should go back to full operation, adjusting their usage so smoothly that users will hardly notice anything is going on. In a 2007 experiment in Washington State, 112 users were fitted not only with a smart meter but with smart switches for thermostats and water heater controls. Power savings amounted to an impressive 15%.

With an increasing push towards electric vehicles and "plug-in hybrid" cars, the smart grid will become even more effective and important -- all the more so because the vehicles that are plugged in could be used as a substantial power storage system, returning power to the grid when demand is high. The distributed power management system would only draw power if the vehicles had an adequate charge, with the threshold set by the end users, and give the end users appropriate credits for the use of their stored power. End users who set up their own renewable energy systems to reduce their power bill will be able to feed home-grown electricity back to the grid for credits as well.

* Enthusiasts feel that the economic stimulus money being handed out by the Obama Administration will do a great deal to kick-start the smart grid. Xcel officials see the smart-metering component of the grid reaching national ignition by 2015.

The power transmission component of the smart grid is a bit more challenging. The political will to set up the network is there at the top, but right now a patchwork of local and region authorities make such projects legally difficult, with lawsuits from citizens and groups screaming "Not In My Back Yard!" further complicating matters. Power companies are pushing for Federal laws to streamline the process, but few see that as easily done. Technology is easy; politics are hard.

ED: THE ECONOMIST also had an article on the smart grid. Much of it covered the same ground as the DISCOVER article, but it added a few interesting details. For example, about 76 million smart meters have now been installed over the world, and the number is expected to double by 2013. Italy is the keenest on smart meters, with over 30 million having been installed by the Enel power utility.

The article does point out that smart meters are expensive, costing hundreds of dollars to buy and install. One estimate gave the cost of converting the USA to smart meters as $50 billion USD. There's also the problem that utilities that sell power have an economic disincentive to help end users conserve. One solution is to provide regulations for industry that "decouple" profits from the sheer volume of energy sales, an approach that California has implemented with considerable success. However, in some cases the business benefits of going "smart" are obvious: Enel spent about 2.1 billion Euros wiring customers up with smart meters but saves 500 million Euros a year, so the payoff for the investment was only five years.

Another difficulty is lack of standards. The smart grid isn't going to work if the servers, smart meters, and smart controls can't talk with each other. Anybody who has even a modest familiarity with technology standards efforts knows that getting agreement on standards can be quarrelsome, tricky, and time-consuming. However, the vision of a working smart grid presents utilities and vendors with such an enormous economic opportunity that they have a strong incentive to push the standards through and get them to work. [END OF SERIES]

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[FRI 04 SEP 09] THE PARASITES (17)

* THE PARASITES (17): The 19th-century British biologist Ray Lankester had judged parasites to be "degenerate" creatures, citing as a prime example the Sacculina parasitic barnacle that attacks crabs, with the parasite ending up resembling something like a fungal infection.

crab with sacculina parasite

At the beginning of its life cycle, the Sacculina barnacle egg hatches into a larva that looks much like any other crustacean larva, not so different from other barnacle or even shrimp larva. While it was once thought that Sacculina was a hermaphrodite, the parasite does have two sexes, and it is the female that performs the assault on the crab. A female Sacculina larva will swim around until sense organs on her legs pick up the smell of a crab, and then the larva descends on the crab. It crawls over the crab's armor until it finds the soft regions of the crab's joints; there are hairs of sorts growing out of holes in these soft regions, and the larva jabs a probe, something like an ovipositor, through one of these holes.

It isn't an ovipositor, however. The larva effectively "moults" in good arthropod fashion, inserting itself as a new form inside the crab while leaving the empty and now useless husk of its old form outside. The new form is a tiny slug that migrates through the crab and settles on its underside, growing into a bulge and extending fleshy tendrils all over the crab's body, even wrapping around its eyestalks, to draw in nutrients along with the crab's blood. The crab otherwise goes about its business unaffected while the barnacle matures to eventually become a knob with a little hole on top.

The uneasy relationship between the crab and the barnacle continues in a more or less stable fashion until a male Sacculina larva arrives, and then the situation gets much worse for the crab. The male larva finds the pinhole, to then "moult" into a small form that burrows through the pinhole down a channel deep into the female, where he finds a well that will be his permanent home. The female has two such wells and so can accommodate two males; they spend the rest of their lives producing sperm to drive the production of eggs, with the female producing a clutch of thousands of eggs every few weeks. The small size of the male and its embedded association with the female was why Sacculina was thought to be hermaphroditic for a long time -- the male was hard to notice, and to the extent that it was, it wasn't easy to see what its relationship to the female was.

So far, a case might be made that Sacculina is a "degenerate" organism, but once the parasite starts reproducing that case becomes less convincing, because the Sacculina then demonstrates the extreme control it has over its host. First, the crab stops moulting and growing; it eats and eats, but only for the benefit of its parasitic freeloaders. It can't even regenerate a lost limb any more. Second, the crab can no longer reproduce, since that would take resources from the parasite as well; the crab has been spayed.

That does not mean the crab has lost its instincts to care for its young, but those instincts are perverted to care for the young of the parasite. A healthy crab keeps fertilized eggs in a brood pouch on its belly, which the crab carefully keeps clean, scraping off algae and fungus. When the crab eggs hatch into larvae, the crab finds a high rock and stands tall on it to let the larvae escape into the sea, waving her claws about to help them on their way. Not coincidentally, the knob created by the Sacculina female is in exactly the same location as would be taken by the crab's own brood pouch, and the crab gives it the same attention -- grooming it and helping to release the larvae into the sea.

That hardly seems like the work of a "degenerate" organism, unless one uses the term in its moral sense -- the reality is that the parasite seems hideously devious. It gets even more devious where the male crab hosts are concerned. Sacculina not only neuters them, it feminizes them, altering their biochemistry to make them act like females, caring for the brood of parasites. [TO BE CONTINUED]

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[THU 03 SEP 09] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: WIRED ONLINE reported on an interesting scheme by Harvard Medical School researchers on contact lenses that could administer drugs. Eye drops are the usual method of eye medication, but they're inefficient, with only a few percent of the medication making it into the eye.

There have been efforts to build drug-dispensing contact lenses before, either by dissolving the drugs in the hydrogel material that the lens is made of, or by incorporating microcapsules of the drug in the hydrogel. The problem was that they couldn't deliver large quantities of the drug for a long period of time. The new contact lens loads the drug into a donut-shaped packet that is "sandwiched" inside the lens, with the hole in the donut providing a field of view for the wearer's pupil. The researchers were able to use the lens to administer antibiotics for a full month, and see no obstacle to developing a commercially practical production version.

* AAAS SCIENCE reports that a collaboration of British and French researchers have come up with a scheme to help protect buildings from earthquake waves, using as a cue the technology of stealthy combat aircraft and ships. Such stealthy vehicles have geometries, coupled with the appropriate materials, that allow them to scatter radar waves instead of reflecting them back to an enemy radar. The researchers wondered if they could scatter earthquake waves using a similar approach.

They came up with a design of an earthquake shield that featured concentric rings of plastic, copper, and four other materials of varying flexibility and thickness. Simulations in which the shield was attacked with surface earthquake waves varying in frequency from 30 to 150 Hz showed that it could absorb or scatter the waves, leaving the zone inside the shield undisturbed. However, the researchers don't believe they have anything resembling a product just yet, and may not for a long time to come; they've just found an interesting idea that deserves further investigation.

* The WIRED GeekDad blog reports that Kotobukiya of Japan, which is in the collectibles & figurines business, is now introducing Jedi lightsaber chopsticks ... well, Jedi knights have to eat too, right? I have to admire the cleverness of this idea, but then again I'd never buy it. It's not like I eat with chopsticks anyway, and I don't think I'd want to make a geek statement if I did.

lightsabre chopsticks

* The WIRED Science blog ran an interesting article about the work of a team under molecular biologist William Shih at Harvard Medical School who have been assembling tinkertoy 3D structures using DNA. DNA, the molecule that encodes the information of life, turns out to be well-suited for such molecular tinkering. It consists of a matched pair of chairs of four nucleic acid bases -- adenine (A), thymine (T), cytosine (C), and guanine (G) -- that have deterministic linkage patterns between the two chains, with A linking to T and C linking to G. Researchers have been able to exploit this selective linkage to build short segments of DNA that will automatically plug into each other in a predictable fashion, building up structures.

The idea of building molecular structures with DNA is not entirely new, but up to now, researchers have only been able to produce two-dimensional structures -- for example folding DNA strands back on themselves to form flat sheets. The Harvard team used this approach, but added small segments of DNA that could "staple" the folds together, forming elaborate 3D shapes. Shih believes that DNA structures might be designed to deliver precisely-targeted drugs or provide highly specific biological diagnostics. For the moment, however, the structures are strictly "proof of concept" and they can't do anything useful just yet. Give it time.

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[WED 02 SEP 09] THE NEW GREEN WORLD

* THE NEW GREEN WORLD: There was a time, billions of years ago, when the Earth did not have oxygen in its atmosphere. Oxygen is reactive and any free oxygen drifting about is gradually removed by binding with other elements; the oxygen in our atmosphere would vanish except for the fact that it is continuously replenished by plants. As reported by an article in AAAS SCIENCE ("On The Origin Of Photosynthesis" by Mitch Leslie, 6 March 2009), researchers are intensely curious about the origins of the process of "photosynthesis", by which early plants generated oxygen to help create the atmosphere as we know it today. That reactive oxygen atmosphere helped support the emergence of elaborate multicellular organisms, and by contributing to an ozone layer that blocked harmful radiation, permitted life to take root on land. Ultimately, the emergence of photosynthesis created a planetary biosystem driven at the base by solar power.

The Green Earth

Researchers believe that early photosynthetic processes were different from that used today; while modern photosynthesis produces oxygen from water, the earliest solar-powered bacteria used a different scheme, possibly based on hydrogen sulfide (H2S). Over time, the early scheme evolved into the modern one, leading to the green world we know today. Biochemists are now trying to trace back the steps of this process, while other researchers argue over how long ago photosynthesis emerged -- was it 2.4 billion years ago, or much earlier? The geological and evolutionary traces of the long-past event are hard to follow.

* How modern photosynthesis works is well understood. Chlorophyll pigment collaborates with about a hundred other proteins to convert carbon dioxide and water into food. Plants, some protists, and cyanobacteria embed their chlorophyll into two large protein clusters named "photosystem I" and "photosystem II", employing both systems to use water as an electron source. Light kick-starts an electrical "circuit" in which electrons flow from the photosystems through protein chains that assemble the energy-rich molecules "ATP" and "NADPH". These two molecules then power the synthesis of sugars that organisms depend on to grow and multiply. Photosystem II, which is the strongest oxidant that occurs in nature, restores its lost electrons by snatching them from water -- and releases oxygen in the process, ironically as a waste product.

Some bacteria don't use water as the electron source, instead using H2S or other alternatives. Today, such organisms live in extreme environments such as hot springs. They do not produce oxygen. The photosynthetic proteins of such "nonoxygenic" bacteria are organized in comparatively simple "reaction centers" that may have been predecessors of the two photosystems.

Trying to figure out the evolutionary emergence of such complicated biochemistry is a challenge. Similarities between proteins in photosynthetic and nonphotosynthetic bacteria suggest that early microbes adapted or "co-opted" some photosynthesis genes from other metabolic pathways. However, research on the genomes of modern bacteria suggests that the genes may also have arisen through "horizontal gene transfer" between different lineages. It is particularly puzzling that modern nonoxygenic bacteria have protein clusters that seem to be predecessors to either photosystem I or photosystem II, but never have both -- and both are required to support modern photosynthesis. Horizontal gene transfer could explain that paradox, though some believe one system evolved from the other.

In any case, the ability to use water as an electron source was a huge evolutionary jump: H2S is relatively scarce, but water is everywhere. Establishing that breakthrough was tricky, and researchers at Arizona State University have been experimenting with the reaction center of the purple bacterium Rhodobacter sphaeroides to see if they can make it more like photosystem II. The researchers initially targeted "bacterio-chlorophyll", the bacterial version of chlorophyll at the core of the reaction center, and tweaked the number of hydrogen bonds; adding bonds increased the reaction center's greed for electrons.

The water-cleaving component of photosystem II contains four manganese atoms that become oxidized, losing electrons, and so the researchers added a manganese atom to the bacterial reaction center -- which then underwent oxidation. Their modified reaction center can't break down water just yet, but the research team believes with some work they might be able to produce a modified reaction center that could break down hydrogen peroxide, which was common on the early Earth.

* While the biochemists tinker with the molecules, an argument continues on when photosynthesis began. The consensus is that nonoxygenic photosynthesis arose first, more than 3.8 billion years ago. Without photosynthesis, life was restricted to volcanic vents and other geologically active sites to obtain energy; once photosynthesis arose, the Sun could power life all over the world.

The dispute is over when oxygenic photosynthesis arose, with the argument focusing on a watershed in the fossil record known as the "great oxidation event (GOE)". Rocks from about 2.4 billion years ago show the first unmistakeable signs of significant, sustained oxygen in the atmosphere, such as "red beds" -- iron oxide, or just simple rust. Geologists have also used a subtler probe that leverages off skewed abundances of sulfur isotopes in an atmosphere without oxygen, with the isotopes clearly shifting 2.4 billion years ago.

Nobody disputes that oxygenic photosynthesis has been around for 2.4 billion years; however, some believe that it has been around for well longer than that, about 3 billion years. Researchers have turned up the remains of what look like cyanobacteria in rocks that are about 2.7 billion years old, and thick shale deposits from western Australia that are about 3.2 billion years old hold rich bacterial remains -- but no traces of sulfur or other possible electron sources, suggesting that water was used instead. It also turns out that there are processes in oxygenic photosynthesis that tends to reject CO2 using with carbon-13 isotope, while nonoxygenic photosynthesis does not. Samples from three sites in Zimbabwe and Canada dating from 2.7 to 2.9 billion years old have been found that have the isotope imbalance.

The evidence for the older date is far from ironclad; there have been criticisms of the observations, and of course there remains the question of why the beginning of oxygenic photosynthesis was so much earlier than the undisputed GOE. However, nobody involved feels like the matter is an insurmountable obstacle, and all believe that the secret of the origin of modern photosynthesis will yield to persistent investigation.

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[TUE 01 SEP 09] ANOTHER MONTH

* ANOTHER MONTH: August was an entirely hectic month. I had been thinking to replace the sorry, decrepit carpeting and flooring in my house since 2004, but I didn't get around to it until this summer, I would say about two years later than I should have. It wasn't any lack of money, it was just a failure to do the job. I have a monthly household repairs budget, and since I couldn't find the time to spend it, it piled up, and I had all the money I could have needed.

I finally just jumped in and signed up a contractor. Having taken the leap, I was left with the task of getting the house cleaned out for the installers. I could cram most of what I had into the garage, though there were three big items that were troublesome to handle:

The old vinyl flooring had also peeled up next to the bathtub, and I'd just ignored it on the basis it would get fixed with the rest. Bad idea. The plywood got wet and rotted, and the installation inspector wanted to replace the floor there. I didn't buy off on that, since the damage seemed superficial and that would have been a lot of expense and hassle. Besides, the installers weren't going to tear out the old vinyl, the asbestos underpad made that problematic from a liability point of view; the plan was to lay down thin plywood over the old vinyl and install the new vinyl over the top of it.

That meant the damage would be covered over, but I didn't want to just leave it, partly because I didn't want to look like an inept clod to the installers and partly because it just bugged me. I scraped out the rot with a small chisel and wire brush, applied wood filler to the damaged areas, then covered it over with primer-sealer and white enamel. Problem fixed at low cost with some labor. I hadn't used spray enamel since I was a kid and I had forgotten what nasty stuff it is: I had to grab a breath, dash into the bathroom, lay down a spray layer, and then dash out again to take a new breath. I would have been sick as a dog if I'd inhaled that stuff.

The installers put in the carpet on Tuesday, the vinyl on Thursday; I had my house completely reassembled on the next Tuesday, doing considerable rethinking of furnishing arrangements while I did so. As is usual for involved projects, there was some collateral damage, the first being that the carpenters broke my thermostat. I didn't make a fuss since it was half-broken already, I just went out and got a cheap digital thermostat to replace it. The other problem was that one of the bolts fitted when they reseated my toilet popped out and I had to put a new bolt through the floor. That was high priority -- the prospect of tipping over my toilet and having to deal with the hassle that would cause was not an idea I liked.

Anyway, I got back on the level faster than I had hoped and my revitalized house was cozy, so it was all entirely for the good -- but turning everything completely upside down for ten days is not something I would enjoy doing on a regular basis.

* And then, while this was going on I got sidetracked into a project: adding illustrations to the old blog entries. It was something I just started tinkering with, getting in deeper until I realized that it wasn't going to be as casual a job as I had carelessly assumed. It was clearly a high-labor / low-priority job, but having started, I dreaded the idea of piling it onto my backlog queue. I put it on the top of my work list in order to kill it off as fast as possible and be done with it.

There were 39 archive files to update, it took over an hour each; I managed to scrounge up 312 illustrations, an average of eight per file. The end result is pleasing, with the illustrations adding a real dimension to the archives. Still, it was a fair amount of effort for a modest payoff -- but it would have, again, bugged me until I did it.

* I'd also been planning to make my fall trip to Spokane in September, but I figured that as long as August was going to be hectic, I might as well do it before the month was out so I could hopefully have a leisurely September. It was a completely routine trip, nothing much to report, I didn't even take spare batteries for the cameras since I had no particular plans to take pictures. It was a pleasant as such things go, the weather seeming a bit more like early fall than late summer; I picked up a few infrastructure shots, pix of aircraft at municipal airports, and shots of miscellaneous items (like an Army HEMTT truck) along the way.

US Army HEMTT truck

Glad to be done with the month. I got back from Spokane on Thursday afternoon, with everything unpacked and sorted out before I went to bed so I would have a clear deck in the morning. I woke up on Friday back on regular schedule, but I felt drained, like all the month's activity had caught up with me at once.

It was a very productive effort, no complaints, but overload is just not sustainable over the long run -- by definition it means having to drop some things to take care of others, and eventually the chaos leads to a train wreck. I recall people who liked to run around all the time as if every second counted. I think it was usually more show than substance.

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