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DayVectors

mar 2010 / last mod dec 2015 / greg goebel

* Entries include: JFK assassination, intracellular immune mechanisms, parasitic wasp genome, history of the pacemaker, silent mutations not so silent after all, advances in optical metamaterials, neural connectomics, extensive amounts of computer code in cars, Craig Venter focuses on algae biofuels & other biofuel efforts, democracy in question, Chagas disease and schistosomiasis, and carbon planets.

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[WED 31 MAR 10] NEWS COMMENTARY FOR MARCH 2010
[TUE 30 MAR 10] A HISTORY OF THE PACEMAKER
[MON 29 MAR 10] ENEMY RECOGNITION (2)
[FRI 26 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (7)
[THU 25 MAR 10] GIMMICKS & GADGETS
[WED 24 MAR 10] NOT SO SILENT MUTATIONS
[TUE 23 MAR 10] METAMATERIALS, THE NEXT GENERATION
[MON 22 MAR 10] ENEMY RECOGNITION (1)
[FRI 19 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (6)
[THU 18 MAR 10] SPACE NEWS
[WED 17 MAR 10] CONNECTOMICS
[TUE 16 MAR 10] RIDE THE DIGITAL CAR
[MON 15 MAR 10] PARASITIC WASP GENOME (2)
[FRI 12 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (5)
[THU 11 MAR 10] SCIENCE NOTES
[WED 10 MAR 10] VENTER DOES BIOFUELS
[TUE 09 MAR 10] WHO NEEDS DEMOCRACY?
[MON 08 MAR 10] PARASITIC WASP GENOME (1)
[FRI 05 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (4)
[THU 04 MAR 10] GIMMICKS & GADGETS
[WED 03 MAR 10] THE CHAGAS THREAT / SCHISTOSOMIASIS RESURGENT
[TUE 02 MAR 10] CARBON PLANETS
[MON 01 MAR 10] ANOTHER MONTH

[WED 31 MAR 10] NEWS COMMENTARY FOR MARCH 2010

* NEWS COMMENTARY FOR MARCH 2010: The Obama Administration finally managed to push a US national health-care plan through Congress this last month. The plan mandates that all Americans will have health insurance, with lower income citizens subsidized by the taxpayers. Insurers will no longer be able to reject applicants because of "pre-existing conditions". Anybody who doesn't get insurance will be fined.

As Vice President Joe Biden put it: "This is a big [BLEEEP] deal." It certainly is, but from the sidelines it's a bit hard to know what to make of it. Even advocates admit that the legislation is inadequate, with no provisions for actually limiting health-care cost escalation. However, the critics were in a weak position, since the US health care system is clearly broken and the government had to get involved. Simply going into denial and saying the government should do little or nothing wasn't realistic; like it or not, something was going to be done. For the moment, simply passing the legislation seems to have scored points for the Obama administration with the public, though the resistance continues -- there's talk of challenging the constitutionality of legally coercing people to buy health insurance.

In any case, the US government was already involved in national health care, with Medicare and Medicaid dollars being the single biggest source of funds for the US medical industry, and it defies simple logic to say the government should not have a strong say over the industry when the government's providing so much of the money. The government has made its move, and with the camel's nose in the tent, more of the camel is likely to follow. It's safe to predict that the result will be more or less a nightmare; the only problem is that a nightmare is what we have now, and the question is only whether the change is going to be in the direction of "more" or in the direction of "less".

* Speaking of nightmares, the long-running fiasco over the US Air Force's attempt to obtain a new inflight refueling tanker aircraft, discussed most recently here in 2008, took a somewhat startling turn in early March the Northrop Grumman / EADS team that was offering a tanker based on the Airbus A330 decided to abandon their effort to win the award, leaving the field to Boeing with a tanker based on the 767 or 777 jetliners.

That was surprising since there was so much money at stake, but apparently the Northrop Grumman / EADS team decided that there was no way they were going to win the way the politics were going; and even if they did get the award, it would be challenged again. The obvious conclusion was that it was futile to keep throwing away their resources chasing after a carrot that would always remain out of reach. Some observers believed this left the USAF with an inferior solution that only existed on paper, but there's no particular reason to think the service will be particularly worse off with the Boeing product, which is mostly based on existing technology. Boeing already sells 767-based tankers, and the USAF solution is essentially a different mix-and-match of tech already in hand.

777 & 767 tanker concepts

However, the failure of the competition is an embarrassment for the US government that will taint relations with Europe. It cannot really be blamed on the Obama Administration since the program and its rocky history go back so many years, but the Obama Administration now has to rethink defense procurement policies so the same thing doesn't happen again any time soon.

As lousy as the deal is, it looks like it's what everyone's just going to live with: EADS walks away, Boeing picks up the pot, the Air Force accepts the solution, and the State Department tries to placate irritated Europeans. Well, at least Boeing won't have any problem with it -- and no doubt Air Force brass are relieved to finally have a resolution to an endless fiasco, even if it's not a perfect one.

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[TUE 30 MAR 10] A HISTORY OF THE PACEMAKER

* A HISTORY OF THE PACEMAKER: As discussed in an article from THE ECONOMIST ("The Rhythm Of Life", 5 March 2009), in 1889 John Alexander MacWilliam, a young Scots physiologist, discovered that he could control the heartbeat of a cat. Using a metronome and a needle electrode inserted into the cat's heart, MacWilliam found that he could speed up and restore normal heart rhythms by applying timed electrical shocks. That might have seemed like a somewhat sadistic experiment, particularly to cat lovers, but a half century ago MacWilliam's research led to the first implantable heart pacemaker, which was followed a few decades later by the implantable defibrillator. Now the "heart rhythm management" industry is big business. The basic principles of the technology haven't changed over the decades, but smaller, smarter devices promise to be easier to implant and provide more precise control over the pacing of the heart. The list of conditions that can be addressed by implantable pacemakers and defibrillators keeps growing, with more than a half million patients fitted with them every year.

The first patient to receive a fully implantable artificial pacemaker was a 43-year-old Swede named Arne Larsson. He was facing death from a heart condition; his wife, Else-Marie, had heard about cardiac pacing technology being tested on animals, and decided to see if she could save her husband's life. Else-Marie convinced Ake Senning, a surgeon at the Karolinska University Hospital in Stockholm, and Rune Elmqvist, a medically trained engineer, to build an implantable pacemaker for Arne. What did he have to lose?

The initial prototype was built in Elmqvist's kitchen and was implanted in Arne Larsson on 8 October 1958. It only lasted three hours, but the next morning Larsson was fitted with a second, identical device that lasted two days. Larsson became the "leading edge adopter" of pacemaker technology, being implanted with a total of 26 up to his death at age 85, from causes unrelated to his heart condition.

* An artificial pacemaker works by restoring the function of a faulty "sinoatrial node", the heart's normal pacemaker. Normally, the sinoatrial node produces steady electrical pulses that spread across the heart, causing it to beat in synchrony. When the sinoatrial node malfunctions, it can produce dangerously slow or erratic rhythms. By inserting electrodes into one or more of the chambers of the heart, via a large vein, it is possible to mimic the action of the sinoatrial node by applying small electrical shocks at regular intervals. Power leads link the electrodes to a small hermetically sealed metal box, called the "generator", that contains the battery and electronics. Modern generators are slightly bigger than a matchbox.

pacemaker

Arne Larsson's first pacemakers were the size of a can of shoe polish, which is what Elmqvist used as molds for his epoxy-resin generators. However, most pacemakers that followed were well bigger than that. Elmqvist's early device was designed to be recharged from outside the body, using an electrical induction loop, but the need to periodically recharge the generator was judged unsafe, due to worries that patients might fumble the job or forget to do it. That meant packing batteries into the generator that could keep it going for years at a time, and so pacemakers ended up being five times bigger than they are now. Mercury-zinc batteries were selected early on; they could provide power for two years, but they also produced hydrogen gas that could diffuse into the body. As imperfect as the early pacemakers were, they were still a huge benefit: before their development, patients had to be paced by external devices so big they had to be rolled around on carts.

In the mid-1960s, a company named Nuclear Materials & Equipment Corporation, of Apollo, Pennsylvania, developed an atomic pacemaker, using a tiny bit of radioactive plutonium-238 isotope to generate heat through radioactive decay, with a thermocouple converting the heat into electricity. The battery was sealed with three layers of casing that could stand up to a rifle bullet. The design lifespan of the device was ten years. The first atomic pacemaker was implanted in France in 1970. Some atomic pacemakers actually survived for almost two decades, but they had significant drawbacks, even beyond the potential threat to the patient. When a device was removed, it had to be handled as nuclear waste, with disposal being a troublesome and expensive process. Eventually, lithium-iodine batteries provided lifetimes of eight to ten years with no need to worry about disposal of radioactive materials; the new batteries also didn't produce hydrogen or other exhaust gases.

Better power sources also led to a beefed-up version of a pacemaker that could restart the heart or correct "fibrillations" -- irregular or dangerously fast heartbeats. These devices, known also as "implantable cardioverter defibrillators (ICDs)", hit the heart with a shock to get it beating or correct fibrillations. A team of researchers at Sinai Hospital in Baltimore, Maryland, began work on the ICD in the late 1950s, with the first ICD implanted in 1980 at Johns Hopkins Hospital by Dr. Levi Watkins.

ICDs are much "smarter" devices than pacemakers, with an ICD using a computer processor chip to monitor heart activity and determine when and how to administer a proper shock. The latest ICDs have wireless telemetry capability that allows doctors to monitor their operation. ICDs are now very popular, and implantation has become a routine outpatient procedure that can take less than a half hour.

* Heart pacemakers and ICDs are one of medical technology's real success stories, and there's room for improvement. The power leads of the implants tend to be the weak link in the technology. There have been recalls due to manufacturing defects, and estimates have been produced that suggest 20% of ICDs will suffer from lead failures within ten years. In one case from Boston in 2001, a doctor was running a routine check on a 79-year-old patient whose IDC exploded during a test, generating a blue flash and a loud pop. The patient, though alarmed, was unharmed. The insulation on a lead had worn away, resulting in a short circuit. That was an unusual failure mode, but there are plenty of others.

Usually lead failures give plenty of advance warning, but replacing the implant itself is dangerous. The ends of the leads are barbed to ensure a secure purchase in the beating heart, and getting them out can be tricky. If they don't come out easily, which happens about once in every 50 cases, the only recourse is open heart surgery, with a fair chance of killing the patient. Replacing the generator, incidentally, is straightforward, involving only a small incision in the chest, with complications in only about 1 out of 100 operations.

Work is underway to develop implants that don't require leads to be stuck into the heart. A California company named Cameron Health has developed a "subcutaneous ICD (S-ICD)", which features electrodes placed outside the heart, just under the skin, making the device easier and safer to implant or replace. The S-ICD is also less prone to false alarms due to electrical noise. Being on the receiving end of an ICD shock is like being kicked in the chest, and with current ICD technology about a third of the firings are due to false alarms.

Another California firm named EBR Systems eliminates electric shocks entirely, using a generator module that focuses ultrasonic waves on a receiver implanted in the heart that generates a physical shock in response. Details are confidential; company officials say they are only working a pacemaker for the moment, defibrillation having proven too much of a challenge. Researchers at the German Heart Center in Essen are working on a comparable wireless approach, but instead of ultrasound they are using electromagnetic induction to stimulate a receiver implanted in the heart. It took a 70 years to turn MacWilliam's pioneering technology into the implantable heart pacemaker, but in the next 50 years the technology has matured dramatically, and it seems poised for significant advances in the 21st century.

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[MON 29 MAR 10] ENEMY RECOGNITION (2)

* ENEMY RECOGNITION (2): Once our cytoplasmic defenses spot an intruder, the cell has several options for response:

Of course, where there are measures, there are likely to be countermeasures, and some pathogens have acquired means to undermine cellular defenses. The hepatitis C virus produces an enzyme that breaks the molecular mechanism by which RIG-I sounds the alarm against the virus, while the bacterium that causes Legionnaire's disease can resist autophagy, and the tuberculosis bacterium has acquired some mysterious mechanism to head off an inflammation response.

* Even though not much is known about our cytoplasmic immune defenses just yet, researchers have still found the knowledge acquired so far to be useful. It has helped deal with the extremely rare "fever syndromes", which afflict a few hundred people worldwide and afflict them with a fever, skin rash, and joint pain if they go outside on a cold day. It turns out that the fever syndromes are due to a mutant NLR gene. This particular NLR, NLRP3, helps promote an inflammation response involving a cytokine named "interleukin-1 (IL-1)". Based on this realization, patients were treated with a drug named "anakinara" that effective disables the immune response provoked by IL-1. Although anakinara was originally developed to treat rheumatoid arthritis, it proved perfectly effective in dealing fever syndrome.

An improved understanding of our cytoplasmic defenses could also lead to better vaccines. Vaccine mixes often include "adjuvants", which are substances that help promote a strong immune response. The only adjuvant currently authorized for use in the USA is aluminum hydroxide, or alum; it's effective, but it can also cause fevers and other side effects. Recent research suggests that alum can provoke cytoplasmic defenses to produce an inflammation response. Better knowledge of our defenses may lead to the development of adjuvants with fewer side effects.

Finally, it is important that we understand exactly what our immune system, all of it, can and cannot do. Our immune system is a marvelously elaborate mechanism that has impressive capabilities, but it's faced with formidable adversaries. Pathogens can be marvelously elaborate themselves, and their life cycles are far shorter than our own, meaning they have an edge in this evolutionary struggle. Says one researcher: "Because the bugs evolve faster, they are always going to stay a few steps ahead." We need to be able to figure out how to outsmart them. [END OF SERIES]

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[FRI 26 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (7)

* THE KILLING OF JFK -- LEE HARVEY OSWALD (7): On 25 January 1963, Lee Harvey Oswald mailed off the last installment on his loan from the State Department. Out of debt at last, on 27 January he was able to then send $10 USD in cash to Seaport Traders of Los Angeles to buy a Smith & Wesson 0.38 caliber revolver. The order was placed in the name of "A.J. Hidell"; the form required a witness, with the name filled in as "D.F. Drittal". Later analysis showed both names to be in Oswald's handwriting. The pistol was shipped via Railway Express, with the balance of $19.95 USD plus shipping charges to be paid COD.

By this time, he was becoming persistently brutal to Marina. She stayed with him because she really didn't have anyplace else to go -- she couldn't speak much English and Lee refused to let anyone teach her, she did not want to return to the USSR, and in fact he used the threat of getting her sent home to intimidate her. The fact that she was pregnant again by this time only increased her dependence.

On 14 February, Oswald saw a story in the DALLAS MORNING NEWS about retired US Army General Edwin Walker, a prominent local Rightist who was active in the ultra-right John Birch Society. Oswald talked about Walker to de Mohrenschildt, who expressed no liking for Walker, suggesting to Oswald that anyone who "knocked off Walker" would be doing society a favor.

Later that month, the Oswalds ran into a couple named Michael and Ruth Paine at a dinner party. The Paines were both American Civil Liberties Union (ACLU) members, liberal activists in conservative Texas. At the time, the couple was separated and Michael had moved out of the house, but they were on fair terms, with Michael often coming by to play with their two small kids and make himself useful with household errands. Ruth, a Quaker, was trying to learn Russian and took a strong, sympathetic interest in Marina Oswald. The Paines would get to know the Oswalds about as well as anyone ever did.

Conspiracy theorists like to paint lurid pictures of the Paines, proclaiming that they were Red agents or part of a US government conspiracy -- one or the other. One of the particularly bizarre notions circulated by conspiracy theorists about the Paines was the fact that Michael was employed at Bell Aircraft in the Fort Worth area and was supposed to have worked for Walter Dornberger, a German expatriate who was employed by Bell.

Dornberger had led the German V-2 rocket program during World War 2, being the boss of the well-known Wernher von Braun, famous in the 1960s for his work on the space rockets for the US National Aeronautics & Space Administration (NASA) that would put Americans on the Moon. Conspiracy theorists describe Dornberger as a "Nazi war criminal", which is a stretch, if not a really big one -- he was indeed a faithful Nazi and his hands were hardly clean, though Dornberger had never been arraigned for and certainly not convicted of war crimes. Almost the same could be said of von Braun, and there was just as much or as little cause to link Dornberger to a sinister conspiracy as there was to link von Braun to one.

More significantly, there was no close link between Paine and Dornberger other than the fact they both worked for Bell. The Bell Fort Worth plant built helicopters -- it was not surprising Michael worked there, since his stepfather was Arthur Young, inventor of the famous Bell Model 47 "MASH" helicopter, one of the key players in the development of the helicopter, and a prime mover in Bell's helicopter business. However, Dornberger was a rocket and space systems engineer who worked at the Bell plant in Buffalo, New York. A personal relationship between a Nazi and a Left-leaning pacifist seems a bit unlikely on the face of it. Conspiracy theorists have a tendency to grasp at straws and build great houses out of them.

Incidentally, some conspiracy theorists have linked Wernher von Braun to the conspiracy. A "William Torbitt" released a document titled "Nomenclature of an Assassination Cabal" in 1970 that claimed von Braun was the boss of the "NASA Security Division". The document was written in a schizophrenic style, consisting of little more than lists of claims and assertions involving almost everything and everybody in the assassination "cabal", without any pretense of validation or even a coherent story. While some conspiracy theorists have taken it at face value, others have found it so preposterous that they suspected it was actually "disinformation" created by the conspiracy to discredit them. [TO BE CONTINUED]

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[THU 25 MAR 10] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: WIRED Online reported on a transportable water cleaning system the US Army is now deploying to Afghanistan that uses bacteria to purify water. That sounds startling on the face of it, but that's essentially how sewage treatment plants clean up their sludge. However, members of the group at Sam Houston State University (SHSU) in Texas say their system is by no means simply a portable sewage treatment plant. The researchers came up with a mix of common bacteria, found in any handful of dirt, that can purify water in less than 24 hours without producing toxic byproducts, in a system packed in an ordinary shipping container. A sewage treatment plant takes much longer and doesn't do anywhere near as tidy a job. The military definitely has use for water cleaning systems in Afghanistan, where lack of access to clean water means having to haul water to field installations. Of course, such systems have obvious use for disaster relief efforts, with consideration being given to getting a prototype to Haiti. The SHSU group claims their "revolutionary" scheme easily scales up to larger installations.

* POPULAR SCIENCE had a note on "Mobile Digital TV (MDTV)", a new digital TV broadcast service now operating in 17 major US cities. Previously, the only way to get video on a mobile wireless device was via download, which could be expensive, but MDTV is a free service, supported by advertising just like regular broadcast. MDTV does of course require that devices have an MDTV receiver chip; MDTV-enabled devices are expected to be available later in 2010, with USB plug-in modules available for laptops and the like.

Mobile Digital TV handset

* BBC WORLD Online had an audio slideshow on a project to refurbish New York City's famous Empire State Building to improve its energy efficiency. The upgrade, which is to cost about $550 million USD, involves replacing all 6,500 windows in the building with insulating windows, and temporarily yanking all the radiators to permit installation of an insulating barrier that will block heat transfer through the walls. One of the big factors in the exercise was that about a third of the building currently isn't air-conditioned, which makes finding tenants more difficult. The plan was to air condition all the public spaces in the structure, with the first thought being to replace the chiller plant. Then somebody suggested "work smart not hard" -- and first determine how energy efficiency planning going on in parallel affected the air conditioning issue. As it turned out, the energy efficiency updates would be enough to permit full air conditioning without replacing the chiller plant. That saved $17 million USD that would have been required to replace the plant, if at the expense of pumping more money into energy efficiency. On the balance, it was a bargain.

* In really off-the-wall gimmick news, DISCOVERY CHANNEL Online reported on a passive near-field communications (NFC) data module named "RosettaStone" from a company named Objecs. NFC is used in RFID systems; the RFID module doesn't require power, the power being obtained from an electromagnetic field generated by the reader device.

The RosettaStone is intended to be embedded in a tombstone; presuming a visitor has an NFC-enabled cellphone, it can be then used to obtain a file of information on the, uh, "occupant". On first sight this seems like a completely ridiculous idea, but then again we're reaching the era of "internet of things" in which any conceivable product will have a digital ID tag, in which refrigerators will be able to query milk cartons to see if they're past their expiration date. Okay, so why wouldn't tombstones be part of atomized internet as well?

Of course there's a long list of practical issues to be considered, for example how long a RosettaStone could be expected to last when exposed to the elements outdoors and, maybe more importantly, if NFC schemes in use now will have any compatibility with the communications tech of the future. Still, it sounds considerably more practical a way to leave a personal memento for the future than having one's head frozen -- though that's admittedly a very low standard of comparison.

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[WED 24 MAR 10] NOT SO SILENT MUTATIONS

* NOT SO SILENT MUTATIONS: The proteins that help construct our body consist of chains of molecular "building blocks" known as "amino acids", with the pattern of the chains defined by the DNA sequences in our genes. DNA is structured around a set of four molecular building blocks of its own, known as "bases", with "triplets" of bases defining specific the amino acids in a protein chain. There are 20 different amino acids and 4 x 4 x 4 = 64 possible DNA triplets to specify the amino acids; there are generally multiple triplets to specify a particular amino acid.

As discussed in an article in SCIENTIFIC AMERICAN ("The Price Of Silent Mutations" by J.V. Chamary & Laurence D. Hurst, June 2009), it was long thought that any genetic mutation that modified a specific DNA triplet in such a way that it coded for the same amino acid before and after the mutation made no change in an organism, and so such "synonymous mutations" were often equivalently called "silent mutations". However, in the 1980s evidence began to accumulate that synonymous mutations weren't necessarily silent.

The first clue that "broke the silence" was statistical. If it didn't matter which of several triplets coded for the same amino acid, then by the simple odds of the matter, all the different triplets that coded for the same amino acid would be roughly as common. In bacteria and yeasts, that didn't turn out to be the case, with some triplets being much more common than others. Investigation showed that though two triplets might code for the same amino acid, the cellular machinery used to synthesize proteins might well work much more efficiently with one triplet than with another.

The difference in efficiency was traceable to an issue of supply. The DNA molecule, as is well known, consists of a "double helix", with two matching chains linked together like a long twisted ladder. The cellular machinery that produces proteins first splits the double chain down the rungs of the "ladder" to produce a half-chain, and then uses one of the half-chains as a template to produce a half-chain of a similar molecule known as "messenger RNA (mRNA)". The mRNA is fed to a cellular organelle known as a "ribosome" that reads the "memory tape" provided by the half-chain of mRNA to assemble the protein, being fed amino acids by triplet chunks of RNA linked to their corresponding amino acids, known as "transfer RNA (tRNA)". As it turns out, a bacterial or yeast cell may contain far fewer tRNAs for one triplet than it does for a second, meaning that protein assembly is much more troublesome for the first triplet than it is for the second. For this reason, proteins that the cell synthesizes in large quantity have genetic codes with a greater bias towards one triplet than those that are synthesized in small quantity.

Later studies for other organisms, such as plants, flies, and worms, revealed that many have similar biases in triplet codings. Mammals feature biases in triplet codings as well, but they don't follow the same pattern: the mammalian genome is roughly organized in blocks, and the biases tend to differ between blocks. Even now, nobody's quite sure what that means, but in any case the general assumption was that, as far as mammals were concerned, synonymous mutations were irrelevant -- truly silent.

Then, in the early 2000s, analysis of the rates of evolutionary change in the genomes of mammals suggested this assumption was wrong. Evolutionary selection pressures tend to "fine tune" the genomes of organisms to make them better adapted to their environment, with "bad" mutations tending to die out while "good" mutations are retrained. If synonymous mutations were truly silent, neither "bad" nor "good", they would be indiscriminately retained -- but the studies showed that they weren't, selection pressures did have an effect on which triplets were retained. That meant the synonymous mutations did have effects.

It required some effort to figure out exactly what. Our genes do not necessarily run continuously on our genome; they may include "noncoding" segments called "introns" that our cellular machinery has to toss out to splice the coding sections of the gene, the "exons", together for producing a protein. Some DNA triplets lead to higher error rates in splicing than other triplets that code for the same amino acid. Dozens of genetic disorders have now been traced, in part or in some cases in all, to synonymous mutations that were once believed to be silent -- for example, synonymous mutations appear to contribute to cystic fibrosis.

Even disregarding the splicing issue, synonymous mutations can make a difference in the folding of a protein. The effectiveness of a protein is not just due to the sequence of amino acids in the protein chain, but also to the way the three-dimensional structure it folds up into. Synonymous mutations can cause a delay in the folding of a protein as it is synthesized, resulting in a misfolded protein that can have disastrous consequences for the organism.

Scientists see the understanding of the possible effects of synchronous mutations as both providing tools to enhance commercial production of proteins by genetic engineering techniques, allowing optimizations of protein production rates; and to obtaining a better handle on genetic disorders. Much more research remains to be done, much more needs to be learned.

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[TUE 23 MAR 10] METAMATERIALS, THE NEXT GENERATION

* METAMATERIALS, THE NEXT GENERATION: Back in 2001, researchers in the US and the UK pulled off a trick that many had assumed impossible: they managed to bend light backwards, developing a "material" with a negative refractive index. The experiment involved shining microwaves -- not precisely light, but the same as light with much longer wavelengths -- at a circuit board topped with an array of rings and wires that represented the "material". It was a funny sort of "material', more like a contraption, but it set physicists to rethinking what they knew about light and optical technology.

As reported by an article from AAAS SCIENCE ("Next Wave Of Metamaterials Hopes To Fuel The Revolution" by Robert F. Service, 8 January 2010), almost a decade later, researchers have made major strides in "metamaterials", as the technology was named, pursuing ideas to create invisibility shields, ultrasharp focusing, and materials that could mimic the ability of black holes to absorb light. Unfortunately, while physicists have been demonstrating ever more clever optical tricks in the lab, they're uncomfortably aware that they haven't been able to come up with anything but laboratory toys. It's predictable that applications will lag major scientific breakthroughs, but those working on metamaterials feel that they really need to show they're actually good for something.

* Traditional optical technology uses mirrors and lenses to focus light. Lenses perform their focusing thanks to their curvature and the "refractive index" of the glass they are made from. The refractive index is relation of the speed of light in different materials; for example, the index change between air and water is what causes a straw in a glass to appear "bent" under the surface of the liquid in the glass.

In conventional optics, the index of refraction is always a positive value. In the 1960s, a Soviet theoretical physicist named Viktor Veselago suggested that it might be possible to engineer structures that had a negative index of refraction. If water had a negative index of refraction, the straw would not seem bent under the surface of the liquid in a glass, it would instead seem to stick back out of the water. Veselago's work suggested that there might be an entire domain of structures that had radically new optical properties.

Veselago's idea, crazy as it sounded, was taken seriously, but it wasn't until 2001 that two researchers -- John Pendry of Imperial College London and David Smith, now at Duke University in Durham, North Carolina -- actually demonstrated a structure with a negative index of refraction. They fabricated an array of metal wires and rings, with a thin slice cut out of the rings, and then shined microwaves onto the array. The microwaves excited electrons in the rings, causing them to slosh back and forth and produce a resonant electromagnetic field to induce a negative index of refraction into the beam.

Since that time, physicists and materials researchers have performed more sophisticated experiments in metamaterials -- but only in the microwave and other parts of the electromagnetic spectrum below the infrared. The problem is that the components of a metamaterials array must have dimensions smaller than those of the wavelength of the electromagnetic radiation they affect. That's not a problem with microwaves, since they have wavelengths in the centimeters, but it is a problem with infrared or visible light, which have wavelengths in the micrometer and nanometer range. Even with modern microchip fabrication technology, it is difficult to fabricate metamaterials arrays at such dimensions.

To make matters worse, metamaterials researchers like to use metal in their work. Metals work fine for microwaves, but are strong absorbers of infrared and visible light. Researchers have tried to dodge this problem by using metal thin films to reduce the absorption, but such thin films are very limited in the effects they can produce.

* To get around the obstacles against working in the infrared and visible regions of the spectrum, researchers have turned to precisely patterned geometrical 3D structures. A team at the University of Karlsruhe in Germany, for example, has used precision laser cutting to carve an array of helical channels turned either clockwise or counterclockwise into a block of polymer. The polymer is then used as a mold, with the channels filled with gold and the polymer removed to a reveal an exquisite array of golden spirals. When exposed to infrared light, the array acts as a polarization filter -- something that can of course be done with conventional optics, but the gold metamaterials array works over a much wider range of frequencies.

A group at the University of California at Berkeley has also built a metamaterials array with a negative index of refraction in the infrared. The array is built from alternating layers of magnesium fluoride and silver, with a precision ion beam used to carve holes into the stack, leaving behind a fishnet pattern. The pattern results in circuits between the alternating layers, with electron movement in the layers setting up a resonant electromagnetic field that produces negative refraction of infrared light shined onto the array. The Berkeley researchers have more recently reported operating a new array that works on similar principles, but built in the form of silver nanowires grown inside a sheet of porous aluminum oxide.

Unfortunately, schemes along such lines only work for light within a narrow spectral range, or shined from very specific directions. Researchers from the US Sandia National Laboratories in Albuquerque, New Mexico, have been working on a new approach that promises to work with infrared coming from any direction. They are depositing metal through a membrane onto a curved polymer surface, with the curved configuration providing structures that work effectively regardless of the orientation of the infrared light beam. The Sandia researchers haven't actually built a full metamaterials array yet, but feel they are making good progress towards one.

Other research groups have tackled the absorption problem by adding nanoparticles or other materials that produce light when illuminated to metamaterials arrays, with the light production compensating for the absorption. So far, researchers haven't had much luck with this approach, but they aren't discouraged. Metamaterials is a new world of physics and researchers have only scratched the surface, with a wide range of possible techniques available for further investigation. Says one: "It's a pretty rich tool set. People are still exploring what you can do."

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[MON 22 MAR 10] ENEMY RECOGNITION (1)

* ENEMY RECOGNITION (1): Our immune system has a powerful capability to recognize dangerous pathogens and work to destroy them. As reported by an article from AAAS SCIENCE ("Internal Affairs" by Mitch Leslie, 13 November 2009), we are still learning more about the molecular mechanisms by which our cells recognize and deal with invaders. While we have become increasingly familiar with the cell's external defenses, we are now finding out that the cytoplasma that fills the interior of the cell includes defenses as well. A better understanding of these cytoplasmic defenses may lead to improved vaccines against pathogens that have so far been evasive targets, as well as treatments for conditions such as gout that seem to be linked to an immune response gone wrong.

* Many animal cells, particularly sentinels of the immune system such as macrophages and dendritic cells, inspect their surroundings with extracellular structures called "Toll-like receptors (TLRs)", more than a dozen of which have been identified to date. Each different TLR can recognize a particular constant ("conserved") feature of certain broad classes of pathogens, with such features referred to as "pathogen-associated molecular patterns (PAMPs)". For example, the Toll-like receptor TLR-5 recognizes a protein named "flagellin", which is a component of the whiplike flagellum that propels many species of bacteria. Once sentinel cells recognize an invader from its PAMPs, the sentinels lead the charge of the immune system against it. The immune system first attacks with a general "innate" immune response and then, using B cells and T cells, an "adaptive" immune response that precisely targets the invader.

Work on plant cells showed that the cytoplasm of such cells contained equivalents of TLRs known as "resistance" or "R" proteins. The immune system of plants is extremely different from that of animals, but the discovery of R proteins made researchers curious about whether we had comparable cytoplasmic defenses. About a decade ago, researchers began to search through mammalian genomic databases to see if they could find analogues of these proteins. They struck gold.

According to immunologist Brad Cookson of the University of Washington (UW) in Seattle, "there's an elaborate intracellular detection array, just like there's an elaborate extracellular array." So far, about 20 intracellular pathogen sensors known as "nucleotide-binding domain & leucine-rich repeat-containing proteins" -- thankfully abbreviated as "NLRs" -- have been found, with the NLRs capable of identifying features of bacteria, parasites, and other intruders. The NLRs aren't alone, either, with other cytoplasmic detectors including:

* Having identified the detectors, the next question for researchers is to determine exactly what they detect, and some progress has been made on the matter. Like TLRs, some of the intracellular detectors bind to PAMPs. RIG-I, for example, zeroes in on viral RNA molecules, allowing it to target killers such as HIV and the hepatitis C virus. Recent research shows that the cell is adapted to assist RIG-I and help it target a wider range of intruders. The cell uses the enzyme "RNA polymerase" to convert a DNA strand into a messenger RNA strand that is then used to synthesize proteins -- but RNA polymerase floating around in the cellular cytoplasm will also convert any stray DNA it finds into double-stranded RNA. Since the cell's own DNA complement is concentrated in the nucleus and in mitochondria, the odds are that stray DNA is from a pathogen. Converting such stray strands into double-stranded RNA allows them to be detected by RIG-I, extending its target range to DNA-based viruses, such as adenoviruses and Epstein-Barr viruses, and even some bacteria.

However, for the most part the action of these intracellular detectors remains mysterious. For example, the intracellular protein NLRP3 not only detects bits of bacterial cell walls in the cytoplasma, but also toxic industrial substances like asbestos and silica, as well as the monosodium urate crystals that torture gout sufferers. The problem is that nobody has been able to figure out how NLRP3 actually does any of this. There's a suspicion that we're only seeing part of the system, that there is an unknown set of intracellular detectors that actually bind to the targets, with the NLRs simply serving as intermediaries. Another idea is that the NLRs do not recognize the intruders as such; they actually recognize the damage the intruders cause in the cell. [TO BE CONTINUED]

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[FRI 19 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (6)

* THE KILLING OF JFK -- LEE HARVEY OSWALD (6): Although Oswald didn't hit it off well with most of the Russian emigres he met in Fort Worth, he did strike up an unlikely friendship with one of them, George de Mohrenschildt. De Mohrenschildt was an oil geologist, wealthy, well-educated, well-traveled, from an aristocratic family of the days of the tsar. He had been friendly with the high-society Bouvier family some years back and had known the current First Lady, Jacqueline Bouvier Kennedy, as a child. Some conspiracy theorists have suggested that there was something sinister about de Mohrenschildt's association with Oswald. Why would somebody like him care about such a loser? Conspiracy theorists also point to the fact that de Mohrenschildt had "CIA contacts".

He did have contacts with the CIA, but there was less to that than meets the eye, and it's well worth discussing in some detail because the matter comes up again. Intelligence services don't get all their information from under the table: they scan through perfectly ordinary sources such as newspapers, books, almanacs, maps, and so on, to help build up a picture of a target country. As part of its "open source intelligence" effort, the CIA had a "Domestic Contact Division (DCD)" -- sometimes also known as the "Domestic Contact Service (DCS)" -- that would interview or get reports from ordinary Americans who had traveled abroad, particularly to East Bloc countries. The DCD talked to tens of thousands of Americans traveling abroad each year. The people interviewed were not on the CIA payroll and the CIA did nothing but ask them some questions. How much value the DCD had in intelligence-gathering might be debated; there is no doubt, however, that it proved a goldmine for conspiracy theorists, providing them with very long lists of "CIA contacts", who could easily be portrayed as "covert CIA agents'.

De Mohrenschildt did a lot of traveling and ended up talking with the DCD, ensuring that he would be eventually smeared with the "CIA agent" brush. Some have also suggested that de Mohrenschildt had been working for the Nazis during World War II, while others claimed he had KGB contacts. De Mohrenschildt said he had actually worked for French intelligence during the war, and there is no evidence to link him to the KGB -- for what it's worth, after the fall of the USSR, the KGB said they'd never had a file on him.

Anyway, so why did a classy guy like de Mohrenschildt take an interest in Oswald? It was not as unlikely as it looked. Those who knew de Mohrenschildt found he had an obnoxiously contrary streak, for example going to black-tie parties in a swimsuit; he would provoke Leftists by praising Fascism, provoke Rightists by praising Communism, and people generally regarded him as a "bullshitter". His background might have been aristocratic, but like Oswald he had what would later be called an "attitude" and his behavior was erratic; his flashy wife Jeanne was at least as out-of-control as her husband. De Mohrenschildt had plenty in common with Oswald.

* Oswald was sick of his job at Leslie Welding Company and simply stopped showing up for work on 9 October. On being told that employment prospects were better in neighboring Dallas than they were in Fort Worth, he started job-hunting there. In October 1962 the Texas Employment Commission managed to place him with Jaggars-Chiles-Stovall Company, a graphics-arts firm, working in photoprinting. Conspiracy theorists have made much of this: while the company mostly put together ads for print media, it also had a contract with the Army Map Service, and so the claim was made that Oswald had "extensive access to classified materials". In reality, only a small part of the company's work was classified, and that part was only handled by employees with a government security clearance. Oswald didn't have a security clearance, and given his past history there was no way he was ever going to get one, either.

Conspiracy theorists have pointed out that Oswald wrote "microdots" next to the entry for Jaggars in his address book. In reality, at the time he was incorporating "playing spy" into his already elaborate fantasy world. He liked tinkering with the company's equipment and worked after hours on forging official documents, for example producing a crude facsimile of a Marine Corps Certificate of Service under the name of "Alik Hidell" -- an alias he cooked up from his nickname while in the USSR, "Alek", and a Marine named Heindel who he'd known in the service. Oswald liked this alias and would keep on using it or variations of it.

Oswald moved his family to a dingy apartment in Dallas at the beginning of November. The move led to particular tensions between husband and wife, with Marina beaten repeatedly. The move generally broke the family's contacts with the emigre community, though he did still see de Mohrenschildt on occasion. The family had Thanksgiving dinner at Robert Oswald's house; in the interests of harmony, Robert made a point of not inviting Marguerite. John Pic was there, the first time Lee and John had met in ten years. It was also the last. [TO BE CONTINUED]

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[THU 18 MAR 10] SPACE NEWS

* Space launches for February included:

-- 02 FEB 10 / PROGRESS 36P (ISS) -- A Soyuz booster was launched from Baikonur to put a Progress tanker-freighter spacecraft into orbit on an International Space Station (ISS) supply mission.

-- 09 FEB 10 / ENDEAVOUR (STS-130) / ISS -- The NASA space shuttle Endeavour was launched from Kennedy Space Center on "STS-130", an International Space Station (ISS) support mission. This was the 130th shuttle flight and the 24th flight of Endeavour. It was the last scheduled shuttle night launch. There were six crew, including:

Endeavour carried the "Tranquility" connecting node and the "Cupola" observation deck module for the ISS. The shuttle docked with the ISS on 10 February, with the shuttle crew joining the ISS "Expedition 22" crew of commander Jeff Williams and engineer Oleg Kotov. The shuttle returned to Earth on 22 February, landing at Kennedy Space Center after 13 days 8 hours 8 minutes in space.

-- 11 FEB 10 / SOLAR DYNAMICS OBSERVATORY -- An Atlas 5 401 booster was launched from Cape Canaveral to put the NASA "Solar Dynamics Observatory (SDO)" into geostationary orbit. SDO had a launch mass of 3,200 kilograms (7,000 pounds) and carried a payload suite based on three elements:

The instruments returned data at a rate of 150 megabits per second, requiring use of a Ka-band downlink and dedicated receiver systems on the ground. The mission was planned to last five years but the spacecraft had enough consumables for ten years of operations. SDO was the first mission in the "Living With A Star" program to analyze the Sun, with an eye on solar influence over the Earth's environment and human technological systems. The Atlas 401 launcher had a 4 meter (13 foot) payload fairing, no solid rocket boosters, and an upper stage with one Centaur engine.

Solar Dynamics Observatory

-- 12 FEB 10 / INTELSAT 16 -- A Proton Breeze M booster was launched from Baikonur to put the "Intelsat 16" geostationary comsat into orbit. The spacecraft was built by Orbital Sciences, carried a payload of 24 Ku-band transponders, and had a design life of 15 years. It was placed in the geostationary slot at 58 degrees West longitude for direct-to-home services to Latin America, being operated by Intelsat on behalf of SKY Mexico and SKY Brazil, local subsidiaries of DirecTV of the US.

* OTHER SPACE NEWS: The Iranians recently put on display a mockup of their new "Simorgh (Phoenix)" two-stage liquid-fueled satellite launch vehicle. It is 27 meters (88 feet 6 inches) long; has four engines on the first stage and one on the second stage; and can put a 60 kilogram (132 pound) payload into orbit. The Iranians also displayed information on a new small telecommunications satellite, a reconnaissance satellite, and a satellite that was presented but not described.

There were concerns that the Simorgh represented Iranian progress in development of long-range missiles, but Pentagon intelligence reports have downplayed Iranian progress in the missile field. Conservative assessments of Iranian missile capabilities led the Obama Administration to cancel deployment of heavy antimissile interceptors to Poland, much to the joy of the Kremlin and disgust of American conservatives. However, the Obama Administration was simply stepping back to a less ambitious plan, and is now pushing for deployment of smaller SM-3 interceptors in Romania. The Russians are once more annoyed.

* AVIATION WEEK reports that Globalstar, owner of the Globalstar satellite world-wide mobile communications system, is planning to launch an initial set of six second-generation replacement satellites in the coming summer, with a total of 24 satellites in place by the middle of 2011. The new satellites will replace half the 48 satellites of the original constellation, which has been in operation since the late 1990s. Ground system improvements are being implemented in parallel. While the new satellites support channel speeds of 256 kilobits per second (KBPS), up from 9.6 KBPS of the current system, the higher data rates won't be available until the ground system is up to speed in 2012.

The first-generation network provided circuit-switched voice and data connections, but the second-generation satellites will supply packet-switched Internet Protocol-based voice, messaging, video, and other communications services at higher data rates. The second-generation spacecraft are being built by Thales Alenia Space of Italy and will be shipped to Baikonur in Kazakhstan for launch on a Soyuz booster.

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[WED 17 MAR 10] CONNECTOMICS

* CONNECTOMICS: As discussed in an article in THE ECONOMIST ("Wired", 8 April 2009), the 2008 Nobel Prize in chemistry was awarded to three researchers -- Osamu Shimomura, Martin Chalfie, and Roger Tsien -- for discovering "green fluorescent protein (GFP)" in jellyfish and determining how it could be used to trace the biological functions of various other organisms. A neurobiologist named Jeff Lichtman has followed up on this discovery to develop a way to tag the nerve cells of mice with genes that produce proteins fluorescent in red, green, and blue. Using the full color imagery provided by the "brainbow" proteins, Lichtman was able to obtain insights into the elaborate wiring of the mouse brain. He intends to use the brainbow mice to investigate neurological development, which besides being interesting in itself could help deal with the occasions when brain wiring doesn't develop as it should, resulting in the afflictions lumped as "connectopathies".

Lichtman's work is one of the most famous examples of the emerging science of "connectomics". Just as every organism has a "genome", a set of genetic codes to define its architecture and operation, they also have a "connectome", a network of nerve cells with a particular pattern of connections, though unlike the genome the connectome alters over time as new connections are formed and older ones break. Lichtman and others in the field dream of a "Human Connectome Project", analogous to the Human Genome Project, to unravel the map of the human connectome.

The science of connectomics actually began well before the word itself existed. In 1972 Sydney Brenner, a biologist then at Cambridge University in the UK, decided to unravel the nervous system of a small roundworm named Caenorhabitis elegans. The roundworm seemed like an excellent subject for such an investigation, since it only has about a thousand cells overall, with about 300 of them neurons. It is also hermaphroditic, capable of breeding itself, producing generations of generally identical roundworms, and it is easy to breed them in large numbers. Brenner's research team embedded the roundworms in blocks of plastic, then sliced the blocks into thin sheets and stained them to permit detailed examination under an electron microscope. After fourteen years of exhausting study, the research team was able to produce a complete map of the nervous system of C. elegans. For this and other work, Brenner shared the 2002 Nobel Prize for medicine.

Such an approach is flatly not practical for mapping the connections of, say, the brain of a mouse. The cerebral cortex -- the part of the brain that "thinks" -- is made up of two-millimeter-long elements known as "cortical columns"; Winfried Denk of the Max Planck Institute for Medical Science in Heidelberg estimates that to map out one cortical column would take a graduate researcher, using Brenner's methods, about 130,000 years. Call it job security.

Of course, automation has come a long ways from the 1970s and 1980s, and machines can now do much of the grunt work far faster and more cheaply than a grad student. Brenner's group, for example, used a transmission electron microscope (TEM), in which the electron beam passes through the sample to be picked up by the imaging sensor. The problem is that a TEM has to work one carefully-prepared slide at a time. In contrast, a scanning electron microscope (SEM) images the reflection of an electron beam off a sample. Denk's group uses a SEM with an automated slicing mechanism; instead of imaging a slide at a time as with a TEM, a researcher can feed the SEM an entire block, with the SEM scanning the surface, then slicing off the top layer to image the next layer.

Researchers have also figured out clever ways to tag particularly interesting parts of the brains. A single neuron has dendritic tendrils that branch wildly through a brain; Denk's research team uses an enzyme, derived from horseradish of all things, that coats the surface of a selected neuron and then reacts visibly to a stain. Ed Callaway of the Salk Institute in La Jolla, California, has even made use of the rabies virus, a notorious assailant of the nervous system, with the virus jumping from neuron to neuron to trace nerve connections.

Brenner's team also had to make do with the "Mark One Eyeball" to determine the patterns in the roundworm nervous system, but in the 21st century image analysis software is well developed and in widespread use. Sebastian Seung, a computational neuroscientist at the Massachusetts Institute of Technology, is writing a program to sift through the sets of data and build up a map of neural connections by trial and error.

The mouse is the primary target for current work in connectomics, since it is cheap, breeds fast, and its brain is relatively simple -- half a gram in mass, with only 16 million neurons. Compared to the roundworm nervous system, the mouse brain still remains an ambitious target, four orders of magnitude bigger. Once the mouse brain is mapped, the tools should be in place to take on the next target, the human brain, which weighs 1.4 kilogram and contains 100 billion neurons. That may seem like an intimidating goal, but the potential rewards are great enough to make it worthwhile.

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[TUE 16 MAR 10] RIDE THE DIGITAL CAR

* RIDE THE DIGITAL CAR: As reported by an article from IEEE SPECTRUM ("This Car Runs On Code" by Robert N. Charette, February 2009), the new Lockheed Martin F-35 Joint Strike Fighter features about 5.7 million lines of program code to run its systems, while the new Boeing 787 Dreamliner has about 6.5 million lines of code. Sounds impressive? Then consider that a luxury auto with deluxe bells and whistles runs on 100 million lines of code, executing on 70 to 100 microprocessor-based "electronic control units (ECUs)" distributed around the car.

The radio and navigation system alone of the current S-Class Mercedes Benz runs to 20 million lines of code, and the car has about as many ECUs as an Airbus A380 super-jumbo jetliner -- excluding the jetliner's in-flight entertainment system. Even low-end cars now have 30 to 50 ECUs. ECUs are found in subsystems for airbags, antilock brakes, engine ignition and control, windshield-wiper control, automatic transmission, climate control, power steering, and of course entertainment / communications systems. In a few years, it is likely that the amount of code in a car will double or even triple.

One of the drivers for the explosion of code in a car is the need to save energy, reduce emissions, and improve safety by making the car "smarter". For example, a car's airbag system has to reliably operate for years in a range of environmental conditions, from very cold to very hot, without deploying airbags on a false alarm -- and then deploy them, in a sequence appropriate to the impact direction, in a fraction of a second when they're needed. Now work is in progress to allow the airbag system to inform emergency responders just how severe the crash was.

The first automotive ECU was a single-function controller used for electronic ignition timing in the 1977 General Motors (GM) Tornado. The next year, 1978, GM offered as an option a "Cadillac Trip Computer" based on a Motorola 6802 processor for the Cadillac Seville that provided data on fuel use, speed, and engine information. By 1981, GM cars had about 50,000 lines of code, and other car manufacturers were getting on the digital bandwagon.

At the time GM began to put advanced electronics into its cars, electronics was about 5% of the cost of a car's hardware; now it's over 15% on average, and up to 45% for hybrids, with their more complicated propulsion scheme. Some believe that the electronics is likely to easily run to half the cost of car hardware in the not-too-distant future. Even at present, software development contributes up to 15% of the sticker price of a car.

This greater complexity is absolutely not without its drawbacks, with major manufacturers forced to perform expensive recalls to fix software problems. Even though a good portion of a car's firmware is devoted to diagnostics, it's still hard to fix such a complicated system, and industry stats show that half the ECUs that mechanics swap out actually work perfectly well. Automotive designers have hopes that remote diagnostics -- ultimately performed by a car over wireless at home in the garage -- may help deal with the growing maintenance problem.

Others may be very skeptical of that idea, but like it or not, cars are going to keep on getting more complicated as sensor systems are incorporated to keep an eye on traffic and obstacles, and wireless systems are added to link into traffic control systems. The ultimate goal is a car that drives itself -- which most will agree is an interesting idea in principle, but drivers are going to need a lot of convincing before they'll be willing to give up the wheel to a car running on hundreds of millions of lines of code with a statistically known fraction of defects.

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[MON 15 MAR 10] PARASITIC WASP GENOME (2)

* PARASITIC WASP GENOME (2): The vast numbers of parasitic wasp species seems to be linked to the fact that 90% of known wasp species are "picky eaters", targeting only one or two host species. That implies a lot of wasp species. As Warren points out, while caterpillars are seen as the stereotypical target of the wasps, they're hardly restricted to them: "Virtually every arthropod on Earth is attacked by one or more of these parasitoid wasps."

The target selectivity of parasitic wasps makes them potentially useful for pest control. Cassava is a leafy edible plant that is a staple in many African countries, having been imported from South America 400 years ago. In the 1970s, the cassava mealybug, which lives on cassava, followed the plant to Africa from South America; by the 1980s, the mealybug was laying waste to cassava fields. However, the mealybug was not all that common in South America. Something was keeping it in check, and investigation showed it was the parasitic wasp Apoanagyrus topezi. After testing the wasp to ensure that it wouldn't become a pest itself, it was released in African countries where the mealybug was a problem. The mealybug was all but wiped out.

The idea of using a precisely targeted wasp species as a "magic bullet" to selectively kill off pests is a tempting one, but it's not as easy as it sounds. The cabbage butterfly was introduced into the USA late in the 19th century and quickly made a nuisance of itself. A parasitic wasp that targeted the butterfly was imported from England in 1881, but it wasn't suited to climate where the introduced butterfly ranged, and proved ineffectual. Another wasp imported from Yugoslavia in the 1970s proved no better. Finally, a wasp was imported from China in the 1980s that was better suited to the climate, and has proven highly effective in killing off the butterflies. However, private companies have never been particularly interested in using parasitic wasps for pest control because, once the wasps have been introduced, they're self-supporting and so there's no more sales to be made. Governmental and non-governmental agencies have also become more reluctant to take chances on the unpredictable results of introducing foreign species. In short, it's not something people are inclined to do if they don't absolutely have to.

* In contrast, enthusiasm for the parasitic wasp as a lab animal has been increasing. One species of wasp has been a particular favorite, the fly hunter Nasonia vitripennis. It's easy to raise in the lab, has a short life-cycle, and can be interbred with closely related species -- if treated with antibiotics first, since species-specific Wolbachia bacteria will otherwise render the couplings sterile.

The prominence of N. vitrepennis made it a high-priority target for genomic analysis, and the sequencing of its genome, as well as of two close relatives in the Nasonia genus, attracted a good deal of attention. John Werren pushed the project in collaboration with Stephen Richards of Baylor College of Medicine in Houston, Texas, with Werren pointing out the unique benefits of a hymenopteran for genetic studies. We are "haploid" animals, with two sets of chromosomes in our cells, while the hymenoptera are "haploduploid": the females have two sets of chromosomes, while the males hatch from unfertilized eggs and only have a single set. That means that genetic changes will show up immediately in male hymenopterans, since they don't have parallel second genes that could mask mutant genes. Interestingly, the wasp genome has 450 genes in common with humans not found in the Drosophila fruitfly, long the standard insect for lab studies, meaning the wasp may prove to be a closer genetic analogue to humans than the fruitfly.

* Of course, the Nasonia wasps are also interesting targets of genetic study because of their specific adaptations. N. vitripennis parasitizes larvae of house flies and other "filth flies", and is not too picky about its hosts. However, its sibling species only target blowflies found in bird nests. Work is underway to nail down the wasp genes responsible for host preference, a task that not only promises to reveal new insights into the emergence of species or "speciation", but hints that some day we might be able to genetically engineer parasitic wasps to attack any arthropod pests we want to control.

Another interesting feature of parasitic wasps is that they produce venoms that have a wide range of effects on target hosts, with these venoms having potential applications in biomedicine. Researchers have performed a computer analysis using the new Nasonia genome and mass spectroscopy analysis of the wasp's venom to identify 79 proteins in the genome -- half of which had not been recognized as venoms before, with about a quarter of the total being unlike any seen before.

Wasp venoms appear to evolve very rapidly, with specific venom cocktails often more effective against one host than another. The adaptation of venoms appears to be one of the processes driving the massive diversification of parasitic wasp species. Another process driving the speciation of the wasps appears to be the high mutation rate of their mitochondrial DNA. The cells of "eukaryotic" organisms -- as compared to the "prokaryotes", the bacteria and their sibling group the archaea -- have DNA in the cell nucleus and separate DNA in the cellular organelles known as "mitochondria". It is known that mitochondrial DNA tends to mutate faster than nuclear DNA, with the rate of mutation of mitochondrial DNA in Drosophila running about seven times faster than the nuclear DNA. In wasps, the rate is about 35 times faster. The mitochondrial and nuclear DNA functionally complement each other, and the high mutation rate means that the mitochondria of one strain of wasps quickly become incompatible with the cells of another strain of wasps.

As ghastly as parasitic wasps are, researchers have come to appreciate what they have to offer. As Claude Despan, a geneticist at New York University in New York City, says of Nasonia: "This species is no longer a 'weird' species with interesting features. It has graduated to be of help to address questions that cannot be that easily investigated in flies." [END OF SERIES]

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[FRI 12 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (5)

* THE KILLING OF JFK -- LEE HARVEY OSWALD (5): Conspiracy theorists have wondered why Lee Harvey Oswald was not harassed by American authorities when he came back from the USSR, but the truth was that his temporary stay in the Soviet Union did not break any US laws. He could not have betrayed any secret information to the Reds for the simple reason that he possessed no secret information to betray. Of course, he was now automatically disqualified from ever obtaining even the most casual security clearance -- but since he wasn't in any position to obtain a job that required a security clearance, or for that matter any job that required more than menial skills, that wasn't an issue either.

American authorities did have some interest in him, which of course conspiracy theorists also try to make out as suspicious. Not long after Oswald had arrived in Fort Worth, the FBI gave him a call; the bureau had opened up a file on him when he went to the USSR and wanted to talk to him. The interview, with Agent John Fain, was on 26 June 1962 and it was confrontational, with Fain finding him evasive and uncooperative. Later Lee told Robert that the FBI had asked him if he was a US government agent; he laughed at them and replied: "Well, don't you know?!"

In July, Marguerite Oswald showed up in Fort Worth, rented a tiny apartment, and asked that Lee move in with his family. Lee didn't like the idea but Marguerite was as always inflexible, and they moved in on 14 July. He got a job as a sheet-metal worker with Leslie Welding Company three days later. Marguerite got to picking on Marina, with the tension escalating until Lee took his family out of the apartment on 10 August, with Marguerite throwing a screaming fit, running after the car when Robert Oswald took them away.

Lee took his family to a broken-down rental house. On 16 August, the FBI dropped by; they wanted to talk to him again. Agent Fain was still not satisfied with the evasive answers Oswald gave him, but when he asked Oswald if the Soviets had asked him, Oswald, to do them any favors, Oswald replied: "No. I was not that important." Fain saw the truth in this and, despite his continuing distrust, decided to close Oswald's file. It could be opened again when needed, but for now Oswald had disappeared off the FBI's screens. Some conspiracy theorists insist that the FBI visited Oswald in order to recruit him, but given his residence in the USSR, the bureau had legitimate reason to check up on him and there's no evidence that the FBI did any more than question him. Ironically, even though the FBI had filed him away for the time being, Oswald would see the bureau's malign hand in his personal troubles from then on.

Oswald was frustrated. He and Marina were not getting along well, leading to quarrels and occasional sessions of wife beatings. He was involved with a group of Russian emigres through Marina; the emigres found him erratic, "not quite right in the head". Oswald remained a noisy Communist -- although he didn't have a high opinion of the USSR, he shrugged it off as a bad implementation of a good idea -- which didn't go over well with the emigres either, since most were anti-Communist. Oswald remained in character in his ability to win friends and influence people. [TO BE CONTINUED]

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[THU 11 MAR 10] SCIENCE NOTES

* SCIENCE NOTES: It is known that the human genome includes some sequences that were obtained from "retroviruses" -- the class of viruses, the best-known member being the HIV pathogen that causes AIDS, that have a genome made of the RNA molecule instead of the DNA molecule, and insert their genome into a host cell genome. At some occasions in the past, retroviruses inserted their genomes into the human germ cell line and left their markers with us. Fortunately, the genomes of all such retroviral hitchhikers in our genome are broken by mutations, so they can't be expressed and produced.

Somewhat to their surprise, a team of Japanese researchers found copies of the genome of a "bornavirus", a virus that causes diseases in horses and sheep, inserted into the human genome in several places. The bornavirus is an RNA virus but not a retrovirus: it normally does not insert its genome into that of a host cell. The bornavirus genome has also been found inserted into the genomes of other mammals, with bornavirus "fossil" patterns common to us and other animals indicating that such insertions went back when we shared common ancestors. Using that for a very rough clock, the oldest insertions are about 40 million years old.

* DISCOVERY CHANNEL Online had an interesting little photo-essay on the Hawaiian bobtail squid, a charming little thumb-sized creature that has an interesting relationship with symbiotic bacteria. The bacteria, Vibrio fischeri, live in an organ provided by the squid; the microorganisms, which are luminescent, return the favor by illuminating the bottom of the squid so that predators looking up don't see a shadow going overhead.

The squids are active at night. In the morning, they eject a large portion of the bacteria, allowing them to "infect" other squids, and then bury themselves in sand to hide out for the day while their bacteria replenish themselves. Once the Sun goes down, the squid venture out, camouflaged by the bacterial light, which is reflected downward and, it seems, modulated to a degree to match lighting conditions by the structure of the organ in which the bacteria live. The squid otherwise does not need the bacteria to stay alive.

Incidentally, humans have tinkered with using illumination for camouflage as well. During World War II, the US rigged up aircraft with lights arranged so that they wouldn't be as easy to see from a distance in daylight conditions, allowing them to sneak up on German submarines cruising on the ocean surface before they could dive and escape. The scheme actually worked as planned, but nobody could figure out a really satisfactory way to mount the lights on the aircraft and it was judged generally impractical.

* There was a buzz in the science blogosphere concerning the "Dark Energy Camera (DECAM)", being developed by the US Fermi National Laboratory in Batavia, Illinois. The DECAM is no ordinary camera: it has a resolution of 570 megapixels, is cooled to -100 degrees Celsius, and is the size of a minicar. The DECAM uses an array of 74 CCD imagers to achieve its high resolution; it has to crunch so much data that it takes 17 seconds to obtain a single image. In 2011, the DECAM, will be installed in a 4 meter (157 inch) telescope known as the "Blanco" at the Cerro Tololo Inter-American Observatory in Chile. Using the DECAM, the telescope will map the southern skies, obtaining floods of data on the reddening of light or "redshifts" of distant galaxies and other cosmic objects due to the expansion of the Universe. The detailed redshift maps are expected to provide new insights into the mysterious "dark energy" that seems to control the expansion rate of the cosmos.

pathogens in glass

* While the arts and the sciences don't have a reputation for getting along well, there are those who do make the attempt to bridge the gap. One interesting example is UK visual artist Luke Jerram, who has taken to rendering pathogens -- the flu virus, HIV, and so on -- as glass sculptures. Jerram's work tends to illustrate the mixed feelings we have towards pathogens: as deadly as they are, they can be absolutely fascinating and even, to the properly tuned eye, downright beautiful.

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[WED 10 MAR 10] VENTER DOES BIOFUELS

* VENTER DOES BIOFUELS: The rush to develop biofuels over the last few years seems to have slowed somewhat, partly due to fluctuations in oil prices and partly due to the fact that expectations for biofuels have proven a bit overblown. However, as reported in THE ECONOMIST ("Craig's Twist", 15 July 2009), oil giant Exxon is now investing $300 million USD in biofuel research and, if things seem to work out, may invest $300 million USD more. The money is going to Synthetic Genomics, a startup in San Diego, California, run by Craig Venter. Venter's credentials are good, since he ran Celera Genomics, the for-profit firm that helped decipher the human genome.

Synthetic Genomics has a different target: algae. Currently, biofuels are made by fermenting corn or sugarcane to produce ethanol, or processing plant oils to make biodiesel. Both processes leave something to be desired in terms of delivering a cost-effective product. Venter would like to "biomanufacture" fuels using algae that have been genetically modified to directly produce fuels with little or no additional processing.

Many startups are tinkering with biofuels from algae, some species of which produce oils that can be used for biofuels. One of the issues in this process is to get the oil out of the algae; Venter's team has managed to genetically modify algae so it actually releases the oil, which floats to the surface of the culture tank. The oil still needs processing to turn into fuel, and that's where the Exxon money comes in. The oil produced by the algae is a "triglyceride" that contains oxygen atoms, along with carbon and hydrogen; Synthetic Genomics plans to further tweak the genome of the algae to get rid of the oxygen, resulting in a pure hydrocarbon that could, in principle, be used as a fuel with no need for chemical alteration.

Once Synthetic Genomics has the genetic tweaks in place, the last task is to find a species of algae best suited for biomanufacturing, capable of handing intense sunlight and the associated heat so it can photosynthesize like mad. Since the algae will be cultivated in large batches, it will also need to be disease resistant. If no one algae species has all these desireable properties, Synthetic Genomics will cut-&-paste the genomes of several to come up with one that does.

Carbon dioxide will be needed to drive the growth of the algae, and since the atmosphere can't provide enough, it will be obtained from the exhaust of a power plant or other major industrial facility. Since the power plant is driven by coal or other fossil fuels, the process is not carbon-neutral -- the CO2 ends up escaping in the end when the biofuel is burned in an automobile or other vehicle. However, there's no additional carbon footprint from burning vehicular fuels obtained from the ground.

Venter believes that his biofuel scheme can turn out at least ten times more fuel per hectare than can be turned out from corn or sugarcane, and will not take up land needed for food production. That's not an entirely level comparison, since the production system for algae biofuels will be more complex and capital intensive, more like a chemical plant than a farm, and will need to be sited near power plants or other facilities to provide the CO2 -- though if it works out, admittedly a big "if", it might be profitable to simply build pipelines to pump the CO2 to the fuel synthesis plants. Right now it's a dream, but it can pay off sometimes to dream big.

* SCIENTIFIC AMERICAN Online had several other articles on efforts in biofuels:

The last item included a comment that could apply to most biofuel efforts -- the researchers pointing out that at present what they have is essentially a blue-sky idea, one saying: "With R&D, it can look easy on paper, but you can run into all sorts of challenges."

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[TUE 09 MAR 10] WHO NEEDS DEMOCRACY?

* WHO NEEDS DEMOCRACY? As reported by an article from THE ECONOMIST ("Crying For Freedom", 16 January 2010), international human rights activists have noticed an unsettling trend: democratic rule seems to be on the decline around the world. Twenty years ago, with the fall of the Soviet empire, it seemed like the rule of authoritarians had been given a sharp rap that would, thanks to the unfortunate lessons of the past, provide a new drive to liberalize societies with open elections, the rule of impartial law, respect for the rights of individuals, freedom of expression and association, and free enterprise.

Even then, the sensible were keeping their fingers crossed, understanding that a hopeful outcome is not an inevitable one. They were wise to be cautious. Many of the states that arose from the rubble of the USSR are authoritarian, some downright tyrannical, and authoritarian states are now collaborating on how to maintain their grip on power. Worse, democratic states have lost their bubbly optimism, and have even become somewhat apologetic.

That weary spirit of apology partly owes its origins to the US war to oust Iraqi dictator Saddam Hussein, which early on was enthusiastically proclaimed as a campaign for democracy. That wasn't the way things worked, and in fact much of the world saw American talk of democracy for Iraq as a cover for overbearing imperialism. The attempt to set up a democratic regime in Afghanistan has similarly proven rocky, with the corruption of the Afghan government undermining efforts to bring peace to the country. In contrast, emerging China seems to show that authoritarian rule can work, with countries such as Syria and Cuba taking China as a role model. Many poor countries are also fond of China, since the Chinese are inclined to do business with them without pestering them about little defects, like miserable records on human rights and gross misgovernance.

That leads to the question of whether democracies are still a reasonable option for the undecided. Arguments can be made that they are, the most significant one being that authoritarian rule tends to be so bad. It is a concentration of unrestrained power in the hands of a few that is all but inevitably corrupting, the worst examples being the "kleptocracies" of the nastiest African states, with leadership that loots the country and crushes anyone who dares protest. Even in their milder forms, authoritarian states are not usually fun places to live, their merits generally being enthusiastically praised by those who give the orders, but not by those told to obey them.

Authoritarian regimes like to defend their ways by pointing out they ensure stability and promote efficiency. There is no strong evidence that they do either, and fair evidence that they don't. It has been observed that India, with its many ethnic groups and their tensions, could not have survived except as a democracy; stability imposed by repression is brittle, prone to fracture when the pressure finally becomes too great, and rigid authoritarian rule in India would have led to violent disintegration. Authoritarian states are particularly bad at transitions of power, with the passing of a strongman ruler often leading to chaos. As far as promoting efficiency goes, the reality is that authoritarian states are much more interested in denying accountability and perpetuating the rule of the leadership class than getting things done, tying up day-to-day life in long lists of rules and overbearing bureaucracy.

Corruption and inefficiency also seemed to be bred by state control over the economy. China has, as noted, been doing very well for itself economically, but that is very much due to the government releasing its grip over commerce. To the extent that it hasn't, is Chinese success due to the repressiveness of the leadership, or in spite of it? Does a country that spends such resources trying to monitor its citizens on the internet really seem all that efficient or forward-looking? Is a government that is so neurotic, so confused in its priorities, that it hands out stiff prison sentences to harmless citizens who politely suggest nonviolent reforms really a model worth emulating?

On the best face of it, democracies have authoritarian states beaten in every way. Checks and balances dilute concentration of power; representative government ensures that different groups have a say in their own governance; transparency helps suppress corruption; free enterprise releases the energies of entrepreneurs; abuses of law are uncovered and corrected; transitions of power are orderly. Certainly, though elections don't always produce good leaders, they help prevent bad leaders from staying in charge indefinitely. The problem is that it is possible to have all the formalisms of a democracy and end up with a system that is indistinguishable from the worst authoritarian states. Modern Russia is an unfortunate example: much care has been put into setting up a structure that resembles a Western parliamentary democracy, but the reality is a system that is notably corrupt and repressive. Freedom of speech on paper means little if it translates in reality to being gunned down on the street by goon squads.

The obvious truth is that democratic formalisms amount to nothing if underlying conditions to make them work aren't there. There has to be a culture where corruption, though it may exist, is not a normal and tacitly condoned practice; where differences of opinion, however acidly expressed, do not lead to violence; where there is a spirit of tolerance, however grudging, for individual expression; where factions are willing to make meaningful concessions and not insist on imposing their will on everyone else at any cost; and where the basic principle of government, however muddily expressed in practice, is that the state serves the citizens and not the reverse.

The ultimate fact is that while democracies can go bad, authoritarian states are on the wrong track from the outset. As Winston Churchill once observed, democracy is the worst form of government, except for all the others. Democracy, for all its failings in practice, still remains worth defending -- though the defense has to be tempered by the realization that it's not always particularly easy to attain.

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[MON 08 MAR 10] PARASITIC WASP GENOME (1)

* PARASITIC WASP GENOME (1): Parasitic wasps are not charming beasts: they lay eggs on or in insect or spider hosts that hatch to devour their hosts alive. As reported by an article in AAAS SCIENCE ("The Little Wasp That Could" by Elizabeth Pennisi, 15 January 2010), however unpleasant they are, parasitic wasps are far more common and ecologically important than we realize. Says Daniel Janzen, an ecologist at the University of Pennsylvania: "You get one in your eye and you pull it out with your finger and think it's a piece of dust. There's millions of individuals out there, and you don't know they exist."

Despite their obscurity, parasitic wasps are significant in human affairs. The US Department of Agriculture (USDA) estimates that parasitic wasps save the US about $20 billion USD a year by killing off vast numbers of insect pests. Scientists have certainly long appreciated the wasps: entomologists are fascinated, in a ghoulish sort of way, by their elaborate life cycles; ecologists are intrigued by their influence in ecosystems; and genetics researchers are increasingly finding them a rewarding and convenient lab subject -- "yeast with wings", as one geneticist put it.

Now an international group of over 150 researchers has published the genomes of three parasitic wasps of the genus Nasonia, which parasitizes flies. Geneticists see the new genomic data as not merely establishing the Nasonia wasps as a genomic model for the "hymenoptera" -- the insect order of ants, bees, and wasps -- but as lab organisms whose importance now ranks equal to traditional favorites like the Drosophila fruitfly and the C. elegans roundworm.

* Daniel Janzen got into parasitic wasps by an indirect path. He'd been a butterfly collector since boyhood, capturing caterpillars to see what kind of moth or butterfly they ultimately changed into. While engaged in this pursuit in Costa Rica in the early 1980s, he was confounded to find too many of his caterpillars turning to mush, with parasitic wasp larvae emerging from the debris. Instead of getting frustrated, however, Janzen started collecting the wasps, documenting their target hosts and visiting a wasp expert once a year to get identification on his specimens. Now Janzen has about 20,000 samples of wasps and an appreciation of just how common they are.

Some species of wasps will lay up to 200 eggs on a caterpillar, while others will only lay one egg that hatches to clone itself rapidly. Sometimes the larvae will lie dormant in a host, evading its immune system, and wait for the host to fatten up; when it does, the larvae rapidly eat it up from the inside out. Some treat their host as a nest, with some of the clones in the nest becoming sterile "soldiers" that take on intruders, significantly including other parasitic wasps.

Parasitic wasps also have interesting interactions with pathogens that live in them in turn. Many wasps are infected with the bacterium Wolbachia, which can skew the sex ratio of offspring. Other species of wasps carry a "male-killing" microbe that kills off males in a brood but not females. Some wasps even have a hitchhiker virus that ends up being injected into a host along with an egg to disable the host immune system.

parasitic wasp

One of the problems with the study of parasitic wasps is the fact that the wasps tend to look alike, even when they are different species with very different behaviors. When DNA barcoding began to become popular, Janzen offered his collection of wasps for analysis; 2,597 specimens were analyzed, yielding 313 species, instead of the 171 that had been assumed. Analysis has shown that one wasp believed to be a single species was actually 36. While almost 60,000 parasitic wasps have been identified, that seems to be merely the tip of the iceberg. When researchers sampling insects in a tropical forest fog a tree, parasitic wasps make up a high proportion of the samples collected. Says John Werren, an entomologist at the University of Georgia in Athens: "There's a really compelling argument that these parasitoid wasps may be more common than beetles." [TO BE CONTINUED]

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[FRI 05 MAR 10] THE KILLING OF JFK -- LEE HARVEY OSWALD (4)

* THE KILLING OF JFK -- LEE HARVEY OSWALD (4): After getting married, Lee Harvey Oswald focused on getting out of the USSR. In May 1961, Oswald wrote the US embassy in hopes of arranging his return to the US along with his bride. He had also been informed earlier in the year in a letter from Marguerite that, thanks to his visit to the USSR, his "hardship" discharge from the Marines had been changed to an "undesireable" discharge -- not as bad as a "dishonorable" discharge, but still not good -- and was writing letters back home to get that straightened out. Oswald would never get rid of the undesireable discharge, but in July, he went to Moscow and finally managed to get the embassy to give him authorization to go home. Marina submitted paperwork to obtain an entrance visa to the US as well. Marina was pregnant at the time and gave birth to a baby girl, named June, in February 1962.

Soviet authorities continued to be troublesome, though it is unclear why since the KGB had passed down the word that nothing was to be done to discourage Oswald from leaving. He wasn't wanted; it was the issue of taking Marina with him that made matters difficult. Some conspiracy theorists have read volumes into Oswald's misadventures in his effort to go back home to the USA, but in hindsight it was an ordinary bureaucratic nightmare, the inconsistencies in the process being due to the occasional screwups that occur in a stream of paperwork -- not to mention the fact that the erratic Oswald was not the easiest person to deal with.

He did get a loan from the State Department for $435.71 USD, which has of course been seen as suspicious -- why would the government subsidize a disloyal citizen? However, State Department regulations permitted loans to help resolve situations embarrassing to the USA; once Oswald went home, he would be out of the State Department's hair, and it was all for the good for US propaganda for a defector to find out that the grass really wasn't greener on the Red side of the hill. The loan was minimal, and only granted once Oswald had exhausted other possibilities.

Finally, on 1 June 1962 Oswald and his family left the USSR on a train to Rotterdam. There they took passage on a ship and arrived at Hoboken, New Jersey, on 13 June. Astoundingly, Oswald thought that reporters would flock to him to ask him about his defection and even wrote up a script for what he would say to them. To no surprise of no one but himself, nobody was there. It should be noted that there had been an article in the US news service when Oswald departed for the Soviet Union -- at the height of the Cold War, people noticed such things -- and there was an article when he came back, but he was hardly front-page news. Effectively penniless, he and his little family ended up living in the house of his brother Robert in Fort Worth, until he could get settled.

* Yuriy Nosenko had drifted away from the Oswald case even before Oswald had left the USSR, but after Oswald became globally infamous, KGB brass immediately ordered Nosenko to obtain the files on Oswald from Minsk and determine what official Soviet dealings had taken place with the American visitor. The files would have indicated if there had been any contacts by other Soviet intelligence services, such as the military GRU. Nosenko was able to give the files a reasonable looking-over, finding no evidence of any such contacts, before he was ordered to hand them over to the high-level KGB First Directorate. The KGB wanted to be able to reassure the Kremlin that Soviet intelligence had no interaction with Oswald, and a First Directorate report was felt to carry the maximum weight.

It is possible to have legitimate suspicions about what Oswald had actually been doing in the Soviet Union, that all the information revealed on his activities there was actually bogus, intended to cover the KGB's tracks. It is, however, also hard to dismiss the fact that Oswald was an emotionally unstable nobody; that the KGB had no reason to regard him as anything more than an obnoxious nuisance; and that no credible source of information has ever indicated anything different. Certainly it is difficult to believe Oswald was recruited as a Red agent before he went to the USSR, since defecting would have blown his cover permanently. One hint that makes it hard to believe that he was recruited after he went was the fact that he came back with Marina: sending Oswald back to the USA with a Russian wife in tow would have been like painting a big Red warning sign in blinking neon lights on him.

According to Nosenko, the KGB didn't even think Oswald might be an American spy, since they couldn't believe the CIA or FBI would employ such a loser. Certainly if they had, he accomplished nothing for them in the USSR, since Oswald had no access to anything remotely secret there and he was under surveillance, with the surveillance revealing nothing that suggested he was a spy. The Soviets took a very dim view of spies, and if they had honestly thought Oswald a spy, he would have been treated very harshly.

When asked if Oswald had any KGB connection, Nosenko replied: "Absolutely none. The files were clear. The KGB didn't want Oswald from day one." Unclassified KGB documents later said the same sorts of things. Again, nobody would judge the KGB a good source of reliable facts -- but it should be noted that the Soviet press, an instrument of the government, was publicly critical of the Warren Commission's conclusion that Oswald was a lone operator. Had Oswald been a Red agent, the Soviets would have had an incentive to agree that he had been on his own, lest the trail of investigation lead back to the USSR. [TO BE CONTINUED]

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[THU 04 MAR 10] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: As reported by BUSINESS WEEK, Adobe Systems -- maker of the effectively universal Adobe Reader / PDF and Adobe Flash schemes -- is now increasingly the target of writers of malicious software. Adobe Flash has been manipulated by banner ads to redirect incautious users to malware-loaded websites, while viruses have been written that lurk in Adobe PDF document files.

Adobe is being victimized in part because Microsoft has become a harder target. Adobe has been releasing fixes for and upgrades of its products more recently over the last year, but the company is only a twentieth the size of Microsoft and doesn't have the same level of resources to fight malware. Adobe is trying to release fixed versions of its software quarterly, but has tended to lag behind schedule. Adobe officials say they are gaining on the problem and think they can deal with it; in particular, they've trained their programmers on appropriate design practices to avoid loopholes in the software. Even if Adobe gets the upper hand, however, malware writers have other options; for example, Yahoo's Instant Messenger is now being increasingly targeted. Never underestimate the persistence of parasites -- they never stop trying to find a way in.

* As reported by DISCOVERY CHANNEL Online news, the era of gesture recognition appears to be approaching rapidly. Softkinetic, a Brussels-based software firm, is now collaborating with US semiconductor giant Texas Instruments and several French high-tech firms to introduce cheap 3D gesture recognition for consumer products. The collaborators are shooting for introduction of gesture-driven TVs and other products by Christmas 2010. A gesture-driven TV wouldn't need a remote; changing channels or volume could be performed with a wave of the hand. Gesture-driven videogames wouldn't need a Wii controller, with body movements and any convenient prop able to do the job. Softkinetic's system involves use of a little camera, like a webcam, on top of the TV or other product.

It seems like several other groups are working on related or similar tech -- Microsoft has been pushing a gesture-based Xbox 360 concept codenamed NATAL -- and visualize adding voice input and recognition. Ultimately, the system might be able to recognize specific individuals and operate as per the profiles for the individuals. Although NATAL has been dismissed as a gimmick, for myself I would like gesture-activated consumer products just so I wouldn't have to fumble around for different remotes all the time. Of course that leads to the interesting question of how to "address" a particular device when there's several of them in the room.

* Also as reported by DISCOVERY CHANNEL Online news, two researchers at the University of Minnesota in Twin Cities, Martin Saar and Jimmy Randolph, have come with an intriguing, if admitted speculative, scheme in which carbon dioxide capture and sequestration is used to generate geothermal power, neatly killing two birds with one stone. It turns out that CO2 does a pretty good job of soaking up heat, and so the two researchers envision pumping the gas underground where it gets hot, then drawing a fraction of the hot gas back to the surface to run a steam turbine through a heat exchanger system. The CO2 would then be driven back underground again. Saar and Randolph suggest that the efficiency of CO2 as a "working fluid" would be high enough to permit exploitation of geothermal power from locales where the underground temperature is too low to be useful with current technology. However, even they admit that they need to do much more homework on the idea to determine if it's practical -- but even at that, they certainly get points for a clever idea.

* SCIENTIFIC AMERICAN had a little photoessay on a new crane being worked on by Danish wind-power giant Vestas for servicing wind turbines. The "Tower Crane", as it's named, is a platform about the size of a pickup truck; it winches itself up the turbine tower using cables strung from the top, and locks itself into place against the tower with two oversized sets of clamps when it gets topside. The platform has a crane that can be used to swap out turbine systems like gearboxes and generators. The Tower Crane is stable in wind gusts of up to 54 KPH (33.5 MPH). Vestas is developing the machine because large standard cranes are expensive, hard to come by, and relatively cumbersome to use. Ultimately, Vestas officials would like the Tower Crane to be an unmanned robotic system. Other wind energy companies are investigating comparable crane systems.

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[WED 03 MAR 10] THE CHAGAS THREAT / SCHISTOSOMIASIS RESURGENT

* THE CHAGAS THREAT: In one of the well-known minor stories of the history of science, the 19th-century English naturalist Charles Darwin suffered ill health most of his grown life, laid low by intermittent fits of vomiting, spasms, tremors, skin problems, and general malaise. It is not known what afflicted him, but one of the candidates is "Chagas disease" -- a parasitic infection common in South America, where Darwin may have picked it up after being bitten by the "great black bug of the Pampas" of Argentina in 1835.

As discussed in an article in THE ECONOMIST ("Kiss & Kill", 8 April 2009), the disease is caused by a single-celled protozoan, a spindle-like "trypanosome" with a single whiplike flagellum, the particular species being Trypanosoma cruzi. All the trypanosomes are malign parasites, with others being responsible for African sleeping sickness and the infection known as leishmaniasis. The T. cruzi protozoan is transmitted by a species of biting assassin bug known as Rhodnius prolixus AKA "reduviid bug", which tend to bite sleeping victims on the face -- and so they are also known as "kissing bugs".

Rhodnius prolixus assassin bug

The bug bite itself actually doesn't transmit the protozoan infection; the protozoans are in the bug's droppings and infect a host who rubs the bites, smearing the droppings into the sores. There may be a swelling around the bites early on, and the infection can then be treated. If not, it goes quiet for one or two decades, and then resurfaces with wide range of troubles with the internal organs -- heart, esophagus, colon, peripheral nervous system -- with about a third of the victims dying of heart and bowel problems. The disease was not understood at all until 1909, when a young Brazilian doctor named Carlos Chagas, then working in Buenos Aries, published a paper describing it. The paper was a remarkable piece of work, describing the pathogen, insect vector, circumstances of occurrence, and symptoms; Brazil still honors his memory, having even printed currency with his face on it.

In northern lands, Darwin's mysterious illness is about all most hear about Chagas -- and it's not even clear that Darwin suffered from it, since his symptoms didn't exactly match those of Chagas disease. Latin Americans are not so ignorant of it, since Chagas disease kills more of them than any rival parasitic infection, with about 18 million suffering from it. Two drugs have been available from the 1970s that can kill off the trypanosome infection if it is caught early on, but that's not likely to happen and so prevention is really the key to fighting Chagas disease. The most effective measure is to spray the walls and thatched roofs of adobe houses with pesticides to kill the assassin bug vector, and such measures have reduced the incidence of Chagas disease in the southern "cone" of the South American landmass.

Unfortunately, Chagas seems to be resurging in the north. Fighting the disease has been a low priority, partly because the long latency makes it seem less urgent. Although the incidence of the disease has been rising in the northern provinces of Argentina, there has been more concern about increasing outbreaks of dengue fever. It's the same old story: current hot emergencies tend to shove other worries onto the back burner. With focus and funding elsewhere, Chagas diseases seems to be rallying for an unwelcome comeback.

In Bolivia, up to 70% of children in rural areas are infected with Chagas. Bolivian migrants to northern Argentina have carried the infection there, to be transmitted to assassin bugs that then pass it on to locals. Central America is suffering and Chagas has risen again in Mexico. The Chagas threat is now being increasingly recognized; an awareness program conducted in a poor district of Honduras, funded by the International Development Research Centre of Canada, stopped infections there in their tracks and cured almost 90% of the childhood infections.

That isn't enough: evolution ensures that the threat is a moving target. Assassin bugs are becoming resistant to insecticides, and the trypanosome seems to be acquiring new insect vectors in regions such as the Amazon basin. In Brazil, homemade fruit juice contaminated with insect droppings also seems to be doing its part to spread the parasite. Although traditionally a rural disease, Chagas is moving into urban areas.

Along with renewed and refined preventative efforts, there is a real need for a true cure of the infection. The problem is the will to develop it. All of Latin America's pharmaceutical market is only a tenth that of the USA, and as mentioned Chagas disease is prevalent mostly in rural areas, where people are poor to begin with. Pharmaceutical companies can't afford to find a cure on their own; it is becoming clear that an alliance of governments, commercial firms, and non-governmental organizations will have to be formed to get the job done.

* SCHISTOSOMIASIS RESURGENT: In closely related news, THE ECONOMIST ran an article ("Hello Again, God Of Plague", 20 June 2009) on the threat posed to China by the Schistosoma japonicum fluke, or parasitic flatworm, which causes the disease known as "schistosomiasis" -- the second most common tropical disease after malaria. The fluke is hosted during part of its life-cycle by fresh-water snails; when the worms mature, they leave the snails and then burrow from the water through the skin of mammal hosts. Victims suffer chronic diarrhea, fatigue, and fever; in severe cases, schistosomiasis can lead to swollen bellies, bladder cancer, liver damage, and death.

The better part of a million Chinese suffer from schistosomiasis. Back in the 1950s, the number was 12 million, but the Communist Party instructed the people to spear snails with sharpened chopsticks, with infection rates then dropping rapidly. Chairman Mao, encouraged, wrote a poem to honor the achievement titled "Farewell, God of Plague". Unfortunately, the disease proved harder to completely eradicate, even after the arrival in the 1980s of a drug named "Praziquantel" that can treat the disease. Drugs are all very well and good, but a vaccine would be better, and there is no vaccine against schistosomiasis.

Chinese authorities have been making inroads on the disease as of late by improving sanitation and replacing water buffaloes -- which also can be infected with the flukes, helping propagate them -- with tractors. Alas, it is an uphill struggle. Tractors are expensive and many peasants can't afford them, and peasants are often shockingly ignorant of how to deal with schistosomiasis even though it is prevalent among them. Many refuse to take Praziquantel, believing it will debilitate them, and balk at government programs to use pesticides to kill snails since the pesticides hamper shrimp and eel production in aquaculture. The new Three Gorges dam may prove disastrous to the health of locals, creating new environments where the snails, and their fluke parasites, will proliferate. The God of Plague may be poised to make a major comeback.

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[TUE 02 MAR 10] CARBON PLANETS

* CARBON PLANETS: Our Solar System has given us stereotypes of what planets should look like. We have the rocky Inner Planets like our Earth, and the Outer Planets like Jupiter -- giant gasballs with a rocky core. However, as discussed by an article from SCIENTIFIC AMERICAN ("A Large Lump Of Coal" by George Musser, January 2010), planetologists are now starting to suspect that planets in other star systems may be much more diverse than we have thought.

The range of possibilities is dependent on the ratio of carbon to oxygen in a star system. After hydrogen and helium, carbon and oxygen are the most common elements in the Universe, and in an primordial planetary system the two can join as carbon monoxide. The evolution of the planetary system is heavily influenced by which one of them is in excess.

In our solar system, although we think of carbon as common, oxygen predominates. The Inner Planets are dominated by silicates -- oxides of silicon -- while the Outer Planets are dominated by water, which is of course mostly oxygen in terms of mass. A recent study by researchers at the Planetary Science Institute in Tucson, Arizona, suggests that the predominance of oxygen here meant that most carbon remained in the state of gaseous compounds, to them be blown out of the Solar System by the emerging solar furnace. The carbon that dominates life on Earth is just a fraction of the carbon that once was present in the solar environment.

So what would have happened had carbon predominated instead of oxygen? Then most of the oxygen would have been lost, with other studies showing that the result would be the emergence of "carbon planets", consisting of silicon carbide and carbon instead of silicates. The crust would be primarily graphite, and a few kilometers down pressures would form a stiff shell of diamond and other crystals. A carbon planet might have plains of carbon monoxide or methane ice; it might have oceans of hydrocarbons -- tars.

carbon planet

Carbon planets may actually be common: computer models suggest that in most star systems carbon predominates, and that our oxygen-dominated planetary system may well be in the minority. Regions like the galactic center, where production of heavy elements in stars has led to a higher ratio of carbon to oxygen, may be rich with carbon planets. In fact, since even heavier elements are more common than they are out here in the galactic boondocks, there may be planets with a wide range of bizarre chemistries. However, some are not so sure carbon planets are common, suggesting that on the basis of specific observational data, there's no reason to believe our Sun and its family of planetary bodies are anything but average. Further work on observing planets in other star systems should reveal whether carbon planets are the norm, or the exception.

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[MON 01 MAR 10] ANOTHER MONTH

* ANOTHER MONTH: I'm always a bit puzzled by traffic to my website. Some items that I hope would get traffic end up being ignored -- I put a lot of work into the US Civil War history, but nobody pays it any mind, they don't even belittle it. I get a bit frustrated over the history of balloons, too; there's nothing on the web that comes close to it, but though I never expected it to be a "best-seller" by any means, it doesn't score on Google searches for "balloons" and even the ballooning community ignores it. Nobody seems to pay any attention to the space stuff I've written.

I don't complain too much, since other documents do well for themselves. The document on codes is highly ranked on Google, as is the radar tutorial. There being no other comparable radar tutorial on the web, that shouldn't be surprising -- but then why is the balloons history ranked so low? It doesn't have any real competition either, and it's hard to think there's a grossly different level of interest in radar than there is in balloons. I'm very gratified that the introduction to relativistic physics is high on the Google charts, since that's the one document I would save if I was forced to choose among them all. It doesn't break any new ground in physics of course, but as far as explaining how relativistic physics works ... well, the best way to put it is that it's the document on the subject I wish I'd read 30 years ago, since it would have saved me a lot of headaches trying to understand things.

Google rankings can be funny to figure out. Of course ranking depends on the search term used -- the EVOLUTION PRIMER comes up with different rankings depending on whether I search for "evolution primer", "Evolution Primer", or "primer evolution". Duh, no surprise there. What is strange is that the ranking of the EVOLUTION PRIMER can change so abruptly over a short period of time. One week it's ranked first, the next week it's ranked 30th, and the week after that it can be ranked first again. It's pleasant that it can be ranked so high given that there's so much competing material on the web, but why the drastic changes? Jittering up and down would be expected, but when it drops in rank it ends up below listings for "Evolution of Primer Explosives" and so on.

In the end, I have to concede that whether anyone reads a word I say or not isn't really the point. I write to learn things, if anyone else is interested, great, if not I soldier on. I can't complain about a lack of attention: I get well over a hundred thousand unique visitors a month, and if even only a tenth of the visitors are actual readers, that's a visitor every five minutes, all day, every day. If half are, it's one a minute.

Besides, experience has demonstrated that I have no control over the traffic. I have tried to promote particular documents, but nothing I ever did had the slightest effect -- not surprisingly, if I can figure out a silly promotional trick, so can everyone else, meaning it's back to square one. I rarely try any more. It's more neurotic effort than it's worth.

* Having cleaned up the pile of drawings I had to work on -- as discussed last month -- I have been able to set aside a small block of time to deal with the "picky things I've been wanting to do that demand some effort but are way low priority". The first was to inventory all the files on the website. I do keep a spreadsheet for such an inventory, with thousands of files I need to keep control over them all, but I hadn't validated it with the actual files on the website and on the mirror of the website on my PC.

The tally came to almost 14,000 files -- granted, about 8,500 are in the photo archive, with three files of increasing resolution for each photo, but that's still a pile. The tricky part was picking out the anomalous files from the crowd. I came up with some simple tricks to spot them and kill them -- some of them I couldn't even figure out where they came from. Now the inventory spreadsheet and the two website images match. Next picky task: write up notes from the manuals for the calculators and cameras I use, so I actually know the features they offer. It's annoying to have a piece of gear and know I'm missing tricks with it.

Incidentally, as far as the pile of drawings goes, I was at a bit of loose ends for a few days trying to think of what I needed to draw next, but now the queue's filling up again fast enough to keep me pressured to drain it out. Considering how much work it is to deal with on an ongoing basis, it's not surprising that it took me 14 months to get rid of the backlog.

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