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DayVectors

dec 2009 / last mod nov 2015 / greg goebel

* 23 entries including: immune system, Southwest road trip, battlefield lasers, infrared fluorescent proteins, fake relics on eBay, SMOS satellite, digitizing old astronomical plates, phytoplasmas, ecstasy for PTSD, sterilizing feral pets, and Big Pharma embraces generic drugs.

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[THU 31 DEC 09] NEWS COMMENTARY FOR DECEMBER 2009
[WED 30 DEC 09] SPACEPORT KODIAK
[TUE 29 DEC 09] INFRARED FLUORESCENT PROTEINS
[MON 28 DEC 09] WAR AT LIGHTSPEED (3)
[FRI 25 DEC 09] THE IMMUNE SYSTEM (8)
[THU 24 DEC 09] SCIENCE NOTES
[WED 23 DEC 09] IN PRAISE OF FAKES
[TUE 22 DEC 09] SMOS IN ORBIT
[MON 21 DEC 09] WAR AT LIGHTSPEED (2)
[FRI 18 DEC 09] THE IMMUNE SYSTEM (7)
[THU 17 DEC 09] SPACE NEWS
[WED 16 DEC 09] ARCHIVES OF THE SKY
[TUE 15 DEC 09] TRACKING DOWN PHYTOPLASMAS
[MON 14 DEC 09] WAR AT LIGHTSPEED (1)
[FRI 11 DEC 09] THE IMMUNE SYSTEM (6)
[THU 10 DEC 09] GIMMICKS & GADGETS
[WED 09 DEC 09] ECSTASY RECONSIDERED
[TUE 08 DEC 09] FERAL PET PLAGUE
[MON 07 DEC 09] SOUTHWEST ROAD TRIP (5)
[FRI 04 DEC 09] THE IMMUNE SYSTEM (5)
[THU 03 DEC 09] SCIENCE NOTES
[WED 02 DEC 09] BIG PHARMA GOES GENERIC
[TUE 01 DEC 09] ANOTHER MONTH

[THU 31 DEC 09] NEWS COMMENTARY FOR DECEMBER 2009

* NEWS COMMENTARY FOR DECEMBER 2009: The big news for this month was the UN conference on climate change in Copenhagen, Denmark, which by all reports was fractious. Although an agreement was reached to attempt to limit global warming to 2 degrees Celsius above pre-industrial temperatures and to set up a $100 billion USD fund to help developing countries cope with global warming, the agreement was non-binding and set no specific targets for action.

Critics called the agreement weak to the point of meaningless, but defenders, while not denying the lack of substance in the results, pointed out that the meeting was a start and had its clear positive aspects. It brought together over a hundred world leaders to focus on the issue, with the countries that brokered the agreement including emerging powers such as China, Brazil, India, and South Africa -- reflecting the shift of global power in the 21st century. The summit also reflected the fact that a consensus has emerged that human-caused climate change is happening; that climate change is now part of the global political and economic agenda; and that citizens of countries all over the world are paying attention to the issue.

* The last week of the year was a turbulent one in Iran, with demonstrations against the current hardline government breaking out after the death on 20 December of one of the country's most prominent dissidents, 87-year-old Hoseyn Ali Montazeri. Opposition leaders called out their people, with the demonstrations focused on 27 December, the climax of the Shiite festival of Ashura. Protesters took over the center of Tehran and several other cities; several protesters were killed.

The protesters called for the removal from power of Supreme Leader Ayatollah Ali Khameni, the clerical dictator of Iran, who is backed up by the elected but hardline government administration of President Mahmoud Ahmadinejad. The reelection of Ahmadinejad last summer triggered demonstrations, and the opposition continues to make its displeasure with the current regime felt. However, the government has been challenged before and has survived; what happens next of course remains to be seen.

* On 25 December 2009, the Chinese state gave literary critic Liu Xiaobo a Christmas present: eleven years in prison. The charge was "inciting subversion of state power"; Liu had angered the authorities by writing essays in which he dared to suggest that China would be better off as a multiparty democracy, and worse by being one of the prime movers behind "Charter 08", a document that was circulated on the internet late last year to call for free speech, multiple political parties, an independent legal system, and meaningful elections. Over 3,000 Chinese intellectuals signed it. Chinese authorities found it an embarrassment, since it contradicted vocal government commitments to human rights and followed on the heels of the Beijing Olympics, which had presented China's best face to the world. The leadership was not amused, and on 8 December 2008, even before Charter 08 hit the internet, arrested Liu.

It wasn't the first time the 53-year-old Liu had been arrested. He had been at Columbia University in the USA in 1989, returning home when the Tianemen Square movement began to get involved. After the government crackdown, he spent 20 months in a lockup. In 1996, he was imprisoned for another three years. Other intellectuals associated with Charter 08 have been harassed, but Liu got special treatment. It is suspected the sentence was handed down on Christmas Day to keep it quiet. A US State Department spokesman announced in response: "As far as we can tell, this man's crime was simply signing a piece of paper that aspires to a more open and participatory form of government. That is not a crime." The Chinese government denounced the comment as a "gross interference in China's internal affairs." Translated from Chinese: mind your own damn business.

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[WED 30 DEC 09] SPACEPORT KODIAK

* SPACEPORT KODIAK: While everyone knows about the US space launch facilities at Cape Canaveral in Florida, few are aware of the facility at "the Other Cape" -- the Narrow Cape on the island of Kodiak, Alaska. As discussed by an article in AVIATION WEEK ("Responsive Space" by William Garvey, 24 August 2009), the "Kodiak Launch Complex (KLC)" is a going concern and has been for a decade.

Kodiak is a sparsely inhabited island about 400 kilometers (250 miles) south of Anchorage, the only other significant facility there being a large US Coast Guard (USCG) station; commercial fishermen also call Kodiak home. There is a small airport on the island to service the inhabitants. KLC was originally conceived to launch constellations of polar-orbiting low Earth orbit (LEO) satellites for mobile communications, such as Iridium, that were being promoted in the 1990s. Kodiak is at 57 degrees North latitude, making it an excellent site for polar launches; the fact that the downrange area to the south is uninhabited ocean also makes it a good site. The facility was set up by the Alaska Aerospace Development Corporation (AADC), established by the Alaska state government, and went operational in 1998.

The LEO comsat business didn't take off the way it was expected to, but the KLC was saved by the Federal government, which has contracted with the facility to perform 14 launches to date. Kodiak is not only at a high latitude, its longitude is well to the east of the "Lower 48" US states, and so launches from there can simulate incoming missiles from the western Pacific (read as "North Korea"). As a result, eight of the launches have been of "Strategic Target System (STARS)" missiles, the flights used for tests of anti-ballistic missile interceptors launched out of Vandenberg Air Force Base in California.

Kodiak Launch Facility

The KLC facility has a modern control center, two launch pads, satellite processing and rocket assembly buildings, and a mobile GPS-based tracking and range safety facility. The complex has been recently improved with a dual redundant fiber-optic network. Rockets and payloads are brought in by air or barge and then trucked up the road to the facility. The AADC has a total of 50 staff on Kodiak and at its headquarters in Anchorage. Despite sniping by critics at "Space Pork Kodiak", the management of AADC claims the operation is comfortably profitable, though admittedly dependent on the Federal dollar.

Indeed, KLC is expanding its operation. Although the last time the facility launched a satellite was in 2001, contracts from the Air Force are on the books for two new satellite launches. A new rocket storage facility, consisting of earthen bunkers, is under construction, permitting storage of solid-fuel rockets and allowing KLC to conduct a launch within 24 hours of being told to GO -- with this capability seen as highly relevant to the Air Force's "Responsive Space" effort for quick-response military space missions, discussed here some years back. The AADC is lobbying to build a third pad, which would permit up to four launches a year. With the recent improvement in health of the commercial space business, the KLC may also be able to diversify its customer base. Uncle Sam has been generous to Kodiak, but having more than one client can't hurt.

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[TUE 29 DEC 09] INFRARED FLUORESCENT PROTEINS

* INFRARED FLUORESCENT PROTEINS: As reported by an article in SCIENTIFIC AMERICAN ("Deep Into The Red" by Bianca Nogrady, July 2009), one of the trendy items in the biosciences these days is "green fluorescent protein (GFP)", which as the name suggests, glows green after being exposed to light. The gene for GFP, originally isolated from jellyfish, can be spliced into cells for use as a tracer of their bioactivity. GFP has proven so useful that it won its discoverers -- Martin Chalie of Columbia University in New York; Osamu Shinomura of the Marine Biological Laboratory in Woods Hole, Massachusetts; and Roger Tsien of the University of California, San Diego (UCSD) -- the Nobel Prize for chemistry in 2008.

Unfortunately, GFP has a limitation: it is only excited by visible light in the blue to orange range, and it only emits green visible light -- meaning it is generally useless for tracing bioactivity in organisms, since the light can't get inside an organism and it can't get out. That restricts the use of GFP to test-tube studies. However, Tsien and his UCSD colleagues have now come up with a new fluorescent protein that will absorb light from the deep-red part of the spectrum and emit it in the near-infrared. Such wavelengths can penetrate mammalian tissue and even bone, and so "infrared fluorescent protein (IRFP)" promises to give researchers a tool to look inside organisms.

The UCSD researchers obtained the protein from a bacterium named Deinococcus radiodurans, a well-known "extremophile" microorganism that can survive in very harsh environments. The bacterial protein, known as a "bacteriophytochrome", actually didn't originally generate light; instead, it absorbed light and then switched genes in the bacterium on and off in response. However, the researchers deleted the element in the protein that converted input light into chemical energy, and the truncated protein then glowed in the infrared. They spliced the IRFP into the liver of a live mouse, with the liver lighting up when the mouse was exposed to deep red light.

IRFP promises to permit "in vivo" examination of a wide range of biochemical processes in deeply buried tissues in animals. It isn't likely to be used on humans, however, since it would require genetic manipulation, which is controversial enough -- and gets much more controversial when the suggestion of splicing a bacterial gene into the human genome is thrown in on top of that.

The UCSD researchers are excited about the possibilities of IRFP, but they would also like to restore and modify the protein's gene-control capability. That would allow researchers to, say, control a gene that directs brain function in a mouse by simply shining the appropriate wavelength of light on the mouse's head -- without any invasive procedures whatsoever.

* ED: I get a free local newspaper a few times a week in my mailbox; it's basically just an advertising platform, but I do read it a bit to follow criminal court cases in the area. I was a little surprised to find one issue actually had an article on another application of fluorescent proteins for biological research in work at Colorado State University (CSU), just up the road from Loveland in Fort Collins.

It turns out that several research groups around the USA are working along much the same lines. The concept is to use GFP to tag viruses that infect mosquitos, allowing the paths of viral infection to be traced. Such research has focused on various forms of "equine encephalitis", which as its name suggests is primarily a disease of horses and donkeys, carried by mosquitos. While the GFP gene can be spliced into the equine encephalitis virus, the virus cannot actually emit light itself since a virus has no metabolic activity -- but once the tagged virus infects a host cell the GFP is expressed in the cell, allowing the infection to be spotted in samples with a fluorescent scope.


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[MON 28 DEC 09] WAR AT LIGHTSPEED (3)

* WAR AT LIGHTSPEED (3): While the Pentagon's JHPSSL battlefield laser program has succeeded in developing lasers that can operate at practical power levels, nobody's actually built a system that's ready for fielding. Refining these such systems into practical gear suitable for use on the battlefield remains a challenge.

Some believe that OP-SSLs may not be the winners in the race anyway, and are more enthusiastic about fiber-optic lasers (FOLs). In such lasers, the lasing medium is a special optical fiber with a cladding that guides the pump light along the fiber. High power FOLs are already in use in industrial applications, operating continuously on production lines. Some FOLs have been built that can achieve 30% efficiency, and they tend to be more robust than the relatively elaborate slab lasers. Unfortunately, FOLs can provide high power or high beam quality, but they can't provide both. The fiber core is normally small and can accommodate only so much light energy before photon interactions start to drain off power increase; there's no way to reach 100 kW. It is possible to make the core bigger, but then the beam quality falls off.

Some question whether 100 kW is really needed. In 2006, Raytheon researchers blew up several mortar rounds at a range of a little over 500 meters (1,640 feet) with a 20 kW industrial laser. Raytheon has integrated a commercial laser as a complement to the Phalanx Gatling cannon used for shipboard defense. Such a laser doesn't generate a really powerful or high quality beam, but on the other hand, as one Raytheon official puts it, it doesn't require "guys in white coats running around and coaxing it to work ... You push a button and it comes on."

Boeing has also tested a kilowatt-class industrial FOL in its own Avenger missile launcher, which is built around a Hummer light truck. Such laser systems could be fielded right away, if the military doesn't mind the low power output. But will FOLs ever achieve 100 kW or more? Researchers won't say they can't, but one says the idea "hurts my head".

* DARPA is also interested in FOLs, but is taking the alternative approach of simply ganging multiple low-power lasers together -- a notion that seems somewhat obvious, though getting it to work is not trivial. The agency is investigating an "active array laser (AAL)" system under the "Adaptive Photonics Phase-Locked Elements (APPLE)" program. The objective of APPLE is to build an AAL that could be conformally integrated into an aircraft, becoming a part of the airframe, with phase-shift steering providing a 45-degree field of view. As envisioned, each element of the AAL array is an individual laser, but kept in phase by a common master oscillator. Piezoelectric actuators tilt the fiber tip while an optical system controls the array output. Each element has a detector to sense the return beam.

The AAL will be a laser-based equivalent of "active electronically steered array (AESA)" advanced radar systems. Like an AESA, the elements of the AAL could be used independently, ganged in groups, or employed as a collective, depending on the power requirements for the particular mode of operation. The list of low power operations includes laser communications, search and track, and target identification -- with such functions performed in parallel by subsections of the array if need be. Medium power operations include countermeasures -- for example "blinding" heat-seeking missiles -- while high power uses include defensive intercepts of missiles, and precision attacks.

DARPA officials say that a conformal AAL measuring only half a meter (20 inches) on a side would be able to produce 200 kW with all its array elements firing on a single target. Raytheon is currently working on APPLE Phase 1, developing a 7-element AAL with a single FOL per element. Phase 2, not yet funded, would focus on development of a 21-element AAL. Of course there's no consideration of fielding such a system in the near future; it's seen as enough of a challenge just to get the demonstrators to work.

* For now, the diode-pumped OP-SSL remains in the running. Chemical lasers can produce the power but are inconvenient, to put it mildly, while FOLs are convenient but don't seem to be able to produce the power. There's a certain sense of excitement in the high-power laser field since systems have finally been built that could be practical in principle, but there's frustration in the continuing challenge of turning those systems into something that will actually work in combat. Battlefield lasers have come a long way, but they have some way left to go. [END OF SERIES]

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[FRI 25 DEC 09] THE IMMUNE SYSTEM (8)

* THE IMMUNE SYSTEM (8): The complexity of the human immune system is so extreme that some claim it could not have arisen through evolutionary processes; it had to have been the product of an Intelligent Designer of some sort -- for example, advanced aliens that visited Earth in the distant past.

The idea is entertaining, but not taken very seriously, at least not by the sciences. There's the general problem that invoking an Alien Designer without providing any details about the Designer, or the Design process, is not much of an explanation: Who were the aliens? Where did they come from? What did they look like? What did they do? What happened to them? It's hard to find examples in any of the sciences that suggest invoking mysterious aliens as an explanation actually buys much in the way of useful understanding.

There's also the problem that the human immune system, powerful as it is, hardly seems perfectly Designed, since some pathogens can get around it, and worse it can go wrong -- leading to common nuisances like hay fever, or even disastrous self-destruct actions like lupus erythematosus. There are infections, such as the bacteria that cause leprosy, that are more or less harmless in themselves; it is the vicious immune system response that causes the extremities of the leper to rot away. In addition, it's hard to think of any good reason for why an Alien Designer would create lethal pathogens and then create an immune system to fight them off. It might seem from that point of view that Design suggests multiple Alien Designers, with the Designer of humans in a struggle with the Designers of pathogens. This is one of the difficulties in giving an arbitrary answer to a problem: as complications arise, the only way to resolve them is to pile up more arbitrary answers.

* If the immune system did in fact evolve, then it had to have been preceded by a series of less elaborate (but still effective) immune systems in ancestral organisms. An examination of the branches of the tree of life strongly suggests that it was. Plants and relatively "primitive" animals (in the strict sense of being "primal", having ancestry going back a very long time) such as sponges and earthworms have an innate immune system but no adaptive immune system -- no antibodies, no T and B cells.

Plants can generate chemicals to provide immune system alerts and to fight pathogens, so they do have an immune system of sorts, but it is very different from that of animals. In particular, plants don't have graft rejection, with the interesting consequence that it is possible to graft different varieties of grapes onto the same vine. Another difference is that many plants can either simply kill off an infected area to prevent the spread of pathogens, or "wall off" branches and leaves to allow them to die without affecting the rest of the plant.

Insects do generate antibacterial proteins along the lines of complement. They also have a set of defensive cells known as "hemocytes", which have parallels to vertebrate leukocytes, being capable of ingesting pathogens or bombarding them with toxic granules. More uniquely, insect hemocytes can form "nodules" around clusters of pathogens; when confronted with large invaders, such as the larvae of parasitic wasps, this nodulization process can lead to the encapsulation of the invaders, with multiple layers of hemocytes reinforced with coagulant molecules to form a tough, lethal cocoon.

Vertebrates are the only organisms with an adaptive immune system. To the extent that many vertebrates are large organisms like humans with long life-cycles that breed slowly, it makes a certain amount of sense that they need an adaptive immune system. Small organisms like insects with short life-cycles that breed rapidly can get by without one; there's enough variability among the innate immune responses of members of the population to allow part of the population to survive an attack by an unfamiliar pathogen, and the survivors can quickly rebuild the population. In other words, while individual insects don't have an adaptive immune system, the insect population itself can adapt. Without an adaptive immune system, however, slow-breeding humans would be gradually whittled down to extinction by successive attacks of unfamiliar pathogens.

While all vertebrates have both innate and adaptive immune systems, they do demonstrate a certain hierarchy of immune system organization that matches their perceived evolutionary relationships. For example, while reptiles and their descendants, birds and mammals, have lymph nodes, the more "primitive" amphibians and fish do not. The hierarchical pattern among vertebrates goes down to finer levels of detail. Humans and other mammals all have the five classes of antibodies IgE, IgA, IgG, IgD, and IgM. Birds do not have IgE; reptiles also lack IgA.

One of the interesting case studies in the evolution of the immune system is the lamprey, an eel-like parasitic jawless fish or "agnathan". The agnathans are vertebrates like us, but they split off from the branch we share with most of the familiar vertebrates around us a long time ago. The lamprey does have an adaptive immune system, but research is showing that its underlying mechanisms are very different from those of animals on our branch of the tree. It is unclear if the two branches diverged from a "primal" adaptive immune system or if they were independent evolutionary "innovations" from a common ancestor group that didn't have an adaptive immune system. Scientists are continuing their investigations in hopes of resolving such questions. [END OF SERIES]

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[THU 24 DEC 09] SCIENCE NOTES

* SCIENCE NOTES: As reported by DISCOVERY CHANNEL Online, weather researchers are now looking forward to a new tool that will allow them to track lightning all over the globe. Installation of the "World Wide Lightning Location Network (WWLLN)" began in 2002, and 46 stations have been set up so far; the final network, to be completed in 2010, will have 60 stations.

The stations are spaced roughly 3,000 kilometers (1,865 miles) apart. As anyone who's listened to an AM radio station during a thunderstorm knows, a lightning bolt generates a burst of radio noise, and so the WWLLN stations listen in on the radio band between 1 kHz and 25 kHz for lightning-caused static. The time of arrival of signals received at different stations is compared to give a rough "triangulation" of the location of a thunderstorm. Along with providing more data on the weather, the WWLLN is expected to have practical applications as well -- for example, allowing warnings to be issued to allow air traffic to be routed around storms. Similarly, since volcanic ash clouds generate lightning, the network will be able to pinpoint remote volcanic eruptions, once again giving a warning to allow air traffic to steer clear.

* Paleontology must be an exciting field to be in these days, with remarkable new discoveries popping up like they're coming off an assembly line. The latest discovery was uncovered by an amateur in the UK and is a "pliosaur", a member of the family of marine "plesiosaurs", the classic "Loch Ness monster" sea reptile. However, unlike other groups of plesiosaurs, which had long serpentine necks, the pliosaurs had short necks.

pliosaur

This fossil was very spectacular, with a crocodile-like head some 2.4 meters (8 feet) long. Only the head was found, but the body length was estimated at up to 15 meters (50 feet). One of the paleontologists who obtained the fossil skull said the beast "could have taken a human in one gulp." The fossil skull is still in its rocky unprepared form, but it is clearly in remarkably good condition, likely due to the simple size and sturdiness of the creature.

* Filarial worms are nasty parasites found in tropical regions, causing afflictions such as skin problems, blindness, and elephantiasis -- a gross swelling of the legs or other body parts due to the worms' blockage of the human lymphatic system. Some species of filarial worms can be killed off directly by drugs, but some are resistant. Researchers have figured out a new approach to help deal with resistant worm strains. Filarial worms feature bacterial hitchhikers known as "wolbachia", and so antibiotics such as doxycycline have been administered to worm-infected patients to kill the bacteria. It is unclear how the wolbachia interact with their worm hosts, but in field tests the antibiotics have proven successful in killing off the worms -- which by themselves would have shrugged off the antibiotics.

* DISCOVER magazine's online blog ran an interesting story on "chronic fatigue syndrome (CFS)" -- the mysterious ailment that leaves people chronically weary, tired, feeling crummy, and unable to concentrate. Nobody has ever been able to pin CFS down to a cause, and in fact it has been often dismissed as a psychosomatic affliction, derided as "yuppie flu".

Now a study published by a team of researchers led by Dr. Judy Mikovits -- of the Whittemore Peterson Institute in Reno, a nonprofit set up by the parents of a woman with CFS -- has identified a suspect, the "xenotropic murine leukemia virus-related virus", blessedly abbreviated as "XMRV", normally regarded as a disease of rodents. The paper reported that 68 of 101 patients with CFS were infected with XMRV, while only 3.7% of a control group of 218 healthy subjects was infected with the virus. Follow-on work performed after the paper was written has shown that 98% of 300 patients with CFS were infected with XMRV.

However, as the saying goes, correlation is not causation, and there is no strong proof yet that XMRV actually causes CFS. XMRV may be harmless, no more than an opportunistic infection of people whose immune systems have been suppressed by another agent, or it may be a contributing factor to CFS that works in collaboration with other agents.

XMRV is a retrovirus, like the HIV pathogen that causes AIDs, and so antiretroviral drugs are now being administered to CFS patients. If the drugs prove effective, that would enhance the suspicion that XMRV underlies CFS. For now Mikovits is being cautious, since biomedical research is subtle, tricky, and prone to dead ends -- but she's finding it difficult to restrain her excitement: "I can't wait to tell my patients ... it's going to knock their socks off. They've had such a stigma. People just assumed they were complainers who didn't handle stress well." [ED: As discussed in later issues, this ended very badly.]

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[WED 23 DEC 09] IN PRAISE OF FAKES

* IN PRAISE OF FAKES: WIRED Online cued me to an interesting article by an archaeologist named Charles Stanish from ARCHAEOLOGY magazine ("Forging Ahead", May-June 2009). The article discussed how archaeologists have been worried that eBay provided much too convenient a market for looted cultural artifacts. There's long been a trade in such items, but eBay gives looters a sales channel to cut out the middleman and sell direct for big money, putting antiquities at massive risk.

The reality is that since the number of real artifacts is limited, it ends up being more profitable to deal in fakes. It's much easier and less legally risky to produce a fake than dig up the real thing, and so eBay actually seems to be making the world safer for real antiquities. The trade in archaeological fakes is not new, of course; archaeologists have been peddled counterfeits since the 19th century. However, in the old days the fakes were generally being foisted on experts, and so they were convincing fakes. In contrast, with eBay providing access to a mass market, the fakes now cover a wide range of quality in astounding quantities. The flood of fakes has helped drive down prices, making it even more attractive to make fakes in volume instead of trying to sell real antiquities for much less than they're really worth.

Stanish visited a number of workshops churning out fakes in Peru and Bolivia. Using local materials and drawing on their cultural knowledge, small manufacturers produce pieces that are, in some cases, remarkably accurate reproductions of actual artifacts, and are carefully treated to give them an ancient appearance. Each fake may actually be unique, being an ever-so-slightly modified version of a real artifact that has the look and feel of an authentic ancient object.

Of course, not all the "antiquities" eBay are actually frauds. Roughly 5% really are the real thing. About 30% are obviously not the real thing, easily caught out by looking at the pictures, even fuzzy ones. These are simple pieces manufactured for tourists and sold as replicas, with no pretense of being authentic.

Unfortunately, the eBay market for antiquities still causes archaeologists some difficulties, since the other 65% exist in an uncertain zone where they have to be examined by someone with professional qualifications to determine if they're real or fake, and even the pros are finding it increasingly difficult to figure out which is which. While eBay has created a boom market for low-quality fakes, ironically competition between the fakers has tended to drive up their quality over time. At the top end, some of the fakes are so good as to be very hard to tell from the real thing. To compound matters, some fakes have become established in collections, with experts being trained on them and becoming even more challenged to tell the real thing from the fraud. There are technical means of dating pottery, but they're expensive, and it is much more difficult to authenticate stone or metal objects.

The bottom line is that in the absence of any technical verification, anyone buying an antiquity on eBay can bet it's going to be a fake. If the buyer doesn't care, that's not really an issue, but anyone who pays $200 USD an ancient mask that's supposedly worth $15,000 USD -- and has it shipped by ordinary parcel delivery through customs, instead of smuggled into the country -- has got a reality check that has bounced.

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[TUE 22 DEC 09] SMOS IN ORBIT

* SMOS IN ORBIT: After repeated launch delays due to problems with the Eurocket Rockot booster, the European Space Agency's (ESA) "Soil Moisture & Ocean Salinity (SMOS)" spacecraft was finally put into orbit from Russia's Plesetsk Northern Cosmodrome on 2 November 2009. SMOS was designed to measure the dampness of land surfaces and the salinity of the oceans, with these dual sets of observations intended to help nail down the global circulation of water from the sea into the air and back to land.

SMOS

The more water lost from the atmosphere to the land, the damper the land; the more water lost to the atmosphere from the sea, the saltier the sea. SMOS helps track such changes by measuring the natural emission of microwaves from the Earth's surface, with the emissions modulated by variations in the sogginess of soil or the salinity of the oceans:

In both cases, the spacecraft performs its mapping over a swath 1,000 kilometers (620 miles) across. The measurements only reach down a few centimeters into the soil or sea, however, and so the spacecraft's data needs to be complemented by other sources, for example ocean buoys.

The microwave radiation being mapped is in the long-wavelength "L-band" region around 1.4 gigahertz, which would on the face of it demand an antenna some 20 meters (66 feet) across to obtain the desired resolution. SMOS "cheats" using a scheme known as "interferometry", often used by arrays of ground-based radio telescopes. The satellite's payload, the "Microwave Imaging Radiometer with Aperture Synthesis (MIRAS)", a passive receiver system, has 69 small microwave antennas mounted on three arms, each 3.5 meters (11 feet 6 inches) long, mounted on a central box. The signals picked up by the little antennas are crunched by computer processing to give the effect of a large unitary antenna.

Climatologists will find the data returned by SMOS very useful. Europe suffered a heatwave in 2003; had the pre-existing dryness of the soil been understood, the extreme conditions that resulted would have been easier to predict. Similarly, if soils are waterlogged, further precipitation is likely to result in widespread floods. The salinity of sea waters provides clues about global oceanic water circulation, with the different densities of more saline and less saline water driving oceanic flows.

The SMOS satellite had a launch mass of about 680 kilograms (1,500 pounds) and was powered by twin solar arrays. Support systems included a set of star trackers, a Sun tracker, and a GPS receiver for location and orientation. The spacecraft bus was built by Thales Alenia Space in Cannes, France, while the MIRAS instrument was built by EADS-CASA Espacio in Madrid, Spain. SMOS was placed in a near-polar Sun-synchronous orbit in which it passed over the same locale at the same time each day, to ensure constancy of measuring conditions. Basic mission lifetime was expected to be three years.

SMOS was launched "piggyback" on top of a smallsat designated "Project For On-Board Autonomy 2 (PROBA-2)", which was an ESA technology demonstration satellite with a launch mass of 130 kilograms (285 pounds). PROBA-2 performed 17 different experiments; it followed PROBA-1, which was launched in 2001.

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[MON 21 DEC 09] WAR AT LIGHTSPEED (2)

* WAR AT LIGHTSPEED (2): After the US military gave up on the THEL chemical battlefield laser system, the focus turned decisively to optically-pumped solid-state lasers (OP-SSLs). They were nothing new; in fact, the first laser ever demonstrated was an OP-SSL, using a ruby rod as its core "lasing" element, pumped up by a wraparound flash tube. Modern OP-SSLs work along the same lines, using a crystalline lasing element pumped up by an external light source. However, traditionally OP-SSLs have been plagued by low power output; low efficiency, on the order of a few percent; and an inability to dump waste heat, tending to shatter or fry themselves if run at high power.

However, another branch of laser technology, the semiconductor diode laser, helped address the problems. One of the chokepoints in OP-SSLs is the light source used to do the pumping. A standard flashlamp isn't all that efficient in converting electricity to light in the first place, and it also generates light over a wide spectrum, much of it no good for pumping the lasing element. Diode lasers -- which have been around since the 1980s and are common in CD and DVD players -- are highly efficient and can also be designed to provide light in the range specifically needed by a lasing element. Diode lasers can convert half their electrical input into light, allowing them to drive an OP-SSL with an admirable overall efficiency of 25%.

While the Army had been working on THEL, the service had also been developing a relatively modest OP-SSL system. In 1997, the Army had awarded a contract to a California-based defense contractor named Sparta to develop "Zeus", which was a Hummer light military truck with a laser turret that was to be used to detonate explosive ordnance from a safe distance away. Zeus was deployed to Afghanistan in 2003 for field tests and later saw service in Iraq as well. In operation, the crew of the Zeus system would pinpoint the target with a visible light (green) laser from 25 meters to 250 meters (80 to 820 feet) away -- far enough to be out of the blast zone of relatively small munitions. The crew would then turn on the main infrared laser, which operated at a power level of half a kilowatt.

The Army was impressed by Zeus, at least to a degree: it was small enough to be mobile and was effective in disposing of dud ordnance and the "improvised explosive devices (IEDs)" used by Iraqi insurgents -- as long as the IEDs weren't buried. The original Zeus was pumped by arc lamps, but in 2004 the system was upgraded to a diode-pumped scheme, bringing the output power up to two kilowatts. That still wasn't enough to overcome the limitations of Zeus, but it did point the way forward to better battlefield lasers.

* Zeus had it easy, since it could focus for as long as needed on targets at relatively close range. Developing a diode-pumped OP-SSL that could achieve the magic 100 kW level needed to deal with incoming ordnance was more difficult, but the technology seemed to be within reach. In late 2002, the Pentagon began the "Joint High Power Solid-State Laser (JHPSSL)" program to provide the Army with a battlefield laser, the Air Force with a laser for the new F-35 Joint Strike Fighter, and the Navy with a laser to stop small attack boats. The laser had to run off conventional power systems such as diesel generators.

Northrop Grumman, Textron, Raytheon, and the US Lawrence Livermore National Laboratory (LLNL) competed to develop the HPSSL. The Phase 1 objective of the program was to demonstrate by late 2005 a 25 kW SSL that could maintain tight focus continuously for 300 seconds on a repeatable basis. All four contenders developed diode-pumped OP-SSLs, with the "pump diodes", as they were called, driving thin slabs of crystalline material -- typically made of neodymium-doped yttrium aluminum garnet (Nd:YAG), which produced output in the near infrared.

The slab configuration allowed the crystals to dissipate heat more easily than would a rod; although the lasers had a good efficiency of about 20%, that still meant a lot of heat to dump. Uneven heating in a slab would spread or disrupt a laser beam, and that meant coming up with schemes to get rid of the heat. Lawrence Livermore had already developed a clever if tricky way to deal with the problem, creating what they called a "solid-state heat-capacity laser", using laser slabs mounted on wheels. A slab was pumped up for ten seconds until it got hot, then rotated to cool off while the next slab was pumped up. It worked for the 25 kW laser, but didn't make the cut for the Phase 2 development effort to build a 100 kW laser.

The designs from Northrop Grumman and Textron Systems did make the cut; both used water cooling with heat exchangers, but had different approaches to the optical system. A laser is basically an optical oscillator, with light generated in a "resonant chamber", the lasing element, where it bounces from end to end, with the beam building up in lockstep. There are two ways to boost power: either pump the laser output through amplifiers of excited lasing material, or bulk up the oscillator. The two companies made a different choice in their HPSSL designs:

The Phase 2 HPSSL lasers are encouraging, and those at the leading end of laser research do not see them as the last word by any means. The US Defense Advanced Research Projects Agency (DARPA) is working with the General Atomics company on an advanced slab laser weapon, the "High Energy Liquid Laser Area Defense System (HELLADS)", with the objective of building a 150 kW laser that would weigh only 750 kilograms (1,650 pounds) -- which could easily fit onto a strike fighter. At last notice, a flight demonstration was expected in 2012. [TO BE CONTINUED]

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[FRI 18 DEC 09] THE IMMUNE SYSTEM (7)

* THE IMMUNE SYSTEM (7): Our immune system is highly effective, but its effectiveness creates a difficulty. A pregnant mother carries a child in the womb with genetic components from a father -- meaning the child is not seen as "self" by the mother's immune system, and could in principle be attacked. That doesn't happen, but it isn't clear why not. It is known that the womb is an "immunologically privileged" site where immune responses are suppressed by processes that remain poorly understood. The child does obtain "passive" immunity from the mother, receiving antibodies and selective immune cells.

Of course, it isn't surprising that the immune system will attack and reject transplanted organs, since they're not identified as "self". It is possible to perform "tissue typing" using leukocytes -- white blood cells -- to determine how good a match a transplanted organ is for a host. The leukocytes carry MHC self-markers known as "human leukocyte antigens (HLA)", which come in about 10,000 different variations.

* Pathogens have acquired a number of tricks to defeat the immune system. One approach is to mutate rapidly, altering antigens so that the immune system memory is rendered useless. This trick is associated with the influenza virus, the Plasmodium protozoan parasite that causes malaria, and in particular with the human immunodeficiency virus (HIV). HIV is extraordinarily agile, featuring a mutation rate far greater than that of the influenza virus. Worse, HIV also attacks helper T cells and macrophages, undermining the immune system that is trying to resist the infection.

* As mentioned in an earlier installment, the immune system can go off the rails. Allergies are the most common difficulty; they're troublesome immune responses to common substances that would be otherwise harmless, most notably airborne pollen. These immune responses are often acquired when the body is attacked by a pathogen and simultaneously exposed to pollen or some other harmless substance -- for example, if a person catches a cold while there's plenty of pollen in the air. B cells start producing IgE antibody that targets the pollen, with the IgE accumulating in the mast cells. When the person encounters grass pollen again later, the IgE-primed mast cells go into action, leading to sneezing, sniffling, and coughing.

In some cases, allergens can cause a massive immune response known as "anaphylatic shock", which can be fatal -- usually due to suffocation when the windpipe swells shut. Food allergies can be very dangerous, particularly for small children, whose digestive processes aren't efficient enough in breaking down the proteins in food, allowing them to get into the bloodstream where they cause an immune response. Peanuts and other nuts can be particularly dangerous to some small children.

Antigen-antibody complexes can also cause difficulties. As noted, such complexes are targets for complement peptides, helping to destroy intruders. The complexes are usually cleaned out after they have served their purpose, but sometimes they can build up and accumulate in tissues, inappropriately invoking complement cascades.

When the immune system targets the self, the result is autoimmune disease. Common autoimmune diseases include:

It is not clear how autoimmune diseases get started. One notion is that they can be triggered by antigens from pathogens that have too close a resemblance to "self". Autoimmune diseases are very difficult to treat; nobody has yet figured out a way to "reprogram" a malfunctioning immune system. The most that can be done at present is to slow down the progress of such diseases and alleviate their symptoms.

* There is some evidence that the immune system can suppress cancers, but research along such lines has led to inconclusive results so far. The big problem with an immune response against cancer cells is that such cells are normal body cells whose replication has gone out of control; they're usually still recognizable as "self", and so an immune response against them runs the hazard of attacking the rest of "self" as well. Of course a cancer cell that has lost its MHC I receptors will be destroyed by natural killer cells, and cancer cells may have distinctive "markers" of their own that allow them to be targeted. There has been some work on "training" an immune response against cancers, but so far results of such experimental therapies have been modest.

* There's a puzzle in the adaptive immune response that is not yet well understood. Our bodies are loaded with colonies of benign microorganisms, particularly bacteria in our lower digestive tract. In fact, there are more foreign cells in our bodies than our own cells in our bodies, though the bacterial cells are much smaller. Some of our "intestinal flora" are needed to maintain our health, since they synthesize vitamins needed for us to stay alive. In the case of herbivores, they are important even to basic digestion, helping to break down cellulose.

The puzzle is how the adaptive immune system recognizes the intestinal flora as "friendlies". What makes this particularly puzzling is that when the intestinal flora stray from the digestive tract, they're attacked as "hostiles". Nobody has any clear idea of how the immune system selectively tolerates the intestinal flora. The immunocompatibility of resident microorganisms remains an interesting leading edge of research in immunology. One interesting idea is that the appendix, traditionally thought to be a useless vestigial organ in humans, is actually important in youth as a feature for conditioning the immune system to tolerate resident intestinal organisms. [TO BE CONTINUED]

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[THU 17 DEC 09] SPACE NEWS

* SPACE NEWS: Space launches for November included:

-- 02 NOV 09 / SMOS, PROBA 2 -- A Eurocket Rockot booster was launched from Plesetsk northern cosmodrome in Russia to put the European Space Agency's (ESA) "Soil Moisture & Ocean Salinity (SMOS)" environmental satellite into orbit. SMOS had a launch mass of 680 kilograms (1,500 pounds) and carried a passive microwave radiometer receiver system to measure soil moisture and ocean salinity. The launch also included the ESA "Proba 2" microsatellite, a technology-test platform with a launch mass of 130 kilograms (285 pounds). The Rockot ("Roar") booster was a refurbished UR-100N (NATO SS-19 Stiletto) two-stage intercontinental ballistic missile, fitted with a Breeze-M third stage.

Rockot booster with Proba & SMOS

-- 10 NOV 09 / POISK MRM 2 -- A Soyuz-U booster was launched from Baikonur in Kazakhstan to put the "Poisk [Explore] Mini Research Module 2 (MRM 2)" docking compartment for the International Space Station (ISS) into orbit. It docked with the ISS Zvezda module on 12 November. The Poisk module was intended to provide docking ports for the Russian component of the ISS, and was loaded with supplies for the station.

-- 12 NOV 09 / SHIJIAN 11-01 -- A Long March 2C booster was launched from Jiuquan to put the "Shijian 11-01" technology demonstration satellite into orbit.

-- 16 NOV 09 / SHUTTLE ATLANTIS (STS-129) -- The NASA space shuttle Atlantis was launched from Kennedy Space Center in Florida on "STS-129", an ISS support mission. This was the 129th shuttle mission and the 31st flight of Atlantis. There were six crew, including:

Atlantis carried two Express Logistics Carriers with a load of spare parts for the station. The spares were intended not merely for ongoing operations but to make sure the station could remain operational once shuttle flights ceased, with the shuttle hauling up elements that were too big to fit through the hatch of a Russian Progress freighter spacecraft.

Atlantis landed at Kennedy Space Center on 27 November 2009 after 10 days 19 hours 16 minutes in space. Stott had spent 91 continuous days in space. She was the last ISS resident to hitch a ride home on the shuttle, with all future crew transfers to be via Russian Soyuz capsules.

-- 20 NOV 09 / COSMOS 2455 -- A Soyuz-U booster was launched from the Plesetsk northern cosmodrome to put a secret military satellite into orbit. The satellite was designated "Cosmos 2455", and was believed to be the first of the new "Lotos" series of electronic intelligence satellites.

-- 23 NOV 09 / INTELSAT 14 -- An Atlas 5 booster was launched from Cape Canaveral to put the "Intelsat 14" geostationary comsat into orbit. Intelsat 14 was built by Space Systems Loral and was based on the SS/L LS-1300 comsat platform. The satellite had a launch mass of 5,612 kilograms (12,375 pounds), a payload of 40 C-band and 22 Ku-band transponders, and a design life of 15 years. It also carried an experimental "Internet Routing In Space (IRIS)" payload for the US Department of Defense. Intelsat 14 was placed in the geostationary slot at 45 degrees West longitude to provide communications services to Europe, Africa, and the Americas, replacing the nine-year-old Intelsat 1R comsat in that slot. The Atlas 5 was in the "431" configuration, with a 4 meter (13.2 foot) payload fairing, three solid-rocket boosters, and an upper stage with one Centaur engine.

-- 24 NOV 09 / W7 -- A Proton Breeze M booster was launched from Baikonur to put the Eutelsat "W7" comsat into geostationary orbit. W7 was built by Thales Alenia Space and was based on the Spacebus 4000C4 comsat platform. The satellite had a launch mass of 5,625 kilograms (12,400 pounds), a payload of 70 Ku-band transponders, and a design life of 15 years. It was placed in the geostationary slot at 36 degrees East longitude, joining the existing Eutelsat W4 satellite to provide communications services to Russia, Europe, Africa, the Middle East, and Central Asia.

-- 28 NOV 09 / IGS -- A Japanese H-2A booster was launched from Tanegashima to put a secret optical "Information Gathering Satellite (IGS)" into orbit. It joined Japan's existing constellation of two optical and two radar spysats in orbit.

H-2A launch from Tanegashima

-- 30 NOV 09 / INTELSAT 15 -- A Land Launch Zenit 3SLB booster was launched from Baikonur to put the "Intelsat 15" geostationary comsat into orbit. The satellite was built by Orbital Sciences and was based on the Orbital Star spacecraft bus. Intelsat 15 had a launch mass of 2,484 kilograms (5,477 pounds), a payload of 22 Ku-band transponders, and a design lifetime of 17 years. It was placed in the geostationary slot at 85 degrees East longitude to provide communications services to Russia, the Middle East, and the Indian Ocean regions. It replaced the Intelsat 709 comsat, which had been launched in 1996.

* OTHER SPACE NEWS: The Iridium low-orbit global comsat system, promoted heavily in the 1990s, ended up being a bust -- but since the emergence of the Iridium company from bankruptcy in 2001, it's made a reasonable niche business for itself, mostly providing communications services to government personnel. Iridium currently has 300,000 subscribers.

Of course, the Iridium satellites in orbit aren't getting any younger, and so the company is now investigating replacement satellites, to be launched from 2014. The new satellites will be based on Internet Protocol instead of the voice channel architecture of the current system, and will provide data rates of up to a megabit per second per subscriber.

Iridium is offering to sell space on the new comsats to scientific users. The secondary scientific payloads will be limited to no more than 50 kilograms (110 pounds) of mass and 50 watts of power, but many science users see that as generous -- most of the support facilities for a science payload will be provided by the satellite, with science communications leveraging off the comsat's own communications system. The biggest problem is that while the Iridium comsats are in polar orbit, allowing them to canvass the Earth, they are not in slightly-off-polar "Sun synchronous" orbits handy for Earth remote sensing satellites, since they ensure that observations are made at the same time and same Sun angles for locales under the orbital track. However, there are some sorts of measurements, for example cloud cover surveys, that don't need a Sun synchronous orbit. How much the ride is going to cost is not clear, but it promises to be relatively cheap, and there is considerable interest in the Iridium offer.

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[WED 16 DEC 09] ARCHIVES OF THE SKY

* ARCHIVES OF THE SKY: For well over a century, astronomers have been photographing the sky, traditionally using glass plates covered with a film of photographic emulsion. As a result, astronomical institutions have huge archives of photographic plates that contain an enormous amount of data. As reported in an article from AAAS SCIENCE ("Stars In The Dusty Filing Cabinets" by Yudhijit Bhattacharjee, 24 April 2009), many of those archives are gathering dust, and in some cases are being simply discarded by organizations in need of more office or storage space.

The plates could have great value, however. In 1962, astronomers discovered a radio-bright object designated "3C 273" that turned out to have an enormous spectral shift, implying it was in the distant reaches of the expanding Universe. Obviously 3C 273 had to be bright to be visible from such distances. Examination of archives of photographic plates from 70 years previous also showed that 3C 273 could significantly change brightness in the space of a week, meaning it was a relatively compact object. The old plates helped characterize the behavior of the first known "quasar", demonstrating their worth. It wasn't the last time astronomers have conducted research by examining the archives.

Unfortunately, even when the archives remain available, examining the old plates using manual methods is laborious. A faction of astronomers is determined to preserve the heritage by digitizing old archives of astronomical plates, placing them online so they can be conveniently searched by software, in effect "googling the Universe". For example, the "Digital Access to a Sky Century at Harvard (DASCH)" effort, led by Harvard astronomer Jonathan Grindlay, has the goal of digitizing all half-million plates in the university's collection and placing them online.

The Harvard plate collection takes up parts of three floors of an old brick building at Harvard College Observatory. The images date back well into the 19th century and were taken with 20 telescopes operated by Harvard astronomers all over the world. DASCH began scanning the plates in 2008, using a modified commercial scanner and custom software. The plates are first cleaned -- as one of the workers on the project said, if the grime wasn't removed "there would be ten thousand more stars per plate" -- and are then precisely fed into the scanner on an air cushion bed. It takes about 90 seconds to scan one plate.

However, the $4 million USD needed to complete DASCH hasn't materialized yet, the effort having been kept afloat so far by a $600,000 USD grant from the US National Science Foundation. The problem is that universities in general and astronomers in particular have a lot of competing demands on funding, and though most astronomers think that digitizing old astronomical archives would be "nice", that's not the same thing as "must". Grindlay is optimistic that DASCH will be finished, however, one of his arguments being that clearing out the plates will free up three floors of storage: "You'll never find a more inexpensive way to clear out that much office space in Cambridge."

Other digitization efforts are being conducted on a shoestring in Germany, Belgium, and elsewhere. Still, most of the plate archives remain untouched, and that presents the uncomfortable prospect of seeing them thrown out. The Pisgah Astronomical Research Institute (PARI) in Rosman, North Carolina, is now trying to acquire collections in danger of disposal, having "rescued" half a dozen collections over the last five years. For example, PARI managed to obtain a collection of about 10,000 plates from Case Western University in Cleveland Ohio. The collection of plates had been sitting in shrink-wrapped cabinets in a storage facility behind old office and classroom furniture.

Says one astronomer: "Each of these collections is like a time machine. There's no substitute for having them. Even if you can't think of what can be done with them today, it's tremendously important that they be preserved."

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[TUE 15 DEC 09] TRACKING DOWN PHYTOPLASMAS

* TRACKING DOWN PHYTOPLASMAS: As reported by an article in AAAS SCIENCE ("Phytoplasma Research Begins To Bloom" by Evelyn Strauss, 24 July 2009), every winter holiday season we're flooded with poinsettia plants with their bright red leaves. Poinsettias tend to be gangly, but in recent times growers have been able to produce bushy plants by infecting them with plant bacteria known as "phytoplasmas".

If that was all there was to phytoplasmas, they wouldn't be a very interesting subject, but they're also major crop pests, attacking grapes in Europe and Australia; corn in South America; pears and apples in the USA and Europe; peanuts, sesame, and soybeans in Asia; and elms, coconuts, asters, and hydrangeas all over the world. Phytoplasmas have had disastrous impact on crops all over the world, and are likely to become an even bigger nuisance as the global climate warms, since the insects that carry the bacteria will extend their range.

plant with phytoplasma infection

Worse, although phytoplasmas are a significant problem, they're poorly understood, being difficult to study. In fact, plant pathologists didn't even realize phytoplasmas were bacteria until a few decades ago, having long believed they were viruses. However, researchers are starting to get a handle on phytoplasmas and have made progress in understanding their quirks. They're smaller than most bacteria and also have smaller genomes, but they have a complicated life-cycle that allows them to thrive in both plants and the sap-sucking insects that feed on those plants. The first phytoplasma genome sequence was published in 2004, with three more sequences published since then. There are now hopes for new defenses against plant maladies caused by phytoplasmas.

* The confusion over phytoplasmas began in the 1920s, when researchers tried to pin down the causes of the plant disease called "aster yellow", which afflicts crops, orchards, and ornamental plants. The small size of the pathogen, the symptoms, and its transmission by sapsucking insects all argued for a viral pathogen, and for the next 40 years that was what researchers looked for. So strong was this assumption was that clues suggesting otherwise were disregarded. In 1957, it was observed that insects infected with material containing the aster yellow pathogen would not pass the disease on to plants if the insect vectors were dosed with the antibiotic tetracycline. That should have been a tipoff, since antibiotics have no effect on viruses, but the assumption was that there had been some confounding factor in the experiment.

Finally, in 1965 Yoji Doi and colleagues at the University of Tokyo took electron microscope images of infected plant tissues, turning up structures that looked like the "mycoplasma" bacteria that cause respiratory ailments and other diseases in humans as well as other animals. Like mycoplasmas, the mystery microbes were unusually small and lacked rigid cell walls. Treatment with antibiotics killed off the pathogens; obviously they were bacteria. Having been on the wrong track for decades, researchers started unraveling what was really going on -- though it didn't prove easy. It wasn't until the 1980s that genetic tools became available to zero in on the mystery bacteria. They turned out to be not all that closely related to mycoplasmas, and in 1994 they were named "phytoplasmas".

Why did it take decades to find out that much? The reason was that phytoplasmas don't behave like typical bacterial plant pathogens. Phytoplasmas only reproduce inside cells, while most bacteria that infect plants reproduce outside cells. Phytoplasmas can only reproduce inside their target plant and insect hosts, and are impossible to grow in a pure culture. That made simple lab experiments very troublesome, and it also made it difficult to sort out phytoplasma genomes from host genomes.

* Symptoms of phytoplasma infections suggest they interfere with normal plant development. They tend to promote "vegetative growth", with plants generating extra leaves, shoots, and branches, and also suppress reproductive activities such as flower formation. In addition, they can promote dwarfism, turn normally nongreen parts green, cause general yellowing, and produce "witches' broom" -- a condition in which branches cluster and become dense.

With phytoplasma genomes available, researchers have been hunting for the proteins generated by phytoplasmas that might produce such effects. British researchers have been able to track down one such protein that helps promote witches' broom and other phytoplasma symptoms. Japanese researchers have found a similar protein that causes a disease called "tengu-su" or "tengu's nest", with plants developing short, small branches that resemble the nests attributed to the "tengu" -- birdlike demons of Japanese folklore. The researchers gave the protein the appropriate name of TENGU.

Phytoplasma proteins like TENGU appear to have a wide range of effects on the host genome. The suspicion is that the phytoplasmas are not merely soaking up plant sap, but altering the host's metabolism for their own benefit. It is known that the alterations in plant physiology caused by phytoplasmas can affect insect vectors used by phytoplasmas in ways that benefit the bacteria. For example, experiments have shown that leafhopper bugs fed plants infected by phytoplasmas have significantly greater fertility, meaning more insect hosts to spread the bacteria. Similarly, phytoplasmas can modify plant hosts to make them more attractive meals for insects, and even alter the plants to release chemicals that attract insects.

Much more needs to be learned about the phytoplasma genome. The genomes now available are smaller than those of typical bacteria, but tend to have many repeated genes, suggesting that the varied effects of phytoplasmas are generated by a fairly small genetic toolkit. In addition, phytoplasmas are a diverse group and the four genomes don't provide much coverage.

* The difficulties in understanding the genetics of phytoplasmas are only part of the challenge of these pathogens. For example, although phytoplasma diseases are generally believed to be spread by insects, in most cases nobody knows what particular insect vectors are associated with particular phytoplasmas. Another difficulty is that a small number of phytoplasma species can infect a few or many different kinds of plants and cause a wide range of symptoms. Confusingly, different phytoplasmas can produce very similar symptoms, while one insect can carry several different kinds of phytoplasmas. Concentrations of pathogens in infected plants can be low and unevenly distributed, making it hard to determine whether the pathogens are even present.

Traditional control measures -- pesticides, culling infected plants, or destroying weeds or other plants that could be serving as reservoirs for phytoplasmas -- are only moderately effective against phytoplasma infections. Injecting tetracycline into the trunks of infected trees can work, but it's costly, doesn't always work, and there's an increasing prejudice against unselective use of antibiotics anyway.

Subtler methods are showing some promise. Some researchers are focusing on breeds of plants that seem to resist phytoplasma infections; there is evidence of coconut palms that coexist peacefully with the bacteria. Another approach is to generate crop plants, for example new strains of rice, that taste fine to humans but don't taste good to insect vectors that otherwise feed on them. Infecting plants with mild strains of phytoplasmas also seems to improve their resistance to infection.

Of course, the knowledge obtained from the gene sequence of the pathogens is very likely to help in the battle against phytoplasmas. Understanding the subtle effects of phytoplasmas on their plant hosts also promises to increase broad knowledge of plant physiology, and even possibly lead to practical applications. Maybe in the future we'll be able to genetically modify poinsettias with the genes for phytoplasma proteins that ensure the plants grow up bushy on their own. Whatever the case, researchers have their work cut out for them.

ED: I was amused to see a dry science article discuss tengu, who are common characters in Japanese fantasy stories. They are variable in form, there apparently being several classes of them. They can look like monstrous birds, or humans with Pinocchio noses and (sometimes) wings, who carry folding fans. Tengu masks for performers are distinctive, with a demonic face and a long, phallic nose.

tengu mask

Of course in modern fantasies, tengu have up-to-date features: in the XXXHOLIC manga (comic) series, they look like midget punks in black clothes, boots, and shades with crow wings who fly through the sky on little surfboards and carry oversized fans. I also came across a toy of a sci-fi tengu, with a jetpack propulsion system instead of crow wings. Even tengu, it seems, must keep up with the times.

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[MON 14 DEC 09] WAR AT LIGHTSPEED (1)

* WAR AT LIGHTSPEED (1): When the laser was first invented a half century ago, the popular media played up the potential of the device as a beam weapon or "death ray". In reality, although lasers were very quickly put to use on the battlefield for targeting and range-finding, the use of lasers as actual weapons was well over the horizon at that time -- and everyone who was working on the technology knew it.

As reported by an article in IEEE SPECTRUM ("Ray Guns Get Real" by Jeff Hecht, July 2009), the battlefield laser is now much closer to reality. The US and Israeli armies see the laser as means of providing defense against incoming rockets and shells, nailing the projectiles at the speed of light to detonate or disable them. The US Navy similarly sees the laser as a shield against antiship missiles. The US Air Force wants compact lasers for fighter jets. These are not fantasies, either: in March 2009, an electrically powered solid-state laser pumped out 100 kilowatts (kW) of light power for a full five minutes, placing the battlefield laser in the realm of practical possibility.

Until recently, work on battlefield lasers had focused on "chemical lasers", which obtain their laser energy by burning fuels inside the laser. Chemical lasers are powerful, but tend very much to the bulky and cumbersome. The US Air Force worked for years on the "Airborne Laser (ABL)", a modified Boeing 747 jetliner firing a beam from a "chemical oxygen-iodine laser (COIL)" weapon through a nose turret. The COIL was powered by a chemical reaction of hydrogen peroxide, potassium hydroxide, and chlorine gas to produce energized oxygen, which then interacted with iodine gas to emit light that built up into a laser beam. The ABL was supposed to shoot down adversary missiles during their "boost phase", just after launch, but costs kept rising and the schedule kept slipping, and the ABL program was cut back to an experimental effort in April 2009.

Airborne Laser

Attempting to design high-power laser systems compact and convenient enough for battlefield use has been troublesome, but the new solid-state lasers look like they can do the job. One of the keys is high efficiency in converting electric input power into laser output power. It actually doesn't take that much power focused on incoming projectiles to set them off, a few kilowatts will do the job, but the key word is "focus"-- beyond a certain range, laser beams spread out in a narrow cone that diffuses their power. Experiments have shown that killing a moving target at a range of a kilometer or two requires 100 kW of laser power. A low power conversion efficiency is not such a problem for a small laser, but a 100 kW laser that's only 10% efficient would demand a one megawatt power supply, which wouldn't be easy to mount on a small truck -- and getting rid of the 900 kW of waste heat generated by the process wouldn't be trivial, either.

Earlier work on battlefield lasers was based on chemical lasers. In 1996, the US Army and the Israeli Ministry of Defense tapped California aerospace contractor TRW, now part of Northrop Grumman, to develop a battlefield laser, designated the "Tactical High Energy Laser (THEL)". THEL showed promise, intercepting a battlefield rocket over White Sands Missile Range in 2000. Unfortunately, a chemical laser system simply didn't belong on a battlefield. THEL demanded several trailer-sized containers to store the laser fuels and the waste from burning the fuels. The fuels tended towards the toxic and corrosive; a THEL site would have not only been a logistical nightmare, it would have been a menace to have around. The whole chemical laser scheme was a nightmare from an environmental point of view, something like hauling the Bhopal chemical factory around in a combat zone. THEL was abandoned in 2004. [TO BE CONTINUED]

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[FRI 11 DEC 09] THE IMMUNE SYSTEM (6)

* THE IMMUNE SYSTEM (6): The cell-based arm of our adaptive immune system takes a different approach from that of the humoral arm. The killer T cells of the cell-based arm do not attack pathogens directly; they find infected host cells and then destroy them by sending a chemical message that tells an infected cell: KILL YOURSELF -- a process known as "apoptosis". Killer T cells are effective at dealing with pathogens that live inside a host cell; they are ineffective against pathogens that live outside host cells. Killer T cells are one of the primary weapons against viral infections.

Killer T cells target infected cells using a host cell's MHC I surface molecules. The MHC I molecules of healthy cells contain fragments of "self" components and so the killer T cells ignore them, but if host cells have been infected, they then present pathogen antigens on their MHC I molecules. Killer T cells that recognize these antigens order the infected cells to commit suicide.

The killer T cells are primed to recognize these foreign antigens by helper T cells, which were in turn primed by dendritic cells in the lymphatic organs. Once stimulated by the antigen presented on the MHC II molecules of dendritic cells, the activated helper T cells start replicating into armies of clones tailored to the antigen. These clones generate cytokines, which stimulate killer T cells that are then keyed to the foreign antigen by the helper T cells. The stimulated killer T cells start replicating rapidly in turn, to move through the bloodstream and destroy infected cells.

Incidentally, a pathogen could disable the MHC I receptors on its host cell, preventing the cell from presenting foreign antigens. That might seem to be a good way to sneak around T cell attack, but the immune system has that base covered: the primary known function of natural killer cells is to destroy cells that lack MHC receptors.

T cells can target a wide range of antigens and so it is possible that they may end up targeting self. Through a process that isn't well understood, the immune system screens out T cells that could attack self during the T cell maturation phase in the thymus, ensuring that dangerous T cells don't make it into the operational immune system.

* After B cells and T cells have been activated by an infection, some are retained as memory cells. The next time an individual encounters that same antigen, the immune system is primed to destroy it quickly. This is "active" immunity, the body's immune system having prepared itself for future challenges. Long-term active immunity can be naturally acquired by infection -- or artificially acquired from vaccines made from infectious agents that have been attenuated or inactivated, or made from small components of the intruder. The last option is safest because there is a chance that attenuated or inactivated pathogens may not always be as attenuated or inactivated as believed, though component vaccines also produce the weakest immune response.

There is considerable public resistance to vaccines. To be sure, vaccines are not perfectly effective and all vaccines can cause adverse reactions in a few cases, but the risk level is generally far lower than that presented by the disease they provide protection against. Some anti-vaccine activists even claim that vaccines are unnecessary, that adequate dosages of vitamin D will provide all the immunity needed. The known facts don't support this idea; it is true that vitamin D does seem to be needed for the proper functioning of a healthy immune system, but unlike vaccines vitamin D can provide no adaptive protection against an unrecognized intruder. Similarly, anti-vaccine activists have claimed that injection of vaccines does not produce a "natural" immune response -- but haven't been able to articulate exactly what the significant difference is between the response to an injected vaccine or, for example, pathogens introduced by a mosquito bite.

* By the way, while mast cells, basophils, and eosinophils are generally regarded as components of the innate immune response, they are effectively cued by the adaptive immune response. After a bout of infection, the mast cells stationed in lining tissues are primed with receptors based on IgE antibodies provided by B cells. That means that when a pathogen arrives, the mast cells can immediately begin to attack it. They release cytokines that call in basophils circulating in the blood, and also stimulate the bone marrow to create the similar eosinophils, which back up the mast cells and basophils. The mast cells, basophils, and eosinophils are generally believed to be focused on dealing with parasites, such as worms, that are too big to be ingested by macrophages, but are vulnerable to bombardment with toxic chemicals. [TO BE CONTINUED]

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[THU 10 DEC 09] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: I ran into an ongoing wiki site for a project named "CREATE", standing for "CREating innovative Air Transport technologies for Europe". It was just what it says, blue-sky thinking about where air transport might go next. Some of it was nothing new, for example advanced turbofan and propfan propulsion, composite material airframe construction, and new aircraft configurations. However, some of the other ideas were distinctly unusual:

* On a related note, WIRED Online had a little article on airbags for airliners. While the usual image of an airliner accident is a midair calamity, takeoff and landing accidents are more common, and in some cases jetliners that were disabled in cruise flight have been able to force land. That means airbags could improve passenger survival. They're not actually needed for most passenger seats because the backs of the seats are designed to soak up passenger impact, but there are rows on a plane -- behind bulkheads or emergency exits -- where there are hazardous obstructions, and so airbags would be useful. But where to put the airbags? Seating systems differ considerably from airliner to airliner, and so building them into the seats is impractical. The option being pursued right now is to pack the airbag into the seatbelt buckle, using a module that pops up a pillow-sized airbag on impact.

A connected article demonstrated some "blue sky" concepts for new airline seating arrangements. One featured a two-level scheme for the center row of seats, with a "sleeper" bunk on the bottom and two seats, reached by stairs, above. Another concept took a hint from military troop transports, with seats facing in from the walls and out from a center row. Staring across the aisle at other passengers may be uncomfortable, but it's not so different from riding a subway or commuter train, and the intent is to only use it for short-haul airliners anyway.

* As reported by an article in SCIENTIFIC AMERICAN, while the air transport industry looks toward a whizzy future, it's currently lagging well behind the rest of the society it serves in the mundane art of recycling trash. Statistics show the 30 biggest airports in the USA dump as much trash as the city of Miami, with enough aluminum cans discarded every year to build over 50 jumbo jetliners. Airports and airlines recycle only a trivial 1% of their trash; the average for cities is over 30%.

The problem is structural. While a few US airports have set up recycling programs, it required changing infrastructure and procedures, and so far there hasn't been a strong enough incentive to persuade all to do so. Similarly, sorting out and handling trash on a jetliner is inconvenient -- and once the jetliner gets to an airport, at present there are no facilities for handling the sorted waste, meaning that the airline itself has to do the entire job. Given the sort of economic pressure the airlines have been under, it's hard for them to want to expend resources on recycling.

The trick in changing the mindset is to show that recycling actually saves money, both in reduced dumping fees and returning revenue from valuable trash, such as aluminum cans. The development of improved trash sorting systems that allow airlines to simply toss "commingled" trash and have the machinery separate it is helping push matters along, and a few airlines are becoming more enthusiastic. Some environmental groups don't believe that a voluntary approach is going to work, however, and are lobbying for a law requiring airports that receive Federal funds to perform recycling.

* WIRED's Gadget Lab blog likes to run entries on clever or at least amusing variations on electrical power socket technology. They recently ran one power socket gimmick that looks like it might be a wave of the future: a dual US-style wall socket panel that also has twin USB power sockets, one off to each side to avoid interference between USB and power cables.

I had to think: Hey, I could use something like that! The gimmick only cost like ten bucks and no doubt it would be easy to wire one up. USB was never intended to be a power-plug standard -- but given the painful lack of standardization in power supplies for the flood of little gadgets we own, it's starting to become one by default.

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[WED 09 DEC 09] ECSTASY RECONSIDERED

* ECSTASY RECONSIDERED: As reported by an article in THE ECONOMIST ("Agony & Ecstasy", 18 December 2008), soldiers who have been through intense combat often suffer from severe emotional problems when they come back home from the wars, being plagued by insomnia, anger, broken relationships, an inability to concentrate. In recent decades, the psychiatric community has given the phenomenon a name: "post-traumatic stress disorder (PTSD)". In 2005, the US government was handing out disability payments for 72,000 American veterans afflicted with PTSD. A study released two years later estimated that 12% of American veterans from the wars in Iraq and Afghanistan suffer from PTSD; with 1.8 million troops sent to those theaters so far, that implies over 200,000 potential PTSD cases.

However, nobody has to go to war to encounter violent situations. One in 20 American men suffer from PTSD for some part of their lives; the ratio for women, who are targets for domestic violence and sexual assault, is one in 10. Two in five rape victims are diagnosed with PTSD six months after an attack. Fortunately, PTSD is treatable with drugs and antidepressants such as Zoloft, sometimes coupled with psychotherapy -- one approach being "exposure-based therapy", in which the traumatic events are replayed in safe surroundings to allow the patient to get perspective on the issue.

Unfortunately, conventional treatments fail about one time in four. A clinical trial of a promising new approach has been performed, involving use of an experimental drug along with psychotherapy. The trial, conducted by Michael Mithoefer -- a psychiatrist from Charleston, South Carolina -- involved twenty patients with PTSD who had resisted conventional therapy; after two sessions all demonstrated dramatic improvement. The major problem is that the drug, "methylenedioxymethamphetamine (MDMA)", is illegal almost everywhere. It's better known as "Ecstasy".

* There has been a resurgence of research in recent years in the use of psychoactive drugs like MDMA, LSD, magic mushrooms, marijuana and other banned substances for treating conditions such as anxiety, cluster headaches, addiction and obsessive-compulsive disorder. This work has been supported by private funds from a handful of organizations: the Beckley Foundation in Britain, the Heffter Research Institute, and the Multidisciplinary Association for Psychedelic Studies (MAPS) in America. Such research had come to a halt in the 1970s when the "war on drugs" became politically popular, first in the USA and then in the rest of the world. Over time, the authorities have become more flexible on research into the therapeutic uses of banned drugs, though the topic still remains politically controversial and policy tends towards the confused.

MDMA was first synthesized almost a century ago but was little noticed until the 1960s. Alexander Shulgin, a chemist at Dow Chemical in California who had invented Zectran, the first biodegradable insecticide, had been experimenting -- in every sense -- with mescaline and its chemical relatives. On a tipoff, he tried MDMA and found it "interesting". Shulgin left Dow to work on psychoactive chemistry full time, assisted by his wife Ann; over a few decades he synthesized hundreds of different chemicals, trying them out on himself and a group of volunteers.

In the late 1970s, the Shulgins introduced MDMA to Leo Zeff, a Californian psychotherapist who had worked on LSD therapies in the 1960s when that drug was still legal. Zeff was so impressed that he postponed retirement and became an enthusiastic advocate for the drug, which he called "Adam", introducing it in turn to a network of therapists in America and Europe. However, in the 1980s MDMA leaked out of the therapy network and ended being taken by young people for kicks.

The result was predictable: in 1985, the US Drug Enforcement Agency (DEA) classified MDMA under "Schedule I", the most restrictive category, with the category description including phrases such as "a high potential for abuse" and "no currently accepted medical use". Schedule I also includes marijuana, LSD, psilocybin, mescaline and heroin -- it should be noted that heroin is available under prescription in the UK and a few other countries, though other nations have followed the DEA's lead. Cocaine, amphetamines, opium, morphine and others are in "Schedule II", meaning they can be prescribed by doctors under DEA supervision.

Although a half-million doses of MDMA had been used in therapy to that time, the compound became illegal all over the world. Some therapists kept on using it; as Shulgin points out, it is very cheap and simple to synthesize. Ironically, once it became illegal, its recreational use exploded. The UN estimates that there are about 9 million MDMA users around the globe ingesting about 100 tonnes of MDMA and similar compounds a year -- not far off the estimate of 12 million heroin users and 16 million cocaine users.

In 1986 a student named Rich Doblin founded MAPS to push MDMA through the US Food & Drug Administration's drug-approval process. The process is time-consuming and can be expensive, but Doblin was energetic and took a grass-roots approach to the exercise, initiating a "Phase I" safety study at the University of California at Los Angeles in 1992. The results were positive, but when they were released in the mid-1990s the political climate had become more hostile. It wasn't until 2000 that Doblin met Mithoefer and work went forward towards a "Phase II" efficacy study.

Mithoefer began to perform treatments in 2004, using MDMA obtained from the only legal source, a Purdue University chemist licensed by the DEA to distribute controlled quantities of the drug. Subjects were given MDMA under supervision, lying on a futon, listening to music, and recalling their traumatic experiences. There's nothing new about revisiting a trauma as a therapeutic technique, but there's the possibility that the recollection may make the trauma worse. MDMA gives them a sense of perfect safety. The sessions with patients using MDMA were far more effective than the control experiment, using the same therapy and a placebo.

Several other Phase II studies organized by MAPS are about to start in Israel, Switzerland, and Canada. A "Phase III" trial, in which the therapy will be extended to many more therapists and several hundred patients, is still several years away. However, if Phase III trials work out, the DEA will then consider rescheduling MDMA. Nobody's guaranteeing that will happen, but advocates are confident there won't be any unpleasant surprises in the trials -- after all, the drug is in widespread use all over the world, and it is very well understood from a practical standpoint. In fact, extensive government research into the harmful effects of MDMA has produced a large body of high-quality papers that should be helpful in making the case to the DEA.

* With PTSD being a major concern to the military, clear evidence that MDMA really works in helping traumatized veterans may well get the armed services to sit up and notice -- after all, not only does the military want to keep faith with its people, the armed services also want to get a cure that will get those folks off the sicklist, with its ongoing expense. A military endorsement of MDMA might go a long way to bringing the drug back in from the cold.

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[TUE 08 DEC 09] FERAL PET PLAGUE

* FERAL PET PLAGUE: As reported by an article in AAAS SCIENCE ("A Cure For Euthanasia?" by David Grimm, 18 September 2009), people tend to love dogs and cats, but they don't always take good care of them. It's not unusual for pets to go wild -- there are an estimated 30 million feral cats in the United States alone -- and become a nuisance, with China and India plagued by rabid feral dog packs. Conscientious pet owners will neuter their pets rather than have them breed indiscriminately, but traditionally pets gone wild are simply killed. That's not only a cruel solution, it's not all that effective in keeping their numbers down.

What those concerned with the problem would like to see is a cheap, convenient way to sterilize feral cats and dogs, with a pill or vaccine. It's not an unrealistic idea, since such an approach has been used to control populations of some species of wildlife -- but so far nobody's been able to get the idea to work for feral dogs and cats. Now an American billionaire named Gary Michelson has set up a foundation armed with $75 million USD to address the problem, and researchers are coming out of the woodwork after the grant money. Ideas are being floated and some think there is a chance that progress may finally be made on the issue.

* The story of nonhuman contraception efforts goes back to Billings, Montana, in 1971, when two cowboys walked into the office of an assistant professor at Montana State University named Jay Kirkpatrick. The US Congress had just passed the "Wild Free-Roaming Horses & Burros Act", which restrained the notorious hunting of feral horses for pet food. The two cowboys were horse-lovers and applauded the principle of the legislation, but they were worried about a wild horse population explosion. They asked Kirkpatrick: "Can you make horses stop reproducing?"

Kirkpatrick was simultaneously dumbfounded and intrigued. To his knowledge, nobody had considered the notion of birth control for large wild animals before. Kirkpatrick took on the task, initially focusing on hormone treatments, along the lines of the classic human birth-control pill. His colleagues were skeptical at first, but in 1977 the US Bureau of Land Management granted him $300,000 USD to perform trials. The matter suddenly became much less silly, and over the next ten years Kirkpatrick did his best to get hormone therapies to work.

He did demonstrate that he could sterilize mares with steroid shots for a breeding season, but in the end that proved an impractical approach: catching the horses was troublesome and the steroids were shown to lead to cancers in zoo animals. In 1988, Kirkpatrick decided to follow up another line of investigation: "immunocontraception". The idea was to develop a vaccine to stimulate a female to the produce antibodies that would carpet her eggs, preventing them from being fertilized. The approach had been tried in humans but had proven ineffective. However, Kirkpatrick conducted a trial on Assateague Island, off the coast of Virginia and Maryland, where the horse population was primed to explode. A year later, thanks to baits loaded with vaccine, not a single foal was born. Kirkpatrick's phone began ringing off the hook. Since that time, the same vaccine has been used successfully to control the births of species from urban deer to sea lions.

* In the meantime, a movement for the surgical sterilization of feral cats and dogs began to emerge in the US. This effort proved successful enough to effectively eliminate the feral dog program in America. However, large numbers of strays are still euthanized every year, and it didn't work with feral cats -- they reproduce too fast. Feral cats are big problem in Australia, where they threaten endangered species. As mentioned, rabid feral dogs are a big problem in India and China, where civic workers organize sweeps through towns, using clubs to kill the animals.

Veterinary medical researcher Julie Levy, now at the University of Florida in Gainesville, decided that some better contraceptive approach was needed. She tried Kirkpatrick's vaccine; Kirkpatrick was confident it would work perfectly well in dogs and cats, but as it turned out, it didn't. She then tried a vaccine named "GonaCon", developed in 1994 by a US Department of Agriculture researcher, that produced antibodies against sex hormone precursors. It worked pretty well on deer, prairie dogs, and even kangaroos; a single injection could sterilize a female cat for five years, but it caused a nasty reaction in dogs. Later, she also began to work with a sterilant named "ChemSpay", which destroys eggs; it worked fairly well on feral dogs in a trial on the Navajo reservation, but it required multiple injections with cats, which was impractical because they were hard to catch. Both GonaCon and ChemSpay had potential for further development, but then the funding went dry.

* Enter Gary Michelson. Although his name is no household word, the retired spinal surgeon is one of America's richest men, thanks to a $1.35 billion USD payoff for surgical devices he developed. Frustrated by the whole animal-control problem, in November 2008 he set up the foundation "Found Animals" with $75 million USD to fund more research. So far the foundation has received dozens of proposals. The first to be funded is a research effort by neuroscientists Beverly Davidson of the University of Iowa, focused on developing a virus that would infect regions of the brain involved with fertility, shutting them down permanently.

Michelson believes it's possible there will be a real solution in a decade, but he acknowledges there are challenges: any product that emerges will have to be safe, effective, cheap, and easy to administer. As Levy and others warn, even if such a product appears, pet owners will still need to be responsible and neuter their animals. Everyone involved, however, hopes for success, and it's easy to sympathize: nobody has to be an animal rights advocate to feel uneasy at the slaughter of tens of millions of our household friends because we have let them become a nuisance.

ED: The biotech described in this article is fascinating but a little unsettling. The idea of developing viruses that could sterilize animals sounds like a premise appropriate for a doomsday sci-fi movie, with humanity rendered childless by a virus design gone wrong. No doubt the people conducting such research have considered that potential and understand the threat -- but that doesn't rule out the possibility of researchers deliberately working towards such bioagents under the sponsorship of a malign rogue state.

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[MON 07 DEC 09] SOUTHWEST ROAD TRIP (5)

* SOUTHWEST ROAD TRIP (5): On Saturday, 10 October, I went down to the Commemorative Air Force airshow. Incidentally, it used to be the "Confederate Air Force", but that was judged politically incorrect. Bit of a shame with the name change, really; the original name was just a gag, the organization having nothing to do with Confederate apologists or white trash supremacists. I can understand why the old name got the boot and can't really protest -- but "Commemorative Air Force" just doesn't have the same ring to it.

Anyway, I was thinking of getting there early and taking flightline pictures before the crowd built and crowded into the images, but I hadn't factored on the effect of jumping from the "late" side of one time zone to the "early" side of the next, and it was still dark at opening time. Worse, it was very foggy, not a good sign for an airshow.

Bell Model 47D helicopter

I went over after it started to get light and did some wandering around, taking shots of aircraft and some of the old military hardware -- they had a short-barreled Sherman tank and a DUKW amphibious truck, both of which I had been after for a while. There's a bit of a challenge in static shots, trying to get the best angle and lighting, which isn't always easy when the target is inconveniently positioned. There's a minor hazard, too, in that framing up the target sometimes leads to walking backwards to get it all in view, which if done absent-mindedly can result in an injurious fall. I never have fallen doing it, but I have to remember to be careful.

Unfortunately, the fog and the chill were discouraging, and I half thought to just leave -- but I wouldn't have had much to do at the motel, so that made no sense. After getting flightline shots, I just sat in my folding chair and shivered for a while; I was actually fairly well dressed for the cold, but it was damp and penetrating.

I figured that the fog would burn off about 10:00 AM; it didn't burn off until about 11:00 AM, and then the day turned sunny and pleasant. The aerial displays started after the sun came out. I quickly realized that the concern I had before the trip of simply duplicating the Chino airshow trip was justified; it all seemed slightly tiresome. I thought again of going back to the motel, but once more I realized I had nothing much to do there. So I got shots of the air displays, which is a challenge -- shooting a fast aircraft with a zoom camera is a bit like skewering a fly with a chopstick. I figured I'd endure until about 03:00 PM and then leave a bit early to miss the rush to the exit.

Rockwell B-1B

Most of the flight displays were done by 03:00 PM anyway, the only one I missed was a Navy Hornet fighter demo, which I wasn't that interested in. So, despite my misgivings I got in a full day at the airshow, and picked up some nice shots of aircraft I didn't have in my collection, most significantly of a Russian Antonov An-2 biplane and a brand shiny new EMBRAER Phenom bizjet. I also ended up with some nice flight shots of a B-1 bomber and a C-17 transport. Still, I realized that I wasn't likely to be going to another airshow for some years -- except for local ones, as long as they're free, and then I won't spend much time at them. Enough is enough.

* Sunday, 11 October, was just driving back to Loveland, Colorado, passing through Lubbock and Amarillo on the way north. It was a full day's drive back -- 1,145 kilometers (710 miles) -- and I couldn't take any long stops, but I had doubted even before I left home there was much to see along the way. As it turned out, I really wanted to get back home, and wasn't interested in taking any long stops anyway.

The chilly fog that had been in evidence the morning before lingered through most of the day as I went north, with the flat terrain covered by a sky of hazy featureless gray of indeterminable depth, the gray occasionally descending into mists that fogged my windshield. When I got to Boise City in the Oklahoma Panhandle, roughly the halfway point of the journey, the mist was coating signs with a thin layer of ice -- though fortunately the roads never got icy at all. Had it been a bit damper, the effect would have been murderous. I recall coming up from Corvallis, Oregon, to Spokane one wintry day when there were "black ice" conditions on the road, and it looked like a war zone, with wrecks alongside the road, including burned-out tanker trucks. It was one of the top ten frightening road trips I ever took and I have no wish to repeat it.

I actually found the grayness oddly pleasant -- surreal and hypnotic, making me lose track of time, which is all for the good on a long dull drive. In southeast Colorado I drove through a huge wind turbine farm, but for the most part all that was visible were the base posts of the turbines, climbing up to disappear into the gray. As I drove past the turbines nearest the highway, I could see their rotors spinning slowly in a dark half-invisible fashion through the murk, like eerie giants.

I finally got on Interstate 70 going west into Denver that afternoon, and the haze cleared away to reveal a pretty fall day, with sunshine and a partly cloudy blue sky. When I finally got back to Loveland, however, there was still snow on the ground from a snowfall the day before, and it was cold. I was amused; the snow was trampled up, clearly the neighborhood kids had been playing there. Not that I minded, there was little there they could damage or could do them injury.

The house was chilly. When I left, I figured the simplest thing to do with my new digital thermostat was to turn it off instead of lower the heat, but while coming back I got to wondering: If the heat's completely off, my house could freeze up. I was alarmed for a moment, then I realized that it had to get far colder before my plumbing might freeze and burst. It was a useful lesson to remember for the future, however. I cleaned up and went to bed.

* I had to judge that, overall, I wasn't interested in taking another trip along such lines for the foreseeable future. I wasn't unhappy with it, I had decided to go on the basis of limited expectations, and the trip met spec, even slightly exceeded it. All went well, it was cheaper than I planned, and not very time-consuming. It was certainly interesting to go through a region I'd never visited before. However, my interest in long road trips has clearly faded; it's now seeming more trouble than it's worth.

I did feel a bit better after I sorted through the photo haul, since I found I got some very nice shots. I'll still be doing my twice yearly trips to Spokane and I will probably take some side trips on them -- as long as I have to be on the road, finding interesting things to see is all for the good. I might be inclined to take a few three-day trips as well; indeed, since the drive to Albuquerque is very reasonable, I might just go down and catch the balloon fest some year.

It was certainly nice to get away from the usual routine for five days. When I get home I'm always surprised at how it takes me a couple of days to get back into juggling everything I'm trying to get done. Even with such a short absence, the first day back I had piled up dozens of bookmarks of online articles I needed to sort through. The internet is just a big pipeline for information -- stop draining it off for a few days, and it piles up. [END OF SERIES]

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[FRI 04 DEC 09] THE IMMUNE SYSTEM (5)

* THE IMMUNE SYSTEM (5): The adaptive immune response is subdivided into a "humoral" arm and a "cell-based" or "cell-mediated" arm. They're not entirely distinct, with some immune system players contributing to both and communications taking place between the two arms, but it can be said in general that the humoral arm performs direct attacks on pathogens, the main weapon in the attack being antibodies generated by B cells. The cell-based arm, in contrast, destroys host cells that have been infected by pathogens instead directly attacking the pathogens, with the primary weapon being the killer T cell.

* The humoral arm of the immune response is initially put in motion by dendritic cells, which absorb intruders and then migrate to the lymph nodes, where they present antigens from the intruder on their MHC II receptors. The lymph nodes contain many different strains of B cells, with each strain able to make one specific antibody. The B cells are covered with receptors that are identical to the antibody the cells produce, fixed to the cell surface -- whatever antigen the antibody a particular strain matches, the receptor on that strain matches the antigen in exactly the same way.

Some strains of B cells may have a high "affinity" for a particular antigen and match almost perfectly; others may have a low affinity and barely match at all; while the rest will have intermediate affinities, matching to some greater or lesser degree. If the antigen is from an intruder encountered in a previous infection, there will likely to be a strain of "memory" B cells present that has a high affinity for it and match it easily. If the antigen is unfamiliar, the body not having encountered that specific invader before, there will still be some B cells in the pool that match to an extent.

In any case, the B cell strains with an affinity for the antigen presented by dendritic cells are activated, to then present the antigen themselves on MHC II receptors. The B cells can't do anything just yet; they have to present the antigen to get an OK from a strain of helper T cell that matches the antigen-MHC complex. In effect, a B cell is saying: "Here's a target -- is it OK for me to produce antibodies to attack it?" This arrangement helps prevent "rogue" B cells from accidentally producing antibodies that attack self. Matching helper T cells bind to the MHC II complex and then start producing lymphokines. These lymphokines are a "green light" for the activated B cell strain to start producing antibodies, and also drive the B cell strain to reproduce rapidly. Some are clones of the original B cell, but along the way the clones produce plasma cells, which cannot reproduce; they exist simply to churn out the proper antibodies.

There may be more than one B cell strain with a match, but the strains with the greatest antigen affinity replicate the best and quickly predominate. This scheme is known as "clonal selection", but as described it has a problem. When clonal selection theory was developed in the late 1950s, the general assumption was that there was a massive range of strains of B cells ready-made, and so there was a strain available to meet almost any threat. Doubts began to accumulate when it was realized just how diverse the range of possible antigens was, demanding a comparable diversity of receptors -- the possibilities were astronomical. Doubts got worse when it was realized that the human genome only encodes a few tens of thousands of genes, nowhere near enough to define a huge range of different B cell strains.

From the late 1970s it was realized that B cells have three classes of genes -- designated "V", "D", and "J" -- with dozens to hundreds of members in each class. An antibody configuration is specified by a gene stitched together with one V, one D, and one J segment. The possibilities are appropriately astronomical, and greatly boosted by spontaneous variations in small snippets of DNA that link together the segments. As B cells replicate, "VDJ recombination" generates a range of "mutant" B cells with unique antibody configurations -- billions of possible combinations, enough to cover any possible antigen. Some of the mutant B cells have lesser affinity than their parents and tend to die out; other mutants have greater affinity and will be selected for production of antibodies in the next cycle of the humoral immune system operation. This cycle is repeated over and over, with each generation producing a better match. The adaptive immune response evolves, adapts, over time.

In any case, the antibodies generated by the activated B cells circulate through the bloodstream and link up with the targeted antigens on the intruders. In some cases, the antibodies may gum up the operation of the pathogen; more often, they opsonize the intruder, marking it for attack by macrophages and other immune system weapons. [TO BE CONTINUED]

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[THU 03 DEC 09] SCIENCE NOTES

* SCIENCE NOTES: As reported by AAAS SCIENCE, a team made up mostly of Chinese scientists has published the latest genome sequencing exercise, which targeted one of the most venerable domesticated animals: the silkworm. The study obtained the genomes of 29 domesticated and 11 wild silkworm variants, with an eye towards both learning about the history of the silkworm's domestication and improving silkworm husbandry.

From archaeological evidence, silkworms are believed to have been domesticated about 5,000 years ago. The genetic analysis showed that domesticated and wild variants are clearly genetically different, which is no great surprise -- in contrast to their wild cousins, domesticated silkworms spin giant cocoons, tolerate crowding, don't mind being handled, have no fear of predators, and cannot fly when they become moths. The genetic data also implies the domesticated line was obtained from a single domestication event. The genomic data may be used to make silkworms easier to handle and more productive, or help domesticate other insects.

* In slightly related news, WIRED Online had an article on a beautiful woven cloth, about the size of a double-length beach towel, on display at the American Museum of Natural History in New York City. It is a unique piece of fabric, made entirely from the silk of Madagascar golden orb spiders. The spiders are not adapted to domestication and it took four years of work by 70 people to obtain the golden silk from roughly a million spiders.

spider cloth

The spiders were collected by handlers -- carefully, since the spiders bite -- and yoked in gangs of 24 to a special silk-harvesting machine developed over a century ago by a French missionary living in Madagascar. After the silk was drawn, the spiders were released; they could be harvested again after a week. The silk was spun into 96-filament thread and then woven into the cloth. The cost wasn't mentioned -- one hates to think of it. Work continues on synthesizing the spider silk or genetically engineering more tractable creatures to produce it, but so far no joy.

* Jumping off on another tangent, an amateur fossil hunter named Jamie Hiscocks scrounging the beaches of Sussex in the UK found a beautiful piece of amber with a spider and remnants of the spider's web encased in it. The amber was dated back 140 million years, to early in the Cretaceous period, the last part of the great era of dinosaurs. This is the oldest spiderweb fossil found so far; there's no web in it as such, but the silk is very evident, displaying little sticky "beads" like those on the silk of modern orb spiders. There are other pieces of amber in the deposit discovered by Hiscocks and paleontologists are eager to probe into it. The story is interesting not only in itself, but in its demonstration that amateurs still have a significant place in the advance of science.

spider in amber

* On yet another tangent, the science blogs were running a story on a newly discovered animal named Bagheera kiplingi, a species of jumping spider that has a unique distinction: it is the only known spider that isn't a predator. It feeds on "beltian bodies", which are nutritious little nodules acacia plants grow to attract ants that help defend the plant. The spider is a freeloader, eating the nodules but not contributing to the defense of a plant. It also occasionally eats ant larvae. In addition, it seems to have another unique distinction: it is the only spider known that provides parental care for its young.

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[WED 02 DEC 09] BIG PHARMA GOES GENERIC

* BIG PHARMA GOES GENERIC: As reported by an article in THE ECONOMIST ("Friends For Life", 8 August 2009), the big pharmaceutical companies have been under serious political pressure for being part of the problem of rising health costs -- with the growing availability of cheaper generic drugs only increasing the embarrassment of "Big Pharma". Generics have been such an annoyance to Big Pharma that major pharmaceutical firms have sometime paid off generics companies to delay production of drugs that have gone off patent.

Regulators in the USA and the EU have been cracking down on the "pay for delay" game, while governments have been liberalizing drug markets, giving the generics makers even more of an edge. To make matters worse for Big Pharma, a record number of drug patents are due to expire soon, with one estimate claiming that about half of the almost $400 billion USD of patented drugs sold in 2009 will lose patent protection by 2015. It is estimated that in America, where Big Pharma is least protected from the generics, the price of a drug is likely to fall 85% within a year of patent expiration.

One defense Big Pharma has adopted is to push "branded" versions of drugs that have lost patent protection, selling them for higher prices than generic equivalents. Label recognition actually has a certain amount of value honestly worth a higher price: a drug that doesn't work can be almost as dangerous as one that's defective, so if doctors and patients aren't sure of a generic, they'll stick with the known brand. Such is the power of brand loyalty that even once patent protection lapses, the firm that held the patent can retain half the market.

Some Big Pharma firms have adopted the tactic of "if you can't beat them, join them" -- that is, hooking up with generics makers. The appeal is in penetrating emerging economies, where future growth in sales is expected to take place and generics are seen as the norm. Given that emerging economies have problems with product piracy -- a particular concern to consumers when it comes to drugs, since pirate drugs can be lethal -- a branded product has some appeal that can justify a higher price. Big Pharma firms such as the UK's GlaxoSmithKline and America's Pfizer have been striking deals with generics makers in India and elsewhere.

There's skepticism over such marriages. Big Pharma firms are dinosaur bureaucracies, powerful but slow moving; generics makers are startups, agile but lacking depth. There's a threat of getting the worst of both worlds in such matings. There is also the fact that generics live in a world of thin price margins on which Big Pharma, with its overhead, cannot survive -- but Big Pharma brings the brand name into the game, and the generics know that can count for a great deal.

* In related news, another article in THE ECONOMIST ("Shot In The Dark", 3 October 2009) discussed how Big Pharma has also been jumping into the vaccine business in a major way. Abbott Laboratories, a US-based Big Pharma firm, recently paid Solvay, a Belgian firm, $6.6 billion USD to obtain the company's vaccine and other pharmaceutical operations. Other Big Pharma players, like Johnson & Johnson, Merck, and Pfizer, have also struck vaccine-related deals in recent years.

This is something of a turnaround. While anti-vaccination activists have made a fuss over the massive profits made by Big Pharma in vaccines, in reality vaccines have traditionally been a commodity business with low margins, and not long ago the trend in Big Pharma was to get rid of vaccine production units. However, that meant the vital business of manufacturing vaccines was dying out, and so Big Pharma and governments came to an arrangement, the deal being that paying $100 USD a dose for new vaccines against afflictions like the papilloma virus would help promote investment in production facilities and development -- while being far cheaper than coping with the diseases if they weren't headed off.

With scares in the last few years over bird and swine flu, vaccine production is now immensely profitable. The "antivaxers" like to claim that Big Pharma is pushing governments to accept vaccination programs to give the companies big profits, but that can be seen as sideways read on things: governments are throwing money at Big Pharma as a subsidy so the companies will be willing to work on vaccines.

There are potential pitfalls. Vaccine development tends toward the expensive, but with many players jumping in, the result may be overproduction, particularly if public health scares fall off. The other big problem is popular resentment of seemingly cozy deals with pharmaceutical companies. Big Pharma is already under political pressure to cut vaccine prices and reveal proprietary processes so others can produce them. Unfortunately, if the result is to push Big Pharma to dump vaccine operations, we may end up right back to where we started from.

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[TUE 01 DEC 09] ANOTHER MONTH

* ANOTHER MONTH: The prime movers behind the popular Discovery Channel MYTHBUSTERS show, Adam Savage and Jamie Hyneman, noted for amusing debunkery that often involves making things go BOOM, were part of a group that visited the White House recently for a science-related function. President Obama called out to them: "I hope you've left the explosives at home!" The Mythbusters duo have now been immortalized by Savage and Hyneman's Law: "Blowing stuff up is fun. Blowing stuff up in the name of science is AWESOME!"

Mythbusters

* I finally managed to get all the old blog archives threaded with hyperlinks, mostly to hook up the installments of the Monday and Friday serials. This wasn't just fuss. Traditionally, when I archived newsletters or the like I was just stowing them away to gather dust, and I more or less forgot about them. Now I'm linking back from new blog entries to old entries on a normal basis to provide more "dimension" -- and that means making the archives easier to navigate, not to mention cleaning them up and maintaining them.

* Sigh, the lunatic fringe ... the whole flu vaccine fury seemed to go on the back burner after flaring up in October, but such controversies do tend to mutate off into bizarre directions. For example, there is a faction which is promoting the idea that vaccines are being used to administer, or at least prep, global populations for injections of nanochips. The conspiracy theorists aren't stopping there either, claiming that nanochips are being developed or are available that can migrate into the brain and then implant themselves as mind control devices -- or, to get even more sinister, pull the same trick on a baby in the womb. I would find this premise too preposterous and cheesy to buy as a "made for SyFy Channel" movie plot device.

ALL GLORY TO THE HYPNOTOAD!

Apparently, one of the big proponents of the nanochip vaccine theory is David Icke (pronounced "Ike"), a Briton who was once a footballer, became a sports announcer after being put out to pasture, and then went so far around the bend that he can't find the bend anymore -- claiming among other things that the power elite behind the Global Conspiracy are descendants of reptilian aliens. There are suspicions that by "reptiles" Icke actually means "Jews", but that hardly makes the notion much more palatable.

The British have a tradition of tolerance for eccentrics and seem to find Icke amusing; he ran for a local office and came in twelfth, with 110 votes, probably most of them cast for a laugh. However, apparently not all are so tolerant: Icke has been keeping a lower profile after finding out he couldn't walk the streets without people pointing at him and saying: "Look, there's the nutter."

Incidentally, concerning the relatively recent conversion of the USA to digital broadcast TV, some of the lunatic fringe believe that was a conspiracy too -- the converter boxes that people bought to hook up to their old analog sets were mind-control devices. Well, since I never bought a converter box, I figure I'm safe on that score. But now I'm wondering ... would it be safe to buy the Blu-Ray video player I've been looking at? Hey, if they can put mind-control systems in a set-top box, they can put one in a video player. And what about my phone? Alarm clock? Desk lamp? How about the toaster?

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