sep 2006 / last mod jan 2018 / greg goebel

* 21 entries including: farming infrastructure, Operation MUSKETEER, genetic toolkits, ISS progress, defense contractors and Iraq, ethanol considered, Athabasca tar sands, crooks against car security systems, robot surgeons, Freedom tower, 911 conspiracies, smart buildings, fighting AIDS, London Ring Of Steel, Moscow spammer, and GI blogs.

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* INFRASTRUCTURE -- FOOD & FARMING (8): As described in the last installment, center-pivot irrigation wastes land, but there is a way to cover all the land, using pretty much the same arrangement of pipe segments and A-frames, rolling in a straight line instead of a circle. The difficulty here is that the source of the water to the sprinkler system has to move, so a hose connection is used, or the water is pumped out of a ditch.

The "side-roll" irrigator seems to be along the same lines, with pipe segments mounting sprinkler heads, but the A-frames are replaced by large circular spoked wheels, with the pipe running through the center of the wheel. Since the sprinkler heads are fixed to the pipe segments, it would seem hard to understand how the assembly moves along, since the heads would turn over. The answer is that it's not moving, at least not normally. The farmer operates it one place, then shuts it down and uses a little four-wheeled "cart" operated by a small motor to roll the sprinkler system farther down the field, to be set up and run from its new position.

side-roll irrigator drive motor

One simple approach to field irrigation is to use a big central water cannon. Some are powerful enough to spray hundreds of meters. They can also be mobile, moving across a field on a platform drawn by a cable and winch, with a big water hose trailing behind.

There's a form of irrigation known as "trickle irrigation" that's particularly efficient in its water usage. It involves snaking tubes through the fields, with the tubes fitted with miniature nozzles that are spaced to deliver water precisely to each plant in the field. The scheme, which was invented by the Israelis, puts the water where it's needed, but trickle irrigation is also labor intensive.

* One of the problems with irrigation is "salinization". Irrigation water is never pure, and when it evaporates it leaves behind salts, gradually rendering the soil infertile. That means that some of the water must be allowed to drain off, carrying the salts with it, instead of evaporating in a field. Salinity problems get worse in arid regions, since there's not a lot of water to spare for drainoff, and at low spots in fields, where the water doesn't drain off easily.

In southern California, drainoff water is accumulated in "evaporation ponds" that are fed by underground pipes from the fields. The water in the ponds evaporates and leaves the salts at the bottom. The ponds reduce productive acreage and there is also the problem of dealing with the residues, but it beats ruining the fields. [TO BE CONTINUED]



* GIMMICKS & GADGETS: As discussed here in May, Nicholas Negroponte of the Massachusetts Institute of Technology's Media Lab has been pushing the "One Laptop Per Child (OLPC)" computer, a concept for a laptop computer that would cost about $100 USD and be supplied in the tens of millions to poor communities all over the world. The idea did not meet with universal enthusiasm, and the technological concepts he had been pursuing ran into some obstacles.

Instead of becoming discouraged, Negroponte called in some heavy support, in the form of Yves Behar, a well-known Swiss-born industrial designer who works from San Francisco. Behar came up with a new OLPC design, which was highlighted in the August 2006 issue of WIRED magazine.

Behar's OLPC is reconfigurable, with the tablet configuration providing a good starting point for a tour. In this format, it looks like a tablet computer, with a fixed handle on the near side, which also handily stores a shoulder strap; a speaker grille on one side of the display and a mike grille on the other; a little cursor control; and an unidentified item that looks possibly like an infrared interface. The display provides 640x480 color resolution with LED backlighting indoors, switching to 1200x900 grayscale resolution in direct sunlight.


"Ears" flip up from the top corners to act as antennas for an 802.11b/g wireless networking scheme, with interface jacks for headphones, networking, and so on exposed when the ears are deployed. A wireless mesh networking scheme allows communication with other OLPC machines in the neighborhood, with relays between machines permitting communications over a town. Voice IP facilities are built in, allowing the OLPC to be used as a phone.

If the user needs a laptop configuration, the display module can be pivoted up and turned around to reveal a keyboard with a large touchpad at the bottom. The guts of the machine are in the display module; the baseline is a 366 MHz CPU with 128 MB of RAM and 512 MB of flash ROM, running a stripped version of Redhat Linux. The mesh network links the machine to a local server with 200 GB of disk space and connections to the outside world.

Flip the display back down and the OLPC is packed away in a damage-resistant transport configuration, protected by its rubberized plastic casing. 31 different case colors will be offered, helping reduce theft. The overall weight is about half that of a conventional laptop. The price is given at $140 USD in the short term.

* I've run across other articles on the OLPC, with one pointing out a potential pitfall that seems obvious in hindsight: think of millions, hundreds of millions of cheap computers all over the world, with effectively the same hardware and OS, plus wireless networking ... ahhh, maybe there's a potential security problem there? Work is being performed on the security issue, with the OS designed to resist worms and phishing attacks. Upgrades will be automatically performed over the wireless network and the simple OS will be easy to reinstall if it's corrupted. Applications will be run in a protected environment to ensure that their access to critical system functions is restricted.

* According to an article from CNET.com, Hitachi is now offering a new line of hard disk drives -- for cars. The rugged "EnduraStar" drives can have capacities of up to 50 GB and can tolerate shock or environmental conditions that would wreck a conventional drive. They use fluid dynamic bearings for the motor, not the usual ball bearings. Hitachi has also unveiled a new 6.3 centimeter (2.5 inch) slimline hard disk, the "CinemaStar", with perpendicular recording and a capacity of 160 GB. It is intended for digital camcorders.

* A programmer for Apple Computer named Andrew Carol has come up with one of the gimmicks of the year. In the 19th century, British researcher Charles Babbage came up with a series of mechanical computers, including his "Difference Engines", which were built to crunch through polynomial equations such as:

   f(x)  =  Ax^2 + Bx + C

Carol was inspired by Babbage's Difference Engine Number 2, which Babbage designed on paper but wasn't actually built until 1991. Carol decided to build a new implementation using Lego pieces. Babbage's design was heavily based on vertical rods; Carol couldn't get that approach to work with Legos, but he was able to construct equivalent functionality with Lego gears.

Carol's Lego difference engine

The end result is a framework strung with gears and chain drives. Carol would like to go on and implement his own take on Babbage's general-purpose computer, the "Analytical Engine". It might be a big job: Babbage never got his own engine to work.

* The technical press has been making a bit of a fuss about the latest incarnation of the Universal Serial Bus (USB), the connection scheme introduced in 1998 that took a big step forward in making PCs easier to interface with devices. In maturity, most USB devices simply plugged in and ran, using a straightforward cabling scheme. The fact that this was surprising at the time showed how bad things really were.

The original USB spec ran at 12 megabits per second. It was followed in 2002 by "USB 2.0", which runs at 480 megabits per second. Now manufacturers are preparing to introduce a "wireless USB (W-USB)" scheme that even eliminates the cabling. W-USB uses a spread-spectrum wireless communications scheme, also operating at the 480 megabit per second transfer rate. Initially, a W-USB interface will be implemented as a "dongle" that plugs into a standard USB port, with built-in interfaces available on PCs down the road.

There was some political difficulty in establishing the spec. Manufacturers split into two camp: the Intel-led WiMedia Alliance and the Freescale-led UWB Forum. WiMedia is backed by Sony, TI, HP, and Samsung, and it appears that the UWB Forum has faltered, so the current vision is that WiMedia is going to be the winner in W-USB war. WiMedia backers are now preparing to introduce W-USB devices under the "Certified Wireless USB" tradename.



* ISS IN PROGRESS: The history of the International Space Station (ISS) has featured its ups and downs, but as reported in AVIATION WEEK ("Global Crossing" by Frank Morring JR, 21 August 2006), the outpost is now on track for completion.

When the NASA space shuttle Columbia broke up on reentry in 2003, putting work on the ISS on hold, the station had been built up to a preliminary operational capacity, with four pressurized modules -- two American, two Russian -- powered by a single large solar array, with heat dumped into space by a radiator system using liquid ammonia as a working fluid. The flight of shuttle Atlantis this September, mission STS-115, restarted construction with installation of a "P3/P4 truss" carrying a second solar array. This was a major component of the station; the payload weighed 15.9 tonnes (17.5 tons) and filled up the shuttle's cargo bay. After installation, it extended its solar panels to a span of 73.2 meters (240 feet).

ISS on departure of Atlantis STS-115

The shuttle is the only vehicle with the capacity to fly main ISS assemblies, and 15 more shuttle flights are planned over the next four years to bring the station to completion, lifting payloads that will double the size of the station. The interruption in shuttle missions means that all the elements are now at Kennedy Space Center in Florida, being tweaked, checked, and lined up for launch. They include:

The ISS has long been controversial, with critics charging that it provides no value proportional to its cost, but at least the program is not spinning its wheels for the moment, burning up funds and going nowhere. Given its spotty past, everyone will breathe a sigh of relief when the last elements are put in place in 2010 and the aging NASA shuttle fleet is retired.



* BAD FOR BUSINESS: Although it is something of a slogan on the Left that war is good for defense businesses, as reported in THE ECONOMIST ("Collateral Damage", 26 August 2006), the war in Iraq is now having negative effect on some of America's biggest defense contractors. In the early days of the Bush II Administration's Global War On Terror, there was little limit on defense spending and the revenue of defense contractors grew steadily year to year, with funding provided for the latest high-tech weapon systems. Now the administration is facing fiscal reality and is being forced to make choices.

As long as the US remains in Iraq, the war there will be on top of the priority queue. That would seem to be a nice thing for defense contractors, and it is -- for those who provide services for the military in the combat zone, or supply ammunition and weapons for the fight. The problem is that the US military likes to obtain advanced-technology weapons to make sure that America will be able to keep an edge over an adversary also armed with the latest technology, and that's not the kind of adversary being encountered in Iraq. To be sure, advanced technology is being used in the fight, but not in the form of the big-ticket leading-edge weapon systems.

For example, the US Army had put heavy funding into the RAH-66 Comanche armed scout helicopter program, initiated late in the Cold War. The Comanche was a stealthy, computerized high-tech marvel that featured every whizzy feature short of telepathic mind control, but with the end of the Cold War it was overkill. The Army needed useful, cheaper weapons in quantity quickly and killed off the Comanche, seeking to replace it with an off-the-shelf solution based on existing light helicopters. Another effort to develop a stealthy robot helicopter gunship was also axed, with the Army now instead interested in acquiring the Firescout -- a robot gunship derivative of the long-established Hughes / Schweizer 300 civil helicopter.

Northrop Grumman Firescout

The US Air Force has similarly been spending large amounts on the Lockheed Martin F-22 Raptor fighter, whose development was also begun late in the Cold War, to counter improved fighters expected to be fielded by the Soviets. The threat it was supposed to counter evaporated, and though the Air Force has so far successfully protected the program as insurance against the emergence of advanced threats in the future, the very expensive Raptor has no particular relevance to the war in Iraq. The big aerial star in the conflict has been the Predator, a piston-powered drone that can carry cameras and a few Hellfire missiles. The Predator isn't low-tech either, with the Air Force now obtaining a turboprop-powered Predator B / Reaper that can carry much more warload -- but nobody would put it in the class of sophistication with the Raptor, and it's far cheaper.

The sign that cutbacks for the big-ticket weapon systems were now going to bite came in August, when Boeing announced the shutdown of its California production line for the C-17 airlifter. The Pentagon had no more orders and export sales had been modest for the big transport aircraft. In the meantime the Army has been working to obtain a light cargolifter, in the form of an off-the-shelf twin turboprop machine, under the Future Cargo Aircraft (FCA) program. The FCA is what the service needs in Iraq to move around without being hit by roadside bombs; the C-17 is nice but not the thing needed on the firing line at present.

The Army, however, is under pressure with the development of the "Future Combat System (FCS)", which is not so much a weapon system as a "system of systems" -- a set of vehicles, weapons, electronics, and software all tied together. The cost of the FCS has doubled since its startup, to about $165 billion USD, and Congress has been taking a critical look at the program. The Army has defended it, issuing a report saying that the prime contractors, Boeing and Science Applications International Corporation (SAIC), are meeting schedule and doing a good job. The FCS is likely to be refocused to address the counter-insurgency mission, though given the broad nature of the program that might just be a question of putting the right spin on the existing effort and making a few trims to the wind here and there.

Cutting defense programs is always difficult, not merely because the military wants to be prepared for the next conflict -- which as history shows can't be expected to be along the same lines as the previous one -- but because politicians like to protect defense contracts that feed their constituencies. However, given the need to fight a troublesome Mideast war on a limited budget, something's got to give someplace.



* OPERATION MUSKETEER (2): The French found the collapse of MUSKETEER in the face of US opposition a bitter cup to swallow. Once again, "perfide Albion" had sold them out: when push came to shove, the British would always side with their overbearing American cousins. To hell with the British, then. France would seek alliances elsewhere to counterbalance the damned Americans and neutralize their British stooges.

It didn't take long to find friends, either. According to French Foreign Minister Christian Pineau, when Mollet got the call from Eden on the evening of 6 November calling off MUSKETEER, German Chancellor Konrad Adenauer was in attendance. Adenauer was blunt: "France and England will never be powers comparable to the United States ... Not Germany either. There remains to them only one way of playing a decisive role in the world: that is to unite Europe ... We have no time to waste; Europe will be your revenge." No time was wasted, with the six-member European Common Market created the next year, in 1957.

The European Common Market evolved into the modern European Union, with the French, under Charles de Gaulle, doing everything they could to keep the British out of the emerging alliance, until the UK finally managed to acquire membership in 1973. Even after that, British participation often focused on limiting the influence of the French and Germans in the exercise. During the 1960s, the French also built up their own strength to counter American dominance, acquiring a nuclear deterrent force without US assistance and withdrawing from the NATO command structure in 1966.

* Britain and particularly Anthony Eden suffered the worst from the backlash. Anglophobes had always seen the British as sneaky doubletalkers, and Eden had given them an example of such conduct based in indisputable fact. To complete the ugly circle, he had lied to his own people as well. Eden was forced to resign, crushed in spirit and health. He went to Jamaica to recuperate at the house of his friend, writer Ian Fleming, whose Agent 007 -- "Bond, James Bond" -- would become a 1960s icon.

The adventures of James Bond would portray the "special relationship" between the UK and the US in that era in a way that flattered the British: cool, suave, daring James Bond played off against his CIA counterpart, Felix Leiter, who could accomplish little except reliably charge in at the finale with reinforcements to crush the evil legions of SPECTRE in a grand cinematically choreographed battle. The Tommies had the dash, the Yanks had the muscle.

The reality was not necessarily so inspiring. The Suez Crisis had finally erased the last substantial traces of British imperial ambitions. From that time on, the British would never cross American strategic interests. The next year, in 1957, Harold Macmillan, the new British prime minister, met with Eisenhower in Bermuda to come to an agreement that dovetailed British strategic planning with American plans. Eisenhower did his best to reassure Macmillan that the US valued the relationship with Britain, working to smooth over the rift that the Suez crisis had opened between the two countries, and the British were eager to go along.

Too eager, possibly. It would take time for Britain to even try to differ with the US, with the country long suffering from a "Suez syndrome", in which, as British Prime Minister Margaret Thatcher put it, the leadership "went from believing that Britain could do almost anything to an almost neurotic belief that Britain could do nothing." Lady Thatcher would have none of it, setting a style of spine and assertiveness, even on occasion giving her good friend and ideological soulmate, US President Ronald Reagan, what one witness called a "good hand-bagging" over disagreements in policy.

The old special relationship with the Americans remains in obvious strength, but though it's apparent who the more powerful partner in the arrangement is, it is still clearly a partnership. The British know they have more influence in Washington than any other nation, with an important say in the partnership that commands respect.

* The Israelis had reasons to be satisfied with the 1956 war, having shattered Egypt's new arsenal of weapons to give Israel some breathing space before the Egyptians regrouped. However, the Israelis were forced to withdraw, the US taking a harder line against them than would ever be taken again, and the conflict seeded the perception in the West that Israel was a bully and aggressor. Soviet influence in the Middle East was greatly strengthened, much as Eisenhower had feared.

Nasser was the biggest victor over the short term, coming out as a hero who faced down Western imperialism. The fact that Egypt's army had been thrashed and it was the Americans who had put a stop to things was glossed over. Nasser became overconfident, building up his "Arab nationalist" dreams on the basis of an increasingly authoritarian and bureaucratic society. It was far more show than substance, with the shell shattered in 1967, when the Israelis utterly defeated their Arab neighbors in a six-day lightning war that held up the weakness of Arab nationalism for all the world to see.

* It is difficult to pin down any specific lessons from the Suez Crisis of 1956. George Santayana famously said that those who do not remember the past are condemned to repeat it, but Anthony Eden remembered the past only too well, and ended up condemned anyway. The past has its lessons; but it may not always be easy to apply them through the fog of the present. [END OF SERIES]



* INFRASTRUCTURE -- FOOD & FARMING (7): Irrigation is regarded as one of the foundations of civilization, allowing cities and nations to stay fed by ensuring a relatively stable water supply. Increased agricultural productivity due to irrigation meant that societies could support city dwellers who didn't raise food themselves, allowing specialization of services, and setting up extensive irrigation systems also implied a level of civic organization to plan out the systems and build them.

The oldest irrigation scheme is the "canal and ditch" approach, with water diverted into a canal and then into branching ditches in the fields. It demands considerable planning and work to set up such a system; the canals and ditches must be dug to the right hydraulic grade and the fields carefully leveled to make sure the water is evenly distributed. The task is complicated, and in many locales in the USA it is controlled by a district irrigation board, which occupies a middle ground between private concern, public utility, and elected governmental apparatus.

In the US, farmers are allocated water by the irrigation board in terms of "acre-feet", meaning they get that many feet of water for each acre on their land, the water being parceled out over the growing season. Water distribution is controlled by gates and weirs, with some used to balance the water flow through the network, and others --"headgates" or "delivery gates" -- used to dump water into the fields. The gates are activated according to a preplanned schedule.

The main alternative to canal and ditch irrigation is sprinkler irrigation. Sprinkler systems tend to lose more water by evaporation, but they are easier to maintain and can work on uneven ground. While some agricultural sprinkler systems aren't much different in concept from those used for maintaining lawns, out here in the West and the Great Plains the predominant approach is the "center pivot" sprinkler system.

I recall flying back to Colorado on a jetliner with a family from Massachusetts, with the parents behind me and myself chatting pleasantly with their two cute little girls on the seats next to me. They were all very puzzled by the way the fields were laid out, organized as squares with the crops growing in big circles inside them. I explained the center-pivot system to them, though I got it a bit wrong. The facts are that the scheme was invented in the 1950s by a farmer from eastern Colorado named Frank Zybach. It involves a long string of pipe segments, with an A-frame mounting two wheels at each joint of the segments and spray sprinklers hung from the pipes. They often have an oscillating sprinkler head -- the kind often seen in public parks, spraying back and forth over an arc -- at the end to extend the sprayer's reach.

The sprinkler rig is connected to a fixed pivot at the center that feeds it water as it slowly circles around the field. This was where I dropped the ball in my explanation, thinking that there was a little "pony motor" on the end that moved the thing around. This was a DUH in hindsight, since the rig is too flexible to be moved around in such a way; it would buckle up immediately. The reality is much more interesting.

Each A-frame is actually powered. This immediately leads to the other problem of how to synchronize the motors, since the A-frame on the end will have to move much faster than the A-frame in the center. It was Frank Zybach's genius to make the problem go away. The outermost A-frame is set to the desired operating speed, and it then moves around the circle at its slow pace. None of the other A-frames move at all -- until the joint between the outer segment and the next segment inward reaches a certain deflection, activating a switch that turns on the inner A-frame. This segment rolls until it activates the A-frame on the next inward segment, and so on.

The center-pivot rig doesn't move in nice neat lockstep fashion, but it doesn't have to. The rig can cover a complete circle in as little as half a day, but it usually performs a rotation once every three or four days. It moves so slowly that the rig never seems to be moving at all. The motors running the A-frames don't have to be very big, since they are heavily geared down.

Since the rig moves faster at the end than in the center, if water were dispersed evenly along its length, the field at the end would end up dry and the field at the center would end up waterlogged; in addition, water pressure drops over the length of the line. The trick is to put fewer and smaller sprinkler heads closer to the center. It's a bit hard to observe the spacing since the rig is so long, but when driving down a tall hill with a good view of the fields below, the progressively increasing density of the spray pattern out to the end of the rig is apparent.

center-pivot sprinkler system

Center-pivot irrigation means that the field can be left clear of fixed or semi-fixed irrigation pipes that would be an obstacle to farm machinery. The center-pivot rig does mean a round field in a square plot, wasting about 20% of the land, but it's usually marginal land that wouldn't be worth too much without irrigation and so the loss is tolerable. Center-pivot irrigation is now used in other dry climates elsewhere; in places where land allocation is not based on a tidy rectilinear grid, a hexagonal grid is used instead, cutting the lost land down to 10%. [TO BE CONTINUED]



* ETHANOL CONSIDERED: As discussed by an article in DISCOVER magazine ("Life After Oil" by Robb Mandelbaum, August 2006, 54:61), the attempts by boosters of ethanol production to proclaim it the future for US fuel supplies, capable of eliminating American reliance of fuel imports, have not been overwhelmingly persuasive. However, a closer look at the details suggests that they may have something to say worth listening to.

There was quite of bit of suspicion when US President George W. Bush announced that the goal of Federal work on ethanol was to reduce our oil imports from the Middle East by 75%, but that statement turned out to be not as dramatic as it sounded up front: the US only gets 16% of its oil from the Persian Gulf. Of course, it might be nice to reduce dependency on oil from Venezuela as well -- no use making Hugo Chavez richer -- but that wasn't part of the proposal.

Still, optimists believe that given enough push, ethanol could take care of 30% of US fuel consumption by 2030, and, at least once it's in consistent use, reduce greenhouse gas emissions by soaking up atmospheric carbon dioxide. It could also be used as a feedstock for plastics and other products now made from petroleum. It's not a ridiculous notion vision, since Brazil -- the world's 14th-biggest economy and with a population of 188 million people -- gets 40% of its fuel from ethanol derived from sugarcane. Prices at the pump are half that of gasoline -- though it should be remembered that a liter of ethanol only has about two-thirds the fuel value of a liter of gasoline -- and the Brazilian government claims that the nation will soon be able to do without imported fuel entirely.

ethanol plant

Even here in the US, ethanol production has been rising sharply. There was some interest in the technology in the late 1970s, during the first global energy crisis, with farmers setting up ethanol distilleries -- only to have the rug pulled out from under them when prices dropped again. However, farm states gradually began to move into the vacuum left by the collapse, providing subsidies and assistance for ethanol production, and by the early 1990s the industry was on the rise. As the extent of production has increased, so has the efficiency of production.

That efficiency is critical, since critics have persistently hammered on corn-based ethanol for requiring more energy to produce than it delivers. That seems to be an exaggeration -- a 2001 study by the US Department of Agriculture claimed the ratio of energy in to energy out was more like 1:1.67, at least when "coproducts" of the process, such as feed mash, are factored in. Other estimates have given it as about 1:1.5 or 1:1.34. In contrast, the ratio for gasoline at present is about 1:4.35 -- so even given an optimistic view, ethanol has a long ways to go.

The most prominent of the "negative efficiency" critics have been David Pimentel, a professor of ecology and agricultural science at Cornell, and Tad Patzek, a professor of geoengineering from the University of Berkeley who founded the UC Oil Consortium, an industry-sponsored research group. They claim the ratio is 1.29:1. The discrepancy, according to ethanol advocates, is that Pimentel and Patzek do not factor in coproducts, and also factor in such items as the energy used in building farm equipment and ethanol distilleries in the first place. In other words, they are calculating worst-case outputs and inputs, and so it's not surprising they get a poor ratio. The advocates find the worst-case estimate annoying, in large part because it's been often quoted in the press as gospel, when it's actually on the outliers. Some advocates suspect it's part of an oil-industry smear campaign.

* Whatever the actual efficiency of ethanol production, continuing process improvements are making ethanol more attractive all the time; after all, given the current low efficiency, it would seem to have nowhere to go but up. However, even if all corn production in the USA were converted to ethanol, it would only provide 20% of America's fuel needs. The National Corn Grower's association thinks that US ethanol production will quadruple to over 60 billion liters (16 billion US gallons) by 2015, but that's less than 7% of expected fuel demand.

President Bush's optimism is based on the idea of "cellulosic" ethanol. Corn harvesting leaves behind biomass residue in the form of "stover" -- stalks, husks, and cobs -- and there's plenty of energy in that material. The problem is that the energy is locked up in the tough molecules that make up the walls of plant cells: fibrous cellulose, hemicellulose, and lignin. If there was some way to break these materials down into simple sugars, corn stover could provide tens of billions of liters of ethanol. There would also be no need to limit feedstock material to corn: prairie switchgrass, common in the US and Canada, grows easily in poor soils and dry climates with little fertilizing, and has a high energy value.

The US National Renewable Energy Laboratory (NREL) in Golden, Colorado, has been working on cellulosic ethanol for a quarter of a century, and researchers there feel they are getting close to a solution. Actually, the Germans, with a long tradition of clever industrial chemistry, came up with a way to produce cellulosic ethanol during World War II by bathing the biomass in sulfuric acid at high temperature and pressure. Not too surprisingly, that approach is environmentally messy and energy-intensive. NREL has been working on enzymes -- protein-based catalysts -- called "cellulases" that can do a more efficient job of converting ordinary biomass to something that can go into a fermenter. The lab has been working with industry to put cellulases into production, and the cost of production of cellulosic ethanol has been dropping rapidly. Right now, it's about twice as expensive as corn ethanol.

Getting that far has been tricky. A few decades back, NREL researchers believed they could genetically modify a bacterium to do the job easily, but it's proven hard to come up with a bacterium that can do the full job. Some commercial startups think there's a better way. If biomass or some other feedstock is burned in an oxygen-poor environment, it will product hydrogen, carbon monoxide, and methane. This mix, much like the "coal gas" once heavily produced in the same way from coal, can be used to drive a power turbine, but it can also be catalytically converted to ethanol or other fuels. It's not all that different from the process for converting coal into ethanol.

One other issue with ethanol is delivery. It can't be sent through an ordinary oil pipeline, since it tends to absorb water easily and, since it's a pretty good solvent, will dissolve and absorb residues left in the pipeline from earlier batches of oil sent through the same line. Building pipelines that could handle ethanol would be a major infrastructure investment. Right now it's handled by tanker barges and railroad cars, with delivery to end use with tanker trucks. In places in the US where ethanol is in fairly common use, that element of infrastructure actually hasn't been a problem so far.

One of the biggest issues for improving ethanol production is simply government budgeting. The Bush II Administration, despite the president's optimistic comments about ethanol, has not been particularly generous in research funding. Congress is starting to take the lead on the matter, and NREL researchers think that if they can get the money, they'll have economically competitive cellulosic ethanol by 2012 -- and once they reach break-even, costs will drop further as the technology goes into widespread implementation and further research becomes obviously profitable.

Ethanol still remains controversial, with the critics charging it's a glass half-empty at best, and the advocates insisting that it's a glass better than half-full. The technology is still immature, and the advocates can feel confident in saying that the glass is likely to fill up more in the future.



* ATHABASCA DIRTY BLACK GOLD: An article from WIRED magazine a little while back ("The Trillion-Barrel Tar Pit" by Brendan I. Koerner, July 2004) reported on a visit to the tar pits of Athabasca in the province of Alberta, Canada, with known deposits of 300 billion barrels of oil, and possible access to a trillion more. There's a trick to it, however, in that it's all in the form of tar mixed with sand and buried well underground, a material referred to with a degree of understatement as "heavy oil". It's not a new discovery, local native tribes long used it to caulk their canoes, but in an era of cheap oil nobody had much more use for it than that. The era of cheap oil is over, and evolution of production technology now makes heavy oil a bargain. Oil firms have been commercially extracting oil from the Athabasca tar sands for some time now, and with the promise of massive profits production is now ramping up aggressively.

A process for extracting the oil from the tar sands was developed by a University of Alberta chemist named Karl Clark in the 1920s, who proposed using steam to perform separation. However, in a demonstration that there is a big difference between a lab experiment and a commercial process, it took decades to get things to work, and still longer to actually make money. A group of energy companies working together as "Syncrude" initially began to try to exploit the Athabasca tar sands in the late 1970s, during the first oil crisis, only to start losing money hand over fist when oil prices fell in the 1980s. Syncrude cut staff aggressively but didn't give up, working to improve efficiency so that the operation would be profitable even at low oil prices.

Originally, the digging was performed much like coal strip mining, using huge "draglines" to get at the tar sands. A dragline is a huge machine, like a small hotel on two huge long feet that can scoot itself backward, while throwing out a huge bucket on a long boom and dragging it back to scoop up the earth. The material is then hauled off on conveyor belts for processing. This works fine for coal but didn't work well for tar sands, and the draglines did not like Alberta's harsh winters at all. Syncrude got rid of the draglines, replacing them with oversized power shovels and huge dump trucks. The trucks dump their loads into a crusher, which pulverizes the material. It is then mixed with hot water and put through a "cyclofeeder" that uses centrifugal action to extract the oil-rich component, known as "bitumen". The bitumen is cooked in "cokers" to get rid of sulfur and other impurities. The coker output is crude oil, which can be processed in conventional oil refineries.

The entire operation is as automated as Syncrude researchers can make it, with components of the process linked by fiber optic cables, a dispatching system keeping the big dump trucks moving efficiently, and careful monitoring of the equipment to make sure it is all working right. Syncrude officials think they can reduce costs further.

The trillion additional barrels of fuel mentioned above are trapped too deep to make surface mining sensible. It is possible to inject steam through boreholes into the deposits to force the heavy oil upward, but this is an energy-intensive process. A more experimental process uses gaseous hydrocarbons to get at the deep tar deposits, and there have been some experiments with air injection processes. With a world hungry for oil, there's plenty of motive to keep on hunting for a way to get at all that buried energy.



* JOYRIDE: There is an old joke that goes: "Just when I thought I was winning the rat race, they brought in faster rats." This sort of evolutionary Red Queen's Race, running as fast as one can to stay in the same place, certainly applies to the competition between manufacturers and thieves. An article in WIRED ("Pinch My Ride" by Brad Stone, August 2006) focused on the development of automotive anti-theft systems and the methods crooks have devised to bypass them.

The first car to feature an electronic security system was the 1986 Chevy Corvette. The "Pass Key I" system was about as secure as the old garage door openers with their small range of fixed codes. It featured car keys with a pellet embedded in the base, with the car's computer sensing the pellet in an electromagnetic field generated after the key was inserted. There were only 15 possible configurations.

It did work fairly well at first, but then customers started complaining about lost keys. Dealers and locksmiths were then allowed to stockpile blank keys. There's the old saying that two people can keep a secret if one of them is dead, and opening up access to the keys broke the secret. By the early 1990s, the police were busting car-theft rings that had all 15 types of keys.

Improved security systems were developed. In one of the many unforeseen consequences of the fall of the Soviet Union, in the early 1990s Eastern European black markets for Western cars and car parts sent European auto thefts through the roof. In 1995 BMW, whose high-value cars were of course a prime target for auto-theft rings, introduced a radio-frequency identification (RFID) scheme to foil the thieves. American and Japanese car manufacturers quickly followed. Such modern "transponder immobilization" systems interrogate the key stuck in the ignition using a transceiver built into the steering column, with the key responding with a long code, providing billions of different possibilities. If the system doesn't get the code, the car doesn't start. Some keys had fixed codes, while others had "rolling" codes that changed between insertions, with the transponder system rolling in the same path along with them.

As before, the scheme worked very well at first, with thefts of cars fitted with transponder immobilization systems dropping drastically. Then the thieves began to crack the system. The security system on a Ford could be disabled just by popping up the hood and pulling out a fuse. Sometimes the thieves didn't even have to do that much. Dealers also occasionally left an additional key in the owner's manual without the owners becoming wise to the arrangement. Thieves could simply pick the door lock, using a "jiggle key" filed down to allow manipulation of the lock tumblers; grab the key from the manual in the glove compartment; and drive away.

Then, again, customers started losing keys. In this case, third parties beat the automobile manufacturers to the punch in helping to break security, selling devices with names like T-Code or CodeSeeker that allowed anyone to duplicate fixed-code keys. Manufacturers knew that people might lose keys and so they often also provided a secret "override" scheme, say using a sequence of pulls and releases on the emergency brake, to allow the car to start without an RFID key. Not surprisingly, the secret is out now, and even casual thieves are able break the system with it.

One of the peculiar -- and to those affected, unpleasant -- aspects of the ability of thieves to override automotive security systems is that many auto insurance companies still believe the systems are secure, though the evidence is plain they are not. As a result, victims of car thefts are having their insurance claims disallowed, in essence being accused of fraud. The insurance companies do have a real problem with fraud, but those familiar with the security systems and the ways criminals can crack them call the systems "theft deterrents" that are hardly crook-proof. Says a locksmith who has testified in insurance lawsuits for both sides: "Tell me a car can't be stolen and I'll show you how to do it."



* OPERATION MUSKETEER (1): In 2006, Israel was once again at war, fighting with Hezbollah in southern Lebanon in a conflict whose long-range consequences can barely be understood at present. As discussed in an article in THE ECONOMIST ("An Affair To Remember: The Suez Crisis", 29 July 2006), fifty years previously, in 1956, Israel was involved in another war, in collaboration with Britain and France, in an effort to bring down Egyptian President Gamal Abdul Nasser. The consequences of that war are still unraveling.

Britain had maintained Egypt as a colonial state for decades before World War II, but in the postwar period the "temporary" British occupation was clearly not a going proposition any longer, with the pressure of Egyptian nationalism forcing British Prime Minister Winston Churchill to withdraw British forces to the Suez canal zone in 1951. The troops were finally pulled out completely in June 1956.

The corrupt Egyptian monarchy had been overthrown by Nasser in 1952, who replaced it with a revolutionary nationalist Arab government. Nasser's relationship with Britain was rocky, and got rockier when Nasser tried to obtain loans from the US and Britain to fund the construction of the huge Aswan High dam on the Nile, which Nasser saw as the centerpiece of Egyptian economic development. The Americans seemed inclined to make the loans at first, but US Secretary of State John Foster Dulles decided against it. The dam seemed to him like too much for Egypt to bite off, and the US was also not happy about Nasser's recent major purchases of arms from the East Bloc.

The British were strapped for cash and prepared to follow Washington's lead. Everybody knew that Nasser would go to the Soviets for help, but they were perfectly happy to let the dam fall into the USSR's lap. What nobody counted on was just how Nasser reacted. On 26 July 1956, he gave a passionate public speech to blast British imperialism, with the speech signaling the Egyptian Army to move in and seize the canal. The canal was to be nationalized to provide the funds needed to build the Aswan High Dam.

The British public reaction was loud and angry, with editorials comparing Nasser's action with those of Mussolini and Hitler in the 1930s. British Prime Minister Anthony Eden, who had replaced Churchill in office in 1955, found the comparison only too vivid: Eden had been Prime Minister Neville Chamberlain's foreign secretary in the prewar years and had submitted his resignation in 1938 to protest Chamberlain's appeasement of the Fascist powers. Eden saw Nasser in much the same terms as he had the Fascist leaders of twenty years earlier, and made it clear that the Suez canal was Britain's "great imperial lifeline". Nasser could not get away with having his fingers wrapped "around our windpipe".

The French weren't happy with Nasser, either. Not only were the French major partners in the company which (had) run the Suez canal, but under the new government of Guy Mollet, France had 400,000 troops in Algeria trying to suppress a nationalist insurgency -- which Nasser was backing. The British and French began discussions about what might be done about Nasser.

There was a problem hanging over their options, however. The US government under President Dwight Eisenhower had made clear American disapproval of military action to resolve the crisis over the canal. Eisenhower was running for reelection and wanted to be a "peace president" -- once a high-ranking US Army general, he represented that seemingly contrary aspect of the military mind that hated war. The US also had a long-standing dislike of colonialism, and felt that heavy-handed actions by the European powers would simply strengthen the hand of the Soviets in the Middle East and in other regions that had just emerged from colonialism.

Eisenhower promoted various diplomatic actions to resolve the crisis. They weren't very effective, except to the extent that the British and French felt they had to play along, bogging down the momentum for military action -- which was exactly the effect what Eisenhower, who was rarely as muddled as he sometimes pretended to be, was trying to achieve. Eden in particular felt frustrated; he wanted Nasser "destroyed".

It was the Israelis who broke the impasse. Of course, Nasser had cut off Israeli access to the canal, and the Israelis had already been irritated with him for his backing of raids conducted by Palestinian infiltrators from Egypt into Israel. The Israelis also wanted to crush the Egyptian military before it assimilated all the new weapons that Egypt had recently purchased. In September 1956, an Israeli delegation secretly met with French officials at Sevres outside Paris to suggest action.

The plan was simple: Israel would seize the Suez canal, and then the British and French would militarily intervene to "restore order", with a "peacekeeping force" to then ensure "free access to the canal". When Eden was told of the scheme, he jumped on board without hesitation. The operation went into planning, being codenamed MUSKETEER in honor of its tripartite nature. It was a real coup for the Israelis, since up to that time the French had been trying to be even-handed in their dealings in the Middle East, while the British had been leaning towards the Arabs.

* Eden's government kept the matter a deep secret, both from the Americans and Parliament, with Eden's foreign secretary, Selwyn Lloyd, assuring the House of Commons that nothing untoward was going on. Some British government officials who were briefed on MUSKETEER were appalled, thinking the whole thing too transparent to deceive anybody. Telling lies was something that happens in politics -- telling lies that were certain to blow up disastrously sooner rather than later was another thing entirely.

On 29 October 1956, Israeli paratroopers under a gung-ho officer named Ariel Sharon were dropped into the Sinai to get the ball rolling. The British and French, who were of course, as they say in the movies, "shocked, deeply shocked" by the outbreak of fighting, issued an ultimatum demanding an immediate cease-fire. Nasser rejected the ultimatum, and British aircraft began to pound Egyptian airfields. On 5 November, a joint Anglo-French force under British command went ashore to seize the canal zone.

Nobody was fooled by the farce. Eisenhower was furious, saying: "I've never seen the great powers make such a complete mess and botch of things." The British were informed that if they didn't cease and desist, the US would cut emergency loans to Britain through the International Monetary Fund. Faced with what was seen as imminent financial collapse, on 7 November 1956 Eden called off MUSKETEER. The French were enraged, but there was nothing they could do.

The Americans had pushed a resolution calling for a cease-fire through the UN as well, with the Soviets backing the USA. The General Assembly was called in an emergency session, which prevented the British and French from using their Security Council vetoes; the resolution was passed by a vote of 64 to 5. Canadian Foreign Minister Lester "Mike" Pearson led the effort to resolve the issue over the next few months, with the Israelis withdrawing and one of the first UN "blue helmet" peacekeeping forces, the "UN Emergency Force (UNEF)", created to intervene in the Sinai and help keep the peace. The UN came out of the crisis with enhanced stature. [TO BE CONTINUED]



* INFRASTRUCTURE -- FOOD & FARMING (6): Beef is tasty but people also like pork and chicken, and raising pig and chickens are big businesses. While cattle are usually owned by a rancher and sold to meat packers, pigs and chickens are usually raised directly by meat packers.

Hogs are generally raised indoors in a long, low-roofed shed, with a slotted floor over a waste pit. The shed is organized into pens with 8 to 10 pigs each, the number in a pen being limited by the fact that if more pigs were in a pen, the weaker pigs would be crowded out by the others and would starve. Feed is dumped from overhead bins into a feeding trough simultaneously to reduce jostling for the food. The bins are refilled immediately after the dump, since if it were done just before the bins were dumped, the pigs would go into a frenzy.

Chickens are raised in externally similar sheds, with the hens in cages hung from the ceiling so that the floor can be hosed off easily. There may be two or three tiers of cages, staggered from each other so chickens on one level don't foul the cages of the chickens below. Chickens don't like getting too hot, so the shed is well ventilated with big fans, and a misting system like that used to keep produce fresh in the supermarket is often used as well. There are no windows in the shed; hens normally only lay in the spring and summer, but if the lights are on 14 hours a day, they lay all year long.

factory hens

All animal husbandry generates manure, with pigs and chickens being among the worst offenders in terms of odor. Neighbors complain about being downwind on a hot day, and getting rid of the manure is troublesome. In our energy-limited times, farmers are increasingly making use of manure digester plants to produce methane for heating and power generation. Nobody thinks biogas production is a road to energy independence, but it's a cost-effective source of energy for the farms, obtaining value from what otherwise would just be an overhead.

* Of course, many other animals are raised on the farm. Turkey farming is another big business, with turkey meat eaten not merely on its own merits, but also as filling for hot dogs and even as lean synthetic ham. Sheep are raised mostly for wool, mutton not being all that popular these days.

Horses are raised for riding and pack animals, with mules raised on a much smaller extent for pack use. Here in the mountain states, llamas are bred on a very small scale as well, since they make excellent pack animals for the high terrain. Buffalo -- "bison" to purists -- are also raised in the region on a modest scale for meat. The idea of trying to milk a buffalo cow is something out of a Wild West tall tale, the beasts not being noted in the slightest for their docility. Some of the ranches sell buffalo hunting rights.

Fish farming has long been popular in the Far East, with carp raised in local ponds and fed with food scraps. It is beginning to catch on in a big way in the West. Oceanic fishing is said to the last major domain of the human hunter-gathering, and given the gradual collapse of oceanic fish stocks, the future seems likely to increasingly belong to the fish farmer.

Work is being done on genetically engineered fish that mature faster. There has also been research in general into genetically modifying animals to produce pharmaceutical proteins, in effect turning them into drug factories. Genetically modified goats have been developed, and work has been done on chickens that lay drug-filled eggs. Similar exercises have been performed with tobacco plants, but though the economic return on using farms as drug factories is potentially huge, the whole concept of using GM organisms to produce drugs remains completely experimental and definitely controversial for the time being. [TO BE CONTINUED]



* ROBOT SURGERY REVISITED: An article in US NEWS & WORLD REPORT ("A Guiding Hand" by Michelle Andrews, 31 July 2006) discussed robot surgery, mentioned here in December 2005. The idea is an extension of laparoscopic surgery, in which operations are performed on patients through small incisions using various types of extension tools. Robot surgery replaces the hand-held tools with a remote-controlled robot system, operated by a surgeon using stereo video glasses.

Robot surgery was originally developed for military use, the vision being that surgeons would be able to perform operations on the front lines while working in safety, even half a world away. "Telesurgery" as such remains experimental, but robotic surgery has become very popular for prostate gland removal. Solid evidence shows that robotic prostatectomies are much more effective than other methods, with a lower rate of side effects and quicker patient recovery. However, although the robots are potentially useful for general surgery, evidence hasn't accumulated yet that they work better for other operations than traditional methods.

Heart surgery has proven a difficult target, and a robot is clearly overkill for operations such as repairing hernias, and removing gallbladders, appendixes, or ovaries under relatively benign circumstances. Traditional laparoscopy does the job just fine and is much more cost-effective.

Hospitals are still shelling out $1.5 million USD a pop for the da Vinci Surgical System, the only surgical robot being sold in the USA for the moment. They're willing to pay the price despite the fact that robotic surgery remains largely unproven in general use. That's because surgeons like to be on the cutting edge, so to speak, and many feel robotic surgery will be vindicated as the way of the future. There's also the appeal to customers, some cynics flatly labeling the robots "marketing tools". In fact, for the time being robotic surgery is the most expensive surgical option and some insurers are leery of approving it.

Hospitals that obtain the robots for prostatectomies do get a lot of mileage out of them, though patients should be forewarned that, to no surprise, it takes a fair number of operations before a surgeon masters the technology, with the first 30 patients taking their chances and the surgeon not really flying with full confidence until after performing several hundred operations.

Despite the difficulties, robotic surgery clearly has a big future. Work is now underway to give the machines "tactile feedback", the current technology not providing any "feel" to the surgeon. Another technology under investigation is "data fusion", with ultrasound or other medical imaging data merged into the surgeon's video system. Finally, work is being done on specialized robots that would only be able to perform a limited range of operations, but which would be much less expensive and easier to use than a full-function general-purpose robot.



* PHOENIX RISING: The five-year memorial on the 11 September attacks on the USA has brought attention to the "Freedom Tower", the new skyscraper that will be the centerpiece of the complex of buildings on the site where once the twin World Trade Center (WTC) towers stood. According to an article from BBC.com ("Building A Skyscraper After 9/11" by Rebecca Morelle), the Freedom Tower will rise to 541 meters (a patriotic 1,776 feet) and is to be completed in 2011. To no surprise it will feature innovations designed to improve safety and survivability:

The Freedom Tower was designed by the firm of Skidmore, Owings, & Merrill (SOM). It will feature a parapet at 418 meters (1,368 feet) to mark the height of old Trade Center towers. SOM officials believe the structure is state-of-the-art in terms of the safety of its design, but do not claim it is foolproof. A company official says: "We have learned to deal with threats on buildings, but architecture should be the last line of defense."

* RE-CALL 911: While work proceeds on restoring the WTC site, the conspiracy theorist community is working overtime at less constructive efforts. According to an article in THE WASHINGTON POST ("9/11 Theorists Multiply" by Michael Powell), 36% of Americans think that the US government had passive or even active complicity in the attack. 12% think the towers were hit by cruise missiles.

911 / day of wrath

Welcome to the world of conspiracy paranoia, where reality wavers like images in funhouse mirrors. The "9/11 Truth Movement", as it is known, is quick to seize on any straw to build up their theories. The Trade Towers were such tall structures -- why did they collapse straight down instead of topple over? Doesn't it require carefully controlled detonations to accomplish the same thing in planned demolitions? Obviously charges were arranged through the buildings.

Says Thomas Eager, a professor of materials science at MIT, who has investigated the collapse of the towers: "At first, I thought it was amazing that the buildings would come down in their own footprints. Then I realized that it wasn't that amazing -- it's the only way a building that weighs a million tons and is 95 percent air can come down."

The informal ideological leaders of the Truth Movement include theologian David Ray Griffin of Claremont University; philosopher James Fetzer of the University of Minnesota, who is also a long-time Kennedy assassination theorist; and economist Daniel Orr, retired from the University of Illinois. Steven Jones, a physics professor of Brigham Young University, is the main "technical expert", who insists that the destruction of the towers had to be a controlled demolition.

Griffin's book, THE NEW PEARL HARBOR, is something of a "bible" for the conspiracy theorists. He travels around giving lectures, telling audiences that the plot was an "inside job", claiming that "the welfare of our republic and perhaps the survival of our civilization" depend on unveiling the "conspiracy". The conspiracy theorists like to push the DVD movie LOOSE CHANGE, a "documentary" whose authenticity can be judged by their claim that the Empire State building was struck by a B-52 bomber and stayed up -- when the fact was that it was a B-25, a World War II aircraft about the size of a commuter turboprop and much slower than the massive jet Boeing B-52 or 767.

The conspiracy theorists believe the plot was concocted to justify American intervention in the MidEast. Many label President Bush as a "war criminal", though a surprising number think that he knew nothing of the plot. The CIA is the prime villain, but the Mossad -- the Israeli intelligence service -- or British intelligence are thought by some to be responsible or involved, apparently depending on whether the theorists are antisemites or anglophobes. Some even claim there were no airplanes and insist that New Yorkers who saw the event were all paid actors, or state that the passengers were spirited off elsewhere, to be either eliminated or left to rot in confinement.

As this suggests, while the conspiracy theorists are very strong in their convictions, they are in little agreement over the details. There are two main camps: "let it happen on purpose (LIHOP)" and "make it happen on purpose (MIHOP)", the terms describing the government's involvement in the attacks. The conspiracy theorists make much of pre-911 intelligence warnings, examine seeming discrepancies in the chain of events, and apply elaborate interpretations to obscure remarks of government officials on the day. There is no such thing as incompetence or accident in their Universe; everything that happened was part of an evil plan. When told that these seem like slender threads to hang so much from and that such a major conspiracy would be hard to keep so secret, they claim the murkiness of the trail as evidence in itself of a conspiracy.

The Truth Movement tends to accuse naysayers like MIT's Eager of being government stooges. Another naysayer, analyst Chip Berlet of Political Research Associates in Boston, a left-of-center think tank, does believe, not unarguably but at least with real basis in the hard facts, that the events of 911 demonstrate gross incompetence on the part of government officials -- but he calls the conspiracy theories "charlatanism", with the "evidence" they cite obtained from grainy pictures posted to the Internet and so on. Says Berlet: "I love THE X-FILES but I don't base my research on it. My vision of Hell is having to review these [conspiracy] books over and over again."

* ED: Arizona Senator John McCain recently published an essay blasting the 911 conspiracy theorists, calling their accusations irresponsible and an insult to the government workers who moved mountains to respond to the disaster; an insult to those who were killed on 11 September 2001, particularly the public safety workers who died in the line of duty; and a distraction from the important work of confronting global terror. Alas, some folks cannot tell the difference between the real world and Marvel Comics, accepting the preposterous as obvious truth and doing little more than spreading chaos.



* SMART BUILDINGS: We tend to take buildings and other structures for granted as a technology, but some researchers are considering an eye-opening technological leap forward. An article from WIRED.com ("Smart Buildings Make Smooth Moves" by Lakshmi Sanda) discussed the idea of "responsive structures" that can sense their internal or external environment and adapt accordingly -- compensating for changes in temperature and sunlight, adjusting to winds, modifying themselves to handle crowds.

One researcher working on the concept, Tristan d'Estee Sterk of the Office For Robotic Architectural Media & Bureau For Responsive architecture, is working on shape-changing "building envelopes" using "actuated tensegrity" structures, consisting of a system of rods and wires manipulated by pneumatic "muscles" forming the framework of its walls. The framework is controlled by embedded computing intelligence, resulting in a light, strong, adaptable, and efficient structure. Imagine a high-rise that can brace itself against winds or an earthquake, or a home that will shake the snow off the roof.

As Sterk points out, architects have always known that a building's shape impacts how it is lit, cooled, and heated. He believes that advanced technology allows architects to advance to a higher level, saying that buildings "clad in new generations of energy-making materials could alter their form to track the sun, enable greater shading or sunlight penetration while also producing energy." He adds that such a building "could even eliminate the need for air conditioning by using shape to improve ventilation rates."

Sterk is now designing a set of ultralightweight skyscrapers for Chicago, which is often referred to as the "Windy City" and so provides a challenge to high-rise design. Sterk's concepts use actuated tensegrity to let wind blow through, with the buildings shifting gently to adapt to wind conditions.

This is the sort of blue-sky idea which immediately confronts designers with a long list of problems, and advocates of responsive structures realize they have a lot of proving to do. There is also the problem of persuading people to live in buildings that don't necessarily sit still. Giancarlo Magnoli, a researcher at the Kinetic Design Group of the Massachusetts Institute of Technology thinks that future buildings may require a different mindset, being conceptually more like modern cars, with their integrated climate-control and safety systems. Says Magnoli: "Sophisticated [automotive] systems don't allow any misuse of brakes, wheels or fuel, and air bags instantly appear to protect us in case of extreme events. Our house rarely does all of this for us -- but we believe it could."



* GENETIC TOOLKITS (2): Some of the early work on genetic toolkits focused on fighting two major diseases, malaria and HIV, which the labs of two of the group, Jay Keasling and David Baker, had been trying to tackle for years. There is a treatment currently available to kill the evasive malarial parasite, the drug being based on a small molecule named C-15 sesquiterpene, also known as artemisinin. It is produced by the sweet wormwood plant, found mostly in northern China; it is not easy to produce the drug in quantity from this source and the cost is prohibitive.

Keasling's group has been trying for five years to genetically modify yeast to produce artemisinin. The goal is not just to synthesize the molecule but to do it with vastly greater efficiency. The optimization of the "pathway" requires construction of a range of different genetic sequences, the sum of the set totaling millions of nucleotide bases. Using SPP, that would be a difficult task, but the task is within the capabilities of a DNA microarray chip.

Baker's group is focusing on synthesis of proteins, with a particular target of producing surface proteins from HIV to be used as vaccines, but also for other tasks, such as environmental waste remediation or industrial catalysis. The team has written computer programs to generate candidate proteins, but the proteins still have to be synthesized and tested. Once again, synthesizing the candidates with SPP would be troublesome, but it can be done in a relatively straightforward fashion with DNA microarrays. More generally, DNA microarrays could be used to quickly characterize emerging new pathogen strains, and also rapidly develop vaccines against those strains.

* One of the more interesting avenues of Bio FAB work has been the development of biosystems that parallel electronic devices. In 2000, Jim Collins of the group, working with his colleagues Tim Gardner and Charles Cantor of Boston University, along with Michael Elowitz and Stanislas Leibler of Princeton University, constructed the first "biocircuits", including a ring oscillator and a toggle switch.

Elowitz and Leibler wanted to build a synthetic biological clock in hopes of obtaining some understanding of the biological clocks of natural biosystems. They created a DNA plasmid containing three genes: tetR, lacI, and lambda cI, which encode the proteins TetR, LacI, and Lamda cI respectively. The plasmid was then inserted in the standard "lab rat" for genetic experiments, the human colon bacterium.

Protein synthesis from a gene starts with the binding of the polymerase enzyme to a specific site on the genetic sequence called a "promoter". The polymerase works "downstream" of the promoter into the coding regions of the sequence, transcribing the DNA into "messenger RNA (mRNA)", with each mRNA molecule linking to a single amino acid subunit for the protein. The transcription stops when the polymerase hits a "terminator" sequence.

Elowitz and Leibler ingeniously arranged for the each of the three parts of their plasmid to code for a protein that would bind to and "jam" the promoter of the following part, preventing polymerase from latching on and beginning transcription. This resulted in the actions:

Now this sounds like a useless three-way stranglehold on the face of it, but actually it's more like a genetic "rock-paper-scissors" game:

Digital electronics engineers will recognize this oscillator as conceptually similar to that produced by chaining three inverting gates in a loop. In the lab experiment, a gene for producing a green phosphorescent protein obtained from a jellyfish was introduced into one of the phases of the ring oscillator, the result being bacteria that blinked on and off like microscopic Christmas lights. Collins' toggle switch was a modification of the scheme, transitioning between two different states.

These experiments defined the simplest elements of synthetic biosystems that not only operated like machines but could be used as machines. Work has been done to create "biodigital" components such as counters and logic gates, not in an attempt to duplicate silicon in DNA so much as to provide built-in control logic for synthetic biosystems. Another element of the effort has been to build "biosensors" capable of detecting chemicals or other inputs and providing outputs in response. A third element has been to provide communications capabilities, both to network systems of bacteria and to provide input-output to users, with both light and chemicals used as the communication medium.

Other work has focused on building instruments to test the effectiveness of synthetic biology systems. There has also been research on trying to prevent bacterial mutations from breaking "machines" implemented in their genomes; the more complicated the "circuitry" inserted into the genome, the more quickly it tends to break through mutations. However, on the other side of the coin, some researchers have taken advantage of mutations through artificial selection, breeding the modified bacteria through generations and selecting the strains that survive the best in the target environment.

Ron Weiss of the Bio FAB group has worked on multicellular systems that could check for the presence of explosives or other specific chemicals and provide an alert by emitting light. Imagine bacteria or mix of bacteria that were designed with two mechanisms for sensing the concentration of explosives such as TNT, with one mechanism triggering at low concentrations and another at high concentrations. Below the low threshold, the bacteria would emit green light; above the low threshold, it would emit yellow light; and above the high threshold, it would emit red light. This would allow a minefield to be neutralized by spraying it with bacteria, the safe areas lighting up as green and the mines spotlighted by yellow and red "bulls-eyes". A similar approach could be used to detect pollutants or for use in medical diagnostics.

Group member Drew Endy and colleagues at MIT are now putting together a generalized library of "BioBricks", as they call them, that could be used to put together complicated synthetic biosystems. The "Registry of Standard Biological Parts" now has more than a thousand BioBricks. One of the real pluses of this approach is that two researchers working on completely different applications will be able to produce BioBricks that they can both use, instead of conducting research projects with no real synergy between them.

The goal is to create a synthetic bioengineering capability not all that conceptually different from the technology to create integrated circuits. Since 2003, courses on Bio FAB technology have started to spread through academia. Interest seems split between "engineers" who are thinking first about applications and "biologists" who see the technology as a powerful way to investigate biological processes by building them from scratch.

There are also cautioning voices on the sideline, warning of the possible dangers of tinkering with microorganisms and trying to establish safeguards. The technology is remains in the lab for the moment, but everyone working in the field is highly excited about its potential. [END OF SERIES]



* INFRASTRUCTURE -- FOOD & FARMING (5): The other obvious component of agriculture is raising animals. The cattle industry is split between two distinctly different types of operations, dairying and beef production.

Dairying is of necessity a highly structured operation, since the cows have to be milked twice or even three times a day, every day. Of course they also have to be fed and otherwise cared for. Most US dairy cows are Holsteins, also known as Friesians, with prominent hip bones and coloration of black splotches on white. They are extremely efficient at converting feed to milk. Individual cows wear ear tags with an identifying number; these days, the tag increasingly includes an RFID unit, which is scanned when the cow goes to the feed trough or the milking station, allowing the dairyman to keep accurate track of input and output.

In the old days, cows would be turned out to pasture in the morning and then brought in to milk, but though heifers may still range free for their childhood, usually the cows spend all their days indoors. For a time each was given her own stall, but now they wander freely through an open structure. They are doled out a proper mix of feed to ensure that they stay well fed.

The life cycle of a milk cow is very predictable. At an age of 14 or 15 months, she'll be bred, with the gestation period then lasting nine months, just like in humans. She'll be put to work giving milk for another year or so, and then bred again. Her time in productive breeding and milking will run about five years, maybe seven if she's unusually healthy. The comfortable lives of milk cows all end in the same grim way, however. Although Holsteins aren't bred to give nice juicy steaks, there's no problem in making hamburger out of them, and so once a cow's milk production goes below the profitable threshold, she becomes a patty in a Big Mac.

The milking parlor is a sophisticated operation, with the cows backing up along a trench along the center, which allows the dairyman to work at the level of the udders. The teats are cleaned off and the four suction cups of the "claw" of the milking machine fitted up. The machine works automatically in a rhythmic fashion and then the claw falls off. Europe has been paving the way with completely robotic milking parlors, which allow a cow to be milked any time she feels like it. Robotic parlors are now starting to catch on in the US and Canada as well. Either way the milk is obtained, it is filtered and then dumped into a refrigerated tank. Every day or two a stainless-steel milk truck hauls the milk to a dairy for pasteurization, packaging, processing, and sale.

* If dairying is agribusiness at its most high-tech, cattle ranching remains more traditional, though RFID is making inroads there as it is across all animal husbandry. There are about 10 million dairy cows in the US, compared to about 100 million beef cows.

longhorn cattle, Kansas

Beef cattle spend the first year of their lives on the range. When they reach a mass of about 270 kilograms (600 pounds), they are sorted out, the most promising sent off to do a stint as breeding stock, with the "losers" sent off to a feedlot for "finishing" -- the term having a double meaning in this case.

Cowboy flics suggests a certain nostalgia to life on the ranch, with cattle lassoed from horseback to drag them into the corral for branding, medication, castration, and so on. Rounding up cattle is actually much simpler these days, with the rancher simply dragging a bale of hay behind his pickup. Corrals are usually prefabricated steel pipe arrangements that can be set up on the range wherever they are needed.

There is nothing at all nostalgic about a feedlot, even in principle. Anybody who lives not far from one (as I do) can witness that they are not pleasant to be downwind of on a hot summer day. A feedlot can be simply described as a "cattle concentration camp", with the cattle penned into a lot to be fattened up for slaughter. The biggest feedlots can have tens of thousands of head. The feedlots usually don't own the cattle; essentially the operation is run as a paid service to the actual owners.

The cattle are fed dried corn, not so different from popcorn, that's usually crushed and sometimes also steamed. The corn is then mixed with a little silage and nutrients, to be dumped into a "bunk" -- a trough outside the edge of the feedlot where the cattle can push their head through the wire and eat their fill. The bunk is kept outside the lot so the cattle can't foul it easily. A water trough is also available, often on the other side of the pen to force the cattle to move around at least a bit. The corn-fed cattle grow big and fat quickly. The inmates can reach slaughtering weight, about 540 kilograms (1,200 pounds) before their second birthday.

A feedlot can be rank-smelling but not too nasty to maintain, with the lot raked up about once a year or so. Mud does amount to a problem for all concerned, which is why feedlots tend to be sited in relatively dry areas.

cattle feedlot

Details of the slaughterhouse operation are obscure, probably because it's something few people want to know much about. Obviously it is as well organized process. I once ran into a fellow who had once been employed in the meat-packing industry, working as a technical writer to document the slaughtering and butchering processes. It sounds cold-blooded, but emphasizes the fact that all manufacturing processes run on documentation.

* Cattle are kept on the range by a barbed-wire or electric fence, but the road entries to the range are ungated, with the cattle kept inside solely by a "cattle guard". This is a shallow pit across the road between the fenceposts covered by a spaced set of steel rails. It's easy enough if a bit bumpy to drive across and any reasonably coordinated human can walk across one with no trouble -- but cattle, fearing they may get their hooves caught, won't try to cross.

Nobody seems to remember the name of the clever person who came up with the idea. It is highly effective. Cattle won't even try to cross a set of white lines painted across an asphalt roadway to make it look like a cattle guard. I have heard tales, however, that sheep of all things have figured out how to roll across them. [TO BE CONTINUED]



* AIDS CHALLENGE: As discussed by an article in THE ECONOMIST ("Stand & Deliver", 19 August 2006), for officials working to deal with the AIDS crisis, it is the best of times, it is the worst of times. The good news is that money to fight HIV and AIDs is flowing, with $8.9 billion USD available in 2006 and larger sums expected in 2007 . The bad news is that the challenge still remains intractable. Kevin De Cock, in charge of the World Health Organization's (WHO) AIDS program, believes there is a five to seven year window of opportunity to deal decisively with AIDs; if no major progress is made in that time, donors will despair and the money pipeline will dry up. This last summer, AIDS fighters met at the 16th International AIDS Conference in Toronto, Canada, to socialize with each other, engage in a bit of publicity theater, be pilloried by AIDS activists, present scientific papers, and in particular devise a strategy for their war against the HIV pathogen.

Early on in the struggle, the disease was poorly understood and there were no treatments for it at all. It became quickly obvious that the disease was transmitted by tainted blood, dirty needles used by junkies, and by sexual contact. The tainted blood problem was addressed fairly quickly once appropriate blood tests were developed, though not before many people died, including tennis star Arthur Ashe and science-fiction writer Isaac Asimov. Efforts were made to educate junkies and provide clean needles. To deal with sexual transmission, condoms were distributed and "safe sex" campaigns were conducted, proving effective in places where they were pushed with adequate effort.

Such passive measures helped limit the spread of AIDS, but did nothing to help those who had been infected. However, during the 1990s a new class of drugs known as "protease inhibitors" were developed, which were then used in conjunction with some earlier drugs to result in "highly active anti-retroviral therapy (HAART)". HAART could not kill off HIV, but it could keep it under control. Rich-country AIDS victims were the first to benefit from HAART, and then AIDS activists began to push for delivery of the treatment to less-well-off countries. It took some time, but that's now happening. About 1.6 million AIDS victims in the poorer countries, including about a million in Africa, are now on HAART. The 2005 G8 meeting in Scotland produced a pledge that HAART would be available to anyone who needed it, anyplace in the world, by 2010.

* The problem with HAART is that it's expensive, indefinite, and the drugs have nasty side-effects. It is far preferable to make sure that people don't get AIDS to begin with. Fewer people suffering from AIDS also means fewer people get AIDS, giving the hope that the disease could be pushed down towards extinction. A vaccine would work better, but developing one has proven very difficult.

A vaccine works by arming the immune system to defend spontaneously against a pathogen. The HIV pathogen is tricky, partly because it attacks the immune system itself; it also tends to mutate at a monstrous rate, making it an evasive target for the immune system, and absolutely no person who has been known to have been infected with HIV has been observed to have successfully killed off the virus even with assistance from drugs. However, about a thousand "long term non-progressors" are known who have been infected with HIV and don't seem to be bothered by it much, giving some hope that the immune system can fight the infection, at least to a degree. Organizations such as the Bill & Melinda Gates Foundation have been dumping funds into AIDS vaccine research, but nobody is optimistic that a vaccine will be found soon.

That turns the current focus back to prevention. Condoms are highly effective in themselves, but not only do menfolk sometimes fail to use them -- for example, when they're good and drunk -- in some places, they tend to refuse to use them at all. It's all very righteous to tell women to "say NO to unsafe sex", but in some cultures wives may not have the right to refuse sex to their husbands without risk of violence. That may be an unpleasant reality, but it is the reality, and there is recognized need for something other than condoms, a technology that a woman can "fit and forget". Several such technologies are now in the works.

The first is the "vaginal microbicide", a chemical that a woman inserts in her vagina before sex, with the microbicides killing off pathogens provided by her mate. None are in use yet, but five are in trials. Some are in the form of foams or gels, but the best option seems to be a small ring that can be fitted to the cervix, releasing the chemicals over weeks or months. That would be a "fit and forget" option; but it has been reported in trials of gels that the menfolk tend to find they enhance the sexual experience, meaning their use would be encouraged.

Similarly, investigations are being performed to see if cervical diaphragms might be used to block infected semen and prevent infection. Another approach is to provide drugs for women that prevent the HIV pathogen from taking hold even if it's introduced during sex. This approach has a spotty history, with five trials currently underway but four others halted for various reasons. One issue with this "prophylactic" approach is the toxicity of anti-HIV drugs, which can be tolerated by AIDS victims whose only alternative is death, but which is harder to accept with if the subjects are healthy.

It has also been recognized that a woman with a herpes infection is twice as likely to acquire AIDS than one who is healthy. AIDS is not a highly infectious disease, it usually takes some work to acquire it, but open sores lower the barrier to infection. Although anti-herpes drugs aren't a full cure for AIDS, they can help, and two trials are currently underway. The menfolk who don't or won't use condoms aren't being completely ignored, however. Strong evidence shows that circumcision helps reduce the incidence of AIDS, and some clinics in Africa are pushing them.

* No matter what technologies are being considered, there is the ultimate problem of getting people to use them, which is basically a marketing issue. The real target of any anti-AIDS campaign is youngsters in the 15 to 24 year old range, not a time of life when people are inclined to be particularly careful in their behavior. A number of local studies have been performed on how to conduct effective anti-AIDS campaigns, though not everyone has been impressed; one Brazilian AIDS official mocked the tendency of studies to regard people as "well-behaved research objects". The fight against AIDS has come a long way, but it has a long way to go.



* RING OF STEEL: Anybody who watches British-made suspense flics is aware of the "Ring of Steel (ROS)", the network of security cameras that protects London's central core, the "City", Britain and Europe's financial center. The ROS came online in 1998. Every vehicle that comes inside the ROS is photographed, with its license plate matched against a national police database and an image of the driver stored away for future reference.

According to an article in the July 2006 IEEE SPECTRUM ("Ring of Steel II" by Justin Mullins), the ROS was born out of a string of Irish Republican Army bombings in the early 1990s that killed four, injured dozens, and caused widespread damage. The London police began to put officers on the street to sort out suspicious vehicles, but that was clearly only a short-term fix. The process had to be automated.

At the time, trying to read license plates by machine was very difficult, particularly since plates could be seen at a wide range of angles under widely varying lighting conditions. The answer, obvious in hindsight, was to make things easier for the machine. Access to the City was limited to a few key roads that funneled traffic through specially designed lanes where cars had to slow down and were pointed directly at cameras under controlled lighting conditions. The design goal was successful read rate of 94%, and it was achieved.

The special lanes were something of a chokepoint, but that worked out well. People began to take the Tube more often and traffic fell off, improving air quality. Some roads that were no longer accessible were turned into pedestrian malls. Automatic license-plate recognition has matured and now it can attain a successful read rate of almost 100% under more or less uncontrolled traffic conditions.

The ROS features over 200 cameras, each sending a 3.8 megabit per second feed to a control room at a central police station. The stream from all the cameras has to be monitored in real time, and this requires 122 IBM xSeries servers with a total of 200 terabytes of storage to match imaged plates to a database of 82 million vehicles. The computer system will flag any suspicious vehicle and an officer will determine if action needs to be taken. In 2005, 38 million vehicles were scanned, with 91,000 flagged for infractions recorded on the national database. In 4,161 cases police action was taken, with a total of 539 arrests. An arrest for a small infraction sometimes leads to a major bust. The system flagged a black Porsche Cayenne whose driver had not been paying his leasing bills; when the police stopped the car and searched it, they found $20,000 USD in the glove box, leading to a major money-laundering investigation.

The ROS has taken a dent out of crime in the City, but to an extent the crime has simply moved elsewhere. People are also getting trickier about dealing with the system, for example obtaining license plates with fonts that give machine character recognition systems a headache. There have been concerns over privacy and just how effective the system is for fighting terrorists. In the infamous 7 July 2005 bombings of the transport system, all four suicide bombers were imaged coming through the ROS.

London police officials flatly admit that the ROS can't do everything, but point out that nobody ever thought it would. The idea is catching on elsewhere. The New York City Police Department is now installing 500 cameras and wants to expand the system into a ROS to protect lower Manhattan.



* DEATH OF A SPAMMER: A recent article from WIRED.com ("The Sleazy Life and Nasty Death of Russian Spam King" by Brett Forrest) provided an interesting story of the rise and fall of a bigtime Russian spammer.

Technically, Vardan Kushnir was not Russian, but an Armenian living in Moscow. He had established a business there, the "American Language Center (ALC)", to teach English to Russians. He was also a spammer, sending out 25 million emails a day. He was prosperous enough to be a familiar face on the Russian club scene, where he was noted for his excess and obnoxious manners.

Kushnir grew up in Armenia, where he was raised by his mother Olga, his father having left the family. He was a bright schoolboy and got a slot into the Moscow Technological Institute of Light Industry. On graduation, he went to Los Angeles, returning to Moscow speaking English like a Yank. In 1994 he opened the ALC to pass his skills on to Russian students.

Kushnir really wanted to become a software developer, helping to establish a US-based company named "Sophim", with the help of a partner in Florida. Sophim didn't take off, and Kushnir had to rely on ALC to keep him and his mother -- who had moved in with him in Moscow -- afloat. In 2001, he gave up on Sophim and decided to go into spamming. He found out that China was the best place to get a spam server, with $1,000 USD giving a month's rent on a server that could pump out seven million emails every day.

Kushnir was a quick study and figured out all the dodges. He used spam to promote ALC and brought in students, and though he wasn't what might be thought of as filthy rich in the USA, by Moscow standards he was doing well for himself and was throwing his money around. His spamming was overbearing and people sent him threats, but Kushnir was unmoved. He found such comfort as he needed by reading books on Scientology, and kept pumping up his spam.

In 2003, the Russian authorities began to take an unkindly interest in Kushnir, partly because his spam lists included a government official in the state communications ministry named Andrei Korotkov who didn't like being spammed. When Korotkov complained, he started getting spam addressed to him personally. There were no laws against spamming in Russia, so Kushnir felt free to blow Korotkov off. Korotkov even tried to counterspam, flooding ALC's phones with prerecorded messages, but Kushnir ramped up his spamming against Korotkov, sending him volumes of insulting messages, and Korotkov had to admit defeat.

Kushnir was not quiet about his misadventures with the authorities, boasting about his games to his acquaintances. He was well known in the club scene by that time, easily able to pick up girls who liked his notoriety and fat wallet. He was tiring of the ordinary sex games, however, gradually moving farther away from the mainstream into the sleaze scene. He would boast about his kinky partying to his employees at ALC, which generally annoyed them. They were much more annoyed with him because he often didn't bother to pay them, stringing them along until they finally quit, with Kushnir finding another sucker as a replacement. When one employee confronted Kushnir, Kushnir suggested with a calm, blandly superior demeanor that the employee was overwrought and should obtain peace by reading L. Ron Hubbard. Kushnir was devoted to Hubbard's teachings, feeling that Scientology had brought him to a higher plane of awareness -- which of course translated into a condescending attitude to those around him that Kushnir didn't bother to conceal.

Not surprisingly, Kushnir had a lot of enemies. One night in the summer of 2005 he went to a club and came back to his apartment with a set of girls, one said to be only 15. His mother went to sleep in a studio apartment nearby to give him some privacy. The girls slipped Kushnir a knockout drug in a drink, but it only kept him out for a while; when he woke up, they beat him up. Several men then arrived, and when Olga came back into the apartment in the morning, Vardan Kushnir was lying cold and dead in a pool of blood on the bathroom floor, his skull beaten in. He was 35 years old. Some items had been taken and the police suspected it was a robbery that got out of hand, but there were a lot of people who would have liked Kushnir dead.

Olga Kushnir now runs ALC; the spam operation has been wound down. There were arrests, but the resolution of the case remains unclear. The authorities don't have a lot of incentive to worry about the murder of well-known obnoxious public nuisance. One Moscow tabloid summed up the attitude in a headline: SPAMMER HAD IT COMING.



* GENETIC TOOLKITS (1): The notion of "genetic engineering" has been around for over three decades, but though the technology is in widespread use and clearly useful, its current implementations -- inserting "plasmids" or loops of DNA into bacteria, or blasting gene sequences into the chromosomes of more complicated organisms -- look more like lab procedures than something in an engineer's toolkit.

As described by an article in SCIENTIFIC AMERICAN ("Engineering Life: Building A FAB For Biologists" by the Bio FAB group, June 2006), Now research groups are working to bring genetic engineering into the true biotech engineering age by providing a set of tools that can be connected together to perform complicated actions.

One such group, the "Bio FAB group", consists of David Baker of the University of Washington; George Church of the Harvard Medical School; Jim Collins of Boston University; Drew Endy and Joseph Jacobson of the Massachusetts Institute of Technology (MIT); Jay Keasling of the University of California, Berkeley; Paul Modrich of Duke University; Christina Smoke of the California Institute of Technology; and Ron Weiss of Princeton University. The Bio FAB group acts as an advisory team to Codon Devices in Cambridge, Massachusetts, a company set up to exploit the "synthetic biology" tools the group is working on.

The genes that define the operation of cells are run by deoxyribonucleic acid (DNA), the famous "double helix" molecule. It consists of dual chains of four nucleotide subunits or "bases":

   adenine (A)
   cytosine (C)
   guanine (G)
   thymine (T)

-- with A on one chain matched to T on the other, and C on one chain matched to G on the other. Triplets of nucleotides specify which amino acid is to be linked into a protein chain, and also specify control functions.

In the 1980s, Marvin M. Caruthers of the University of Colorado at Boulder developed a scheme known as "solid phase phosphoramidite (SPP)" chemistry that is now used for most commercial DNA synthesis. SPP starts with a single nucleotide attached to a substrate, usually a polystyrene bead, and suspended in solution. Adding an acid allows the first nucleotide to join to a new nucleotide obtained from a solution of that particular type of nucleotide. The cycle is repeated to add as many nucleotides as desired, with an error rate of about 1 nucleotide in 100. Adding one nucleotide requires about five minutes.

However, even the simplest genes of interest are thousands of nucleotides long, and the most minimal genome for an entire organism such as a bacterium is millions of nucleotides long. SPP is too slow, cumbersome, and has too high an error rate to be useful for building complete DNA sequences. In contrast, the biosystem of a living cell uses enzymes such as "polymerases" to synthesize DNA at a rate of up to 500 nucleotides per second, with an error rate of 1 in a billion. Furthermore, multiple polymerases will work on copying the same DNA strand in parallel, allowing them to turn out about five million bases in 20 minutes.

A team under one of the Bio FAB group members, George Church, decided to take the parallel approach by adapting the current technology of DNA "microarrays". A DNA microarray is a glass slide patterned using SPP with a grid of "dots" of DNA segments from 50 to 70 bases long, known as "oligonucleotides" or "oligos". The density of a microarray goes up to a million dots per square centimeter.

Church's modified microarray had editing capabilities, allowing specific oligos to be cut loose from the slide as needed, and was patterned with dots about 30 microns wide, containing 10 million oligos each. The oligos were known in this case as "construction oligos" because their sequences overlapped, allowing the construction of long DNA sequences. However, since SPP has a high error rate, the microarray had to be validated to eliminate errors before it could be used.

Two error-correction schemes were used. The first used the same technology to create a matching microarray of "selection oligos". These were "complementary" arrays to the original arrays, in which A on one array was swapped with T on the other, and C similarly swapped with G. This meant the dots on the two arrays should match each other, like neighboring pieces in a jigsaw puzzle.

In the error correction process, a dot on the microarray of selection oligos was released and washed across the original microarray. The selection oligos matched up with or "hybridized" with the original oligos; any oligos in a dot that didn't match up could be assumed to be bogus and cut loose for disposal. Of course, the error rate in synthesizing the selection oligos was exactly the same as the error rate in synthesizing the original microarray, but the minority of bogus selection oligos weren't likely to bind to any of the original oligos, and so the bogus selection oligos could be ignored. This proofreading scheme cut the error rate down to 1 in 1,300 bases.

Since natural biosystems also perform error correction in DNA copying, and do an astoundingly good job of it, the second error-correction scheme leverages off nature's error-correction scheme. Another of the Bio FAB group, Paul Modrich, figured out the mechanism in the mid-1990s, naming it "MutS/L/H". When two complementary half-strands of DNA hybridize, if there's an error in base pairing at a particular location, it forms a "kink" in the double helix. A natural protein named "MutS" will bind to the kink and then call in two other proteins, "MutL" and "MutH", to fix the error.

A third group member, Joseph Jacobson, working with Peter Carr of MIT, was able to use MutS/L/H to reduce the error rate in synthetic DNA to 1 in 10,000 bases, which was sufficient for building simple networks of genes. Armed with the microarray technology and error-correcting schemes, the Bio FAB group had the tools to build long, relatively error-free DNA sequences that could be used for experimenting with synthetic genomes. [TO BE CONTINUED]



* GI BLOGS: The fact that US military personnel fighting in Iraq and Afghanistan now have access to the Internet has allowed the troops to keep the citizens back home informed on what's happening in the combat zone. According to an article from BBC.com, the brass sometimes thinks the citizens are being informed too much.

Blogs maintained by soldiers are one thing, but the Pentagon is particularly worried about some of the pictures and videos posted online -- with some of the videos set to rock or hiphop music soundtracks. Says a military public affairs officer: "There's continuing concern about the use of these videos and stills being used by our enemies to propagate the false notion that our military members are barbaric, warmongers -- which is unequivocally not the case. And ... many of these videos and photos can harm force protection and operational security measures."

In one video posted online, American troops are observing a group of suspected insurgents who they believe are hiding weapons in a field. They discuss the situation among themselves, call up the chain of command to request approval for action, and get the green light. They kill three of the insurgents and destroy their two vehicles. To anybody with even a distant familiarity with warfare, this is clearly an ordinary combat scenario and nothing that could be construed as a war crime, but it's also an exercise in voyeurism and not the message military wants to be sending back home to the civilians: "Our mission may involve breaking things and killing people, but it's not in the military's interests to broadcast that fact to the world."

US Central Command does monitor the Web, but officially they only do so to correct inaccurate information. Websites that post shocking videos say that they're not trying to be "notorious", they just want the troops to be able to tell the folks back home what soldiers have been enduring in the field. The military does seem to be soft-pedaling their efforts to control the flow of information. They realize that the heavy-handed approach would likely be counterproductive, instead preferring to provide comments when materials could be construed as doing harm to the collective interests of the military.

* ANOTHER MONTH: I finally got the backlog cleaned out in uploading pictures to the website photography archive. The total came to 795 pix taken from 2004; since I was so close to 800, I went through my CD-ROM archives of raw photos to find useful shots that I had passed over, and was able to get about ten more in the pipeline. Not surprisingly, on second inspection some of the "left-overs" turned out to be pretty good shots.

Building the archive was a lot of time. I figure that it takes at least an hour to process five pix -- sorting them out, archiving them, tweaking them with a photo editor, setting up the web page links to the pictures, uploading them, and verifying the upload. It's helped squeeze me on time since I began the archive on 1 April. Now it's just a question of adding new pix as I take them.

* The Web is such a fascinating place. I was sitting in the tub reflecting on my appalling indifference to local politics, and realizing that I had no clear idea of who my elected representatives were. After I got out of the tub and dried off, I got to thinking: "I wonder if there's a site where I can enter my postal code and get all that information?"

I took me all of a few minutes to find it: "www.vote-smart.org". Works like a charm, too, providing all the information any casual visitor might want. I might actually start hanging around there just to get some data on the folks who send me fliers all the time. It has to be taken with a grain of salt, however. The Vote-Smart site pushes a "National Political Awareness Test (NPAT)" for politicians that tries to nail down where they stand on issues. It's a "multiple-choice" poll that, as is often the case with such things, funnels the answers for complicated issues into sets of more or less simplistic categories. A politician would easily be forgiven for replying: "I do have a voting record available to the public, you know, and if you want to ask my views on particular subjects I will be glad to respond in an articulate fashion."

Wikipedia is actually a fairly good source of information on politicians above a certain modest level of prominence -- finding all my Federal representatives is easy, and I could even find materials on my state representatives. It's fairly neutral on them because the partisans on both sides who try to edit the article end up coming to a compromise, though sometimes only after fighting each other to exhaustion.

I'm really beginning to appreciate the Wikipedia, though I would never post an article to it. I've had run-ins with their bureaucracy; to a degree the bureaucracy is necessary, but it's still obnoxious to deal with, reminiscent of the old joke: "Not all system administrators become egomaniacs, control freaks, and petty tyrants. Some are born that way."

* Which leads to the dark side of the web. I have a utility provided by my ISP that allows me to backtrack hits into the website, and I check it several times a day, both to get some information on people visiting the site and to spot-check the documents they are visiting -- making sure they have been properly uploaded and their formatting is correct.

One backtrack took me without warning into a neo-Nazi forum, with the members spouting off wild antisemitism and talking about the ZOG. "ZOG"? It rang a bell -- Zionist Occupation ... Group? I looked it up on Wikipedia and it popped back into my head: oh right, the "Zionist Occupation Government", meaning the "filthy Jew-dominated US government." It is an indication of how extreme the white-supremacist fringe is that they consider the Bush II Administration to be Left-leaning.