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DayVectors

oct 2010 / last mod feb 2016 / greg goebel

* Entries include: JFK assassination, US fast rail versus freight rail, system updates revisited, improving cassava as foodstuff, overblown Arctic methane scare, domesticating oysters, spider silk from GM silkworms, GM EN-V bubble cars, digital biopsies, Obama space plan finalized, dining in space, and evolutionary adaptation to disease.

banner of the month


[FRI 29 OCT 10] NEWS COMMENTARY FOR OCTOBER 2010
[THU 28 OCT 10] SCIENCE NOTES
[WED 27 OCT 10] IMPROVING CASSAVA
[TUE 26 OCT 10] ARCTIC ARMAGEDDON?
[MON 25 OCT 10] SYSTEM UPDATES REVISITED (2)
[FRI 22 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (14)
[THU 21 OCT 10] SPACE NEWS
[WED 20 OCT 10] BREED A BETTER OYSTER / SPIDER SILK FROM SILKWORMS
[TUE 19 OCT 10] RETURN OF THE BUBBLE CAR?
[MON 18 OCT 10] SYSTEM UPDATES REVISITED (1)
[FRI 15 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (13)
[THU 14 OCT 10] GIMMICKS & GADGETS
[WED 13 OCT 10] DIGITAL BIOPSIES
[TUE 12 OCT 10] OBAMA SPACE PLAN FINALIZED
[MON 11 OCT 10] TRAIN WRECK (2)
[FRI 08 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (12)
[THU 07 OCT 10] SCIENCE NOTES
[WED 06 OCT 10] DINING IN SPACE
[TUE 05 OCT 10] HARD BARGAIN? / EVOLVING FOR THE CITY
[MON 04 OCT 10] TRAIN WRECK (1)
[FRI 01 OCT 10] ANOTHER MONTH

[FRI 29 OCT 10] NEWS COMMENTARY FOR OCTOBER 2010

* NEWS COMMENTARY FOR OCTOBER 2010: There was a little rumble in the political press this last month when US President Barack Obama's National Security Adviser General James Jones announced he was leaving his position at the White House. Jones follows a series of other high-profile exits, most importantly Obama's trusted chief of staff, Rahm Emanuel, who left to run for mayor of Chicago. Some commentators have made it sound like the crew is jumping from the sinking ship.

As suggested by BBC WORLD Online, that's a silly read on things. General Jones never fit in well with the Obama Administration, and the broad opinion of Washington DC observers was that there was no question of whether Jones would leave, it was just a question of when. In any case, turnover in positions at the White House always tends to be high. Staffers put in long hours under intense and often hostile public scrutiny. The pay is poor relative to the responsibilities and public profile, running at top to $172,000 USD. Most Americans would regard that as pretty good money, but most of the staffers could be making many times that elsewhere, and living costs in Washington DC are steep.

General James Jones in conference

Burnout has been unusually high because the Obama Administration took power at a time when things weren't going well, the government confronting two wars and the biggest economic crisis in decades. Even in better circumstances, the White House has an impossible job that drives people out the door. As one political observer put it: "Reagan went through six national security advisers before his eight years were over, and George W. Bush had one each for his two terms. As far as these two administrations were concerned, general stability in that position doesn't necessarily correlate with impressions of their relative success in foreign policy." Similarly, President Clinton and Reagan each went through four of chiefs of staff, and George H.W. Bush had three in just one term. President Obama's public approval ratings are unimpressive, but his ship of state is not about ready to sink beneath the waves.

* As mentioned here last December, the Chinese government made embarrassing international headlines by throwing democracy activist Liu Xiaobo into prison for eleven years. The authorities were further embarrassed recently when Liu won the 2010 Nobel Peace Prize.

Commenters suggest, however, that while the prestige of the Peace Prize is substantial and that it will increase pressure on the Chinese government, it may not accomplish all that much. The government controls communications to the Chinese public, and in the new economic environment, most Chinese don't worry about politics much anyway. As far as foreign governments go, they already have a list of complaints with China that they don't want to push too hard, and it's difficult to see that they will press the matter. Indeed, all the Chinese authorities have to do is wait for things to go quiet for a while, and then announce that Liu has been freed -- to be booted out of the country. That would mean good press, while tidily removing Liu from the scene and effectively eliminating him as a nuisance.

* As reported by BBC WORLD Online, it might not seem obvious that there would be public enthusiasm for paying taxes anywhere. Certainly officials of the Bangladesh National Board of Revenue (NBR) weren't expecting an overwhelming response when they conducted five-day "tax fairs" in the cities of Dhaka and Chittagong in September, where citizens could come to sign up on the tax rolls. However, NBR officials were indeed overwhelmed when people flocked to the tax fairs, standing in long lines to sign their names and get their "Taxpayer Identification Numbers (TIN)", as well as submit returns and pay off the taxman. While the tax fairs did offer convenience -- traditionally, paying taxes in Bangladesh is a bureaucratic pain -- they also had a festive atmosphere, with balloons and bright ribbons decorating the walls; vendors in stalls selling snacks and drinks; and citizens chatting away at each other.

Only 2% of Bangladeshis, 1.3 million people out of a population of more than 150 million, are regular income tax payers in Bangladesh. The government has been trying for years to widen its tax base to boost its revenue, but without much success -- even though Bangladesh has been doing, on the average, fairly well for itself economically over the past decade, with many citizens joining the middle class.

Unsurprisingly, the newfound enthusiasm for paying taxes involved a bit of government arm-twisting. NBR officials say that tax revenues only began to increase after the TIN number was made mandatory to do such things as registering a car, buying a flat, or even opening a bank account. The government expects to triple its tax revenues over the next five years.

Bangladeshis seem to recognize that their government is impoverished and that it really does need the money -- for tasks such as improving the country's decrepit infrastructure and inadequate healthcare system, as well as creating more job opportunities for the younger generation. Said one first-time taxpayer at the fair in Dhaka: "If you're a good citizen, then you should pay taxes. I think everyone should pay tax. Only then will our government have enough resources to invest in infrastructure projects."

However, along with an eagerness to pay taxes comes a demand that the government prove they can make good use of the money. Said another participant in the tax fair: "Like a responsible citizen, I will continue to pay my taxes and it is up to the government to show us the result. I want to see how they are going to accommodate our expectations."

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[THU 28 OCT 10] SCIENCE NOTES

* SCIENCE NOTES: As reported by WIRED Online, a climate simulation produced by Mark Jacobson of Stanford University in California suggests that curtailing soot emissions would be straightforward and would have a strong effect on limiting global warming.

Soot comes from the incomplete combustion of fossil fuels, and also from the burning of wood or dung for fuel. Burning crop waste and forest fires are another major source of soot. When aloft, the dark particles absorb sunlight, raising local temperatures and causing rain clouds to form, which in turn deprives other areas of moisture. When soot lands on snow or ice, its effects are magnified, because melts reveal fresh patches of heat-absorbing dark ground. A 2003 study from the US National Aviation & Space Administration suggested that soot emissions were responsible for 25% of the warming seen over the past century.

Soot could be greatly reduced by widespread use of exhaust filters and clean-burning stoves. Since soot only remains in the atmosphere for a few weeks, once soot control tech was in place, the warming effect of soot would cease almost immediately. In Jacobsen's simulation, due to the thermal inertia of the oceans the effect wouldn't be seen right away, but curtailing soot would have much faster effects than cutting back on CO2 emissions.

Jacobsen admits that limiting soot isn't really a long-term fix for global warming, it's just buys some time at the relatively modest cost of making sure poor people all over the planet get low-cost, effective stoves. There's every good reason to do this since, as discussed here last year, hearths now used by the poor are both inefficient and unhealthy. Even if global warming wasn't a concern, providing people with better stoves and getting rid of soot would pay for itself.

* Flightless predatory birds are not unknown in our own era, the secretary bird of Africa being a well-known example. However, the secretary bird doesn't come close to matching the similar but much bigger and more intimidating "terror birds" that stalked South America from about 60 million years ago until they died out a few million years ago.

Researchers have now performed a CT scan on one of the 18 known species of "phorusrachids", as the terror birds are formally known, to understand more details of its structure and habits. The bird selected, known as Andalgornis steulleti, was a mid-sized terror bird, with a height of about 1.35 meters (4.5 feet) and a weight of about 40 kilograms (90 pounds). It died out about 6 million years ago.

Andalgornis steulleti

The scan revealed that the bird's skull had rigid bones that served as structural support beams, where almost all known birds have flexible joints. The reinforced skull appears to have been adapted to stabbing prey with the sharp tip of the big beak. The beak, however, was hollow, making it relatively fragile, and so it is unlikely the bird struggled with prey -- it just stabbed prey with its beak until it was dead, and then gobbled it down whole.

* The Chornobyl nuclear disaster of 1986 -- last discussed here in 2006 -- continues to have its lingering effects. There were worries in Russia that the wildfires raging over the country this last summer might spread into the Chornobyl exclusion zone, with unforeseen consequences. That didn't happen, but according to a note from DISCOVERY Online, German authorities are seeing a residual effect of their own: radioactive boars.

The radioactive debris spread by the reactor accident has been fading out down the half-life curve, but radioactive cesium-137, with a half-life of 30 years, has migrated into the soil, where it is accumulated by mushrooms and truffles. Boars like to eat such fungi, not to mention root around in the soil a good deal, so they end up concentrating the radioactive materials further.

This is not just some "news of the weird" item, either, it's a real problem. German boar populations have been exploding, it is believed due to increased yields of acorns from oaks and other boar food as a result of climate warming, and hunting of boars has been tracking the population increase. The boars are often too radioactive to be safe to eat, and so the German government pays hunters to hand over the carcasses for disposal. The bill came to the equivalent of over a half million dollars last year, and it stands to get worse, at least until the cesium-137 decays down to a level where it's no longer a nuisance.

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[WED 27 OCT 10] IMPROVING CASSAVA

* IMPROVING CASSAVA: Westerners are not particularly familiar with the cassava plant, but as reported by an article from SCIENTIFIC AMERICAN ("Breeding Cassava To Feed The Poor" by Nagib Nassar & Rodomiro Ortiz, May 2010), cassava -- also known as tapioca, manioc, or yuca (not the same as the yucca plant) -- is a staple food of more than 800 million people in tropical regions of the globe. It contributes more to the world's calorie budget than any other crop except rice and wheat. Families usually raise it for their own consumption on small plots, although in Asia and parts of Latin America cassava is grown commercially for use in animal feed and starch-based products.

The scientific name for the shrubby cassava plant is Manibot esculenta. Cassava and its wild relatives of the genus Manibot originated in Brazil, where indigenous tribes first domesticated it. Portuguese sailors helped transplant the plant to Africa in the 16th century, and from there it spread to Asia, ultimately reaching as far as Indonesia. In the 21st century, Africa produces more than half, 51%, of the 200 million tonnes of cassava produced annually, with Asia producing 34% and Latin American producing 15%.

cassava plant

The roots, which look like elongated sweet potatoes, can be eaten raw or boiled, or processed into granules, pastes, or flour. In Africa and some parts of Asia, people also eat the leaves, which provide protein -- a dry cassava leaf is up to 32% protein -- plus vitamins A and B. Cassava is easy to grow, tolerant of drought or acidic soils, and robust in the face of pests and disease. It's a very efficient food plant: while the proportion of a grain plant that can be eaten is only 35% at most, it is about 80% for cassava. It grows rapidly and can be planted at any time of the year, with the result that subsistence farmers like to keep a crop of it around as an emergency backup if their other crops fail.

Along with all its virtues, however, cassava has some significant flaws:

The authors of the article have been performing work on improved varieties of cassava at the University of Brasilia since the 1970s. The research team scoured the countryside, eventually managing to find and cultivate 35 different wild Manibot species that could be used for hybridization experiments.

One of the first hybrids developed by the group, in the early 1980s, provided more protein. Cassava roots typically only consist of about 1.5% protein, as compared to 7% or more for wheat. The new cassava hybrid had 5% protein. They have since worked on further improved varieties that are more nutritious, recently introducing a variety that has 50 times more "beta carotene", an important source of vitamin A.

The work has also focused on the problems associated with propagating cassava. Some wild Manibot species, for example the treelike M. glaziovii, can reproduce asexually or sexually, with the asexually-produced seedlings being clones of the mother plant -- but not carrying the load of pathogens of cuttings. The Brasilia group has created a hybrid cassava based on M. glaxiovii that can reproduce both asexually and sexually. Some hybrids based on M. glaxiovii also produce long roots that can tap into deeper water sources, as opposed to the big starchy roots of traditional cassava; work is continuing on developing a hybrid that trades off between the root configurations, providing a cassava variety that is more drought-resistant. Still other work by the Brasilia team has focused on disease resistance.

cassava root

Progress has been made on improved cassava varieties, but traditionally the plant hasn't been a high-profile research target -- it's not a major agricultural crop in developed countries, and so there's not so much money to be made in coming up with a better cassava plant. Field research suggests that there should be no obstacle to coming up with a cassava plant that quadruples yield, if the will was there to develop it. Fortunately, the plant is now attracting more interest: its genome is being sequenced, and an international collaboration named "Bio-Cassava Plus", funded by the Bill & Melinda Gates Foundation and Monsanto, is working on genetically modified cassava with properties such as improve nutrition and longer shelf life. Given the expected rise in human population in the next few decades, a better cassava plant could play a major role in keeping people fed.

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[TUE 26 OCT 10] ARCTIC ARMAGEDDON?

* ARCTIC ARMAGEDDON? While the evidence has accumulated that human activities may well be leading to an era of global climate warming, the issue has become emotional, leading in some cases to an excess of enthusiasm for sounding the alarm. An article from AAAS SCIENCE ("'Arctic Armageddon' Needs More Science, Less Hype" by Richard A. Kerr, 6 August 2010), suggests that warnings over massive emissions of methane, a potent greenhouse gas, from the Arctic regions have been exaggerated.

The scenario does sound alarming on the face of it. Methane is over 20 times more effective than carbon dioxide as a greenhouse gas. Warming does seem to be causing emissions of methane from the Arctic sea floor and from permafrost, but there's no evidence that indicates the beginning of doomsday. Geochemist Martin Heiman of the Max Planck Institute for Biogeochemistry in Jena, Germany, says Arctic methane emission "will aggravate the global change problem -- but it's not a catastrophe."

There's certainly plenty of methane out there. Microbes living under the sea floor produce the gas, which is trapped in crystalline cages of water ice to form "methane hydrates", a sort of ice that can be lit on fire. Nobody's exactly sure how much methane is trapped under the seafloor, but it is on the order of several trillion tonnes, about a thousand times more than the methane in the atmosphere. As temperatures increase, the hydrates melt, releasing methane to bubble up through the water into the air. Similarly, as Arctic permafrost thaws, microbes in the soil can convert biomass in the soil to methane. The top 3 meters (10 feet) of Arctic permafrost are estimated to contain about a trillion tonnes of organic matter that could be converted into methane.

In March 2010, oceanographer Natalia Shakhova of the University of Alaska, Fairbanks took samples over the East Siberian Arctic Shelf, to find a flood of methane brewing up from the ocean floor -- with as much methane being generated in the region as had been estimated to be coming from the entire ocean floor. The group's report set off alarms, but the researchers didn't emphasize and reporters didn't notice a significant detail: the methane was coming from permafrost that had been thawing in relatively warm waters that had flooded the area when sea levels rose following the last Ice Age. In other words, it was possible, if not certain, that methane emissions in the region had been at a high level for tens of thousands of years, and had nothing in particular to do with global warming.

Another report attracted less public attention but created more serious professional concern. A paper published by marine geophysicist Graham Westbrook of the University of Birmingham in the UK and his colleagues discussed how they had used sonar to probe the shallow waters of Norway's Svalberg archipelago, halfway between Norway and the Arctic Circle. They discovered that the bottom waters had warmed by about one degree Celsius over the last 30 years, and also found plumes of methane bubbles floating upward from the seafloor.

In the wake of these discoveries, a computer model was constructed by geochemist David Archer of the University of Chicago in Illinois and colleagues to estimate how much methane would be released by a 3 degree Celsius increase in ocean temperature, yielding the conclusion that half the methane in the seafloor would be released. Other researchers gave a "very coarse estimate" that suggested the thawing of northern permafrost would increase atmospheric methane by an order of magnitude.

* So there's the nightmare scenario, but is there evidence that it's really coming true? Atmospheric chemist Edward Dlugokencky of the US National Oceanic & Atmospheric Administration's (NOAA) Earth System Research Laboratory in Boulder, Colorado, and his colleagues examined data on atmospheric methane, collected weekly from 1983 into 2008 at 46 sites around the world. The study showed that methane increased to the late 1990s, then leveled off, to bump up in 2007 -- and level off again in 2008. The NOAA researchers concluded the methane increase observed was due to a variety of factors, but not due to an imminent gusher of methane from thawing Arctic permafrost and seafloor. Says Dlugokencky: "Despite all the media hype, I don't think we're yet at an Arctic tipping point."

Even Archer says that a rise in atmospheric methane won't happen abruptly. It's not a question of the temperature rising a few degrees Celsius and gushers of methane pouring into the sky: it takes time to melt methane hydrate, the methane has to escape from the seafloor, and the methane also reacts with oxygen in air bubbles in the water to form water and carbon dioxide. Even when released into the atmosphere, it's converted into water and carbon dioxide in about ten years.

In other words, methane release is not likely to happen abruptly, and over the long run it's likely to end up as carbon dioxide anyway. Neither is good news, but it's not a recipe for Armageddon. As Archer commented in his blog: "Is now the time to get frightened? No. CO2 is plenty to get frightened of, while methane is frosting on the cake ... Methane sells newspapers, but it's not the big story."

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[MON 25 OCT 10] SYSTEM UPDATES REVISITED (2)

* SYSTEM UPDATES REVISITED (2): My household network needed to link up five PCs -- my desktop and my Acer laptop, both running Win7; plus two Acer notebook computers and my old Dell laptop, all running WinXP. I used the Dell laptop as a node in the BOINC scientific computing network, running all day and night on various science projects; it seemed to be at death's door at one time, so I bought the second notebook to replace it in that role. I managed to get the Dell machine back up to working condition, however, and so all I had been using the second notepad for was as a digital jukebox.

I started out working on the Win7 Desktop, which was hooked up to the DSL modem over an Ethernet hardware connection. I'd run the installation software that came with the modem when I installed it, and it was working fine as far as the desktop was concerned, giving me fast internet access. Now to get the wi-fi going.

As far as configuring the wi-fi capabilities of the DSL modem went, the notes I took were of no use -- everything I found assumed a separate wi-fi router, which was not what I had, and the DSL modem had its own software for configuration, making most of the comments about Windows configuration irrelevant. Though I wasn't sure of myself, I went ahead and checked the DSL modem configuration.

I could get to that by going to Windows Explorer, selecting the "Network" node, and then selecting the "ActionTek PK5000" icon. That gave me a local web page, which I added to "Favorites" in the browser, with the following entries proving important:

Everything seemed to be enabled and set properly for wireless as far as the desktop PC was concerned. Now I went to Win7 configuration issues. First thing to do was validate the computer name; I pressed "Windows_key / Pause" to get the "System" panel and read that I had named it "NIGHTWING". That done, I went on to set up the Windows network configuration.

One thing the notes I took warned me to watch out for was that Win7 includes a concept known as a "Homegroup". This apparently makes it easier to configure a pure Win7 network, but older flavors of Windows don't understand it, and it can make things complicated in a mixed system, which meant disabling that feature. What I really wanted was the "Workgroup", which is normally named "WORKGROUP". However, the notes also said that if it's named that, Windows makes various assumptions about network configuration that can lead to complications, so I changed it to "WIFINET". I did that through "System" as obtained above -- there's hard-to-see "Change settings" link at the right of the screen, which gives a dialogue box. I selected the "Computer Name" tab, then the "Change" button, and change the workgroup name.

OK, for the last step, enabling permissions and the like, I went to "Control Panel > Network and Internet", then selected "Homegroup" at top. This gave a page to enable sharing of various resources from the public folders; I set them all.

I used the same page to shut down Homegroup operation. That could be done with the item on the page marked "Change advanced sharing settings ... " I set "Turn off password protected sharing" and "Use user accounts and passwords to connect to other computers". These changes killed off Homegroup operation -- which I needed to do to clear the decks for integrating XP PCs into the network. I also chose 128-bit encryption and enabled "Turn on network discovery" -- though the discovery feature is really intended for portables. I rebooted the desktop to make sure the new configuration "took".

* With the desktop (hopefully) configured, I went to the Acer Win7 laptop. On booting the laptop, there was an icon for the wireless connection. Clicking on it brought up a small panel that showed there were several connections available, including some from the neighbors, but I wanted "myquest0953", which had a nice strong signal. Before selecting it, however, I made sure that the laptop was properly configured by right-clicking on the "myquest0953" entry. In the dialogue box I got I selected automatic network discovery in the first panel, then WEP (without authentication) security in the second, typing in the network key. I then saved the settings and connected.

That was all I actually had to do to get online with the Win7 laptop, since it connected via wi-fi to the DSL modem and thence to the internet -- the Win7 desktop wasn't in the loop. However, I wanted the two PCs to talk to each other, so I went through the same Win7 configuration steps as for the desktop, though the name of the laptop was "HUNTRESS". I set the workgroup name to "WIFINET", set permissions, and disabled Homegroup operation as above. I rebooted, and then I was able to get into the Public directories of each PC from the other. [TO BE CONTINUED]

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[FRI 22 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (14)

* THE KILLING OF JFK -- THE ASSASSINATION (14): A little before 8:00 PM that Friday, Oswald was put in a third lineup, for the two Davis women who had seen a man running across their yard after the Tippit shooting, dumping empty casings from his revolver; and for Howard Brennan, who had seen a man shooting at JFK from the TSBD window. The two women had no hesitation in identifying Oswald: "That's him!" -- bringing the total of witnesses identifying Oswald as Tippit's killer to five. However, Brennan said Oswald looked like the man he had seen in the sixth-floor window of the TSBD, but wasn't sure.

Brennan later told the Warren Commission that he flatly recognized Oswald as the shooter. Brennan didn't identify him to the Dallas police because he, Brennan, had been worried that as a prime witness to the assassination of a president, he might have made himself and his family a target. Conspiracy theorists made much of the fact that Brennan had to wear glasses, but in fact he was farsighted, and he could see perfectly well at a distance. Still, Brennan was only one witness, his observation wasn't corroborated; besides, he had been at street level, the shooter on the sixth floor of the TSBD, and that was a fair distance to be able to tell a stranger from somebody else who looked broadly like him. The description Brennan gave certainly matched that of Oswald, but it hardly gave a detailed picture of the shooter.

After the lineup, Oswald was hauled away once more. Conspiracy theorists claimed that witnesses such as Domingo Benavides weren't called in for the lineups because they would have contradicted other witnesses. Actually, Benavides had told the cops that day that he wasn't sure he could identify the shooter, which is why he wasn't called. Benavides later told the Warren Commission that the shooter resembled Oswald, and still later said he was absolutely certain it was Oswald. His increasing certainty over time doesn't inspire confidence, but on no occasion did Benavides claim the man he saw didn't resemble Oswald.

Much later, in 1978 the HSCA found another witness named Jack Ray Tatum who said he had seen Oswald kill Tippit as he was driving past. Tatum didn't come forward; he had mentioned the matter to friends, and eventually the story leaked out. Tatum flatly hadn't want to go to the authorities with the matter, feeling there were plenty of other witnesses and that it would just make life troublesome for him if he got involved. Tatum's details were highly consistent with those of other witnesses; Domingo Benavides said there was a red car in front of him when the shooting took place, and Tatum drove a red Ford Galaxie. Tatum had observed the shooter pumping the final bullet into Tippit's head; Tatum had no doubt the shooter was Oswald.

In any case, as Oswald was led off, reporters milling around the jail in hopes of getting a scoop heard him shout out: "I'm just a patsy!" He was put through a third interrogation session. Oswald said he didn't want to talk any more, though he did explain how he had got from the TSBD to his boardinghouse: "I took a bus, but due to a traffic jam, I left the bus and got a taxicab, by which means I actually arrived at my residence."

The police fingerprinted him and performed a paraffin test to determine if he had fired a weapon. The test involved coating the subject's hands with hot wax and gauze, then peeling it off to permit chemical analysis for nitrate residues presumably left by firing a weapon. The paraffin test was also applied to Oswald's right cheek, an unusual procedure.

There was a short press conference at 11:20 PM. Oswald was asked: "Did you kill the president?" He replied: "No. I have not been charged with that. In fact, nobody has said that to me yet." Oswald was taken away, with the reporters then continuing to grill District Attorney Henry Wade. Wade was necessarily vague and noncommittal, refusing to speculate on whether Oswald had been part of a Communist conspiracy, though when asked what kind of rifle the police had recovered, Wade erroneously answered: "It's a Mauser, I believe." That casual and qualified remark would linger down through the decades.

Dallas nightclub owner Jack Ruby was among the crowd at the press conference, suggesting the poor security at police headquarters. 1963 was a different era, at that time only highly secure installations were very careful about who came in the door -- in those days, somebody could have carried a submachine gun onto an airliner in a briefcase without much worry of anyone noticing -- and the Dallas police department had a policy of being as open to the press as possible. For whatever merits such a policy had normally, the situation that Friday was anything but normal; the police had a suspect in custody who they had to be aware was the target of widespread wrath, and who brought in a mob of reporters from all over the world to clog City Hall. In hindsight, the Dallas police failed to understand that they needed to take extraordinary precautions.

After further shufflings, at 1:35 AM on Saturday, 23 November, Oswald was arraigned for the murder of JFK. He got some sleep in a maximum security cell, in which he was the only prisoner -- the police didn't want to let any other prisoners get their hands on him. Officers were posted to keep him under observation in case he tried to commit suicide. Not only did Oswald need to stay alive to allow the authorities to get to the bottom of things, if he died in police custody there would be absolute hell to pay.

The Dallas police had arrested Wesley Buell Frazier that evening. Frazier was cooperative, allowing the police to search his home. Down at City Hall, he told them what he knew, in particular mentioning the bag of "curtain rods" that Oswald had with him when Frazier picked him up that morning. Armed with this information, the police talked with Marina Oswald and Ruth Paine, who were still present, and asked them about the curtain rods. Neither knew anything about the matter. Finally, the police took them back to the Paine house, with Marguerite coming along to spend the night there. Back at the house, Marina remembered the "Fascist Hunter" photos and realized how incriminating they were; she didn't know exactly what to do with them. She also found Lee's wedding ring in the cup where he had left it that morning before going to work. The discovery was another shock to Marina: it was clear that Lee hadn't expected to come back home that night.

After leaving City Hall, Robert Oswald drove around aimlessly for a time. He finally went back downtown and got a hotel room. He then went back to City Hall but still couldn't see Lee. When he was told that Lee was going to be arraigned for killing JFK, Robert went back to his hotel room. He couldn't sleep. [TO BE CONTINUED]

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[THU 21 OCT 10] SPACE NEWS

* September was a busy month for space launches:

-- 02 SEP 10 / GLONASS M x 3 -- A Proton M Breeze M booster was launched from Baikonur in Kazakhstan to put three Russian GLONASS M modernized navigation satellites into orbit. The satellites were designated "Cosmos 2464" / "GLONASS 736", "Cosmos 2465" / "GLONASS 737", and "Cosmos 2466" / "GLONASS 738".

-- 04 SEP 10 / CHINASAT 6A -- A Long March 3B booster was launched from Xichang to put the Chinese "ChinaSat 6A" geostationary comsat into orbit. It was based on the DFH-4 comsat bus and carried a payload of 1 S-band / 24 C-band / 8 Ku-band transponders.

-- 08 SEP 10 / GONETS-M 12, KOSMOS 2467 & 2468 -- A Rockot booster was launched from the Plesetsk Northern Cosmodrome in Russia to put the "Gonets-M 12" civil low-orbit comsat and two secret military payloads into orbit. The two secret payloads were designated "Kosmos 2467" and "Kosmos 2468"; they were suspected to be "Rodnik" class low-orbit military comsats, similar to the Gonets-M series.

Gonets-M comsat

-- 10 SEP 10 / PROGRESS 39P (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. It docked with the ISS Zvezda module on 12 September.

-- 11 SEP 10 / MICHIBIKI -- A Japanese H-2A booster was launched from Tanegashima to place the "Michibiki" navigation satellite into orbit. It provided GPS augmentation signals for Japanese land areas. It was the first of three "Quasi-Zenith Satellite System (QZSS)" spacecraft, intended to enhance GPS navigation in dense city areas and rural mountain valleys. It was launched into an orbit with an inclination of 45 degrees and an altitude ranging from about 32,000 to 38,600 kilometers (20,000 to 24,000 miles), with the orbit forming a figure-8 pattern on the Earth below stretching from Japan in the north to Australia in the south, and the north lobe of the "8" much smaller than the south lobe. The orbit ensured that the satellite would remain high in the sky over Japan for eight hours a day. Michibiki, which meant "Pathfinder" in Japanese, was to validate the technologies for two more QZSS satellites to provide 24-hour coverage.

Michibiki spacecraft

The satellite was built by Mitsubishi Electric Corporation and transmitted four L-band signals compatible with GPS signals. Special receivers were required to make use of its augmentation capabilities. While previously Tokyo's well-known Ginza shopping district only received adequate GPS coverage half the time, adding Michibiki raised the duty cycle to 90%. The H-2A was launched in the "202" configuration, with two large solid rocket boosters and no small solid rocket boosters.

-- 21 SEP 10 / NROL-41 (USA 215) -- An Atlas 5 booster was launched from Vandenberg Air Force Base to put a secret military payload into space for the US National Reconnaissance Office (NRO). The spacecraft was designated "NROL-41" AKA "USA 215". The Atlas 5 501 configuration featured a 5 meter (16 foot 5 inch) fairing, no solid rocket boosters, and an upper stage with a single Centaur engine.

-- 22 SEP 10 / YAOGAN 11 -- A Chinese Long March 2D booster was launched from Jiuquan to put the "Yaogan 11" Earth observation satellite into orbit. Chinese sources claimed it was a civil remote sensing satellite, but it was generally judged to be a military optical imaging satellite. The launch also carried two picosats, "Zheda Pixing 1B" and "Zheda Pixing 1C", developed by Zhejiang University and carrying microelectronics evaluation payloads.

-- 27 SEPT 10 / SBSS BLOCK 10 -- A Minotaur 4 booster was launched from Vandenberg AFB in California to put the "Space Based Surveillance Satellite (SBSS)" Block 10 spacecraft into polar low Earth orbit. SBSS Block 10 was a satellite designed to spy on other satellites, as well as observe debris that could pose a threat to spacecraft in orbit.

The spacecraft had a launch mass of 1,000 kilograms (2,200 pounds) and was based on a Ball Aerospace Commercial Platform 2000 bus, with a image-processing system developed by Boeing Space & Intelligence Systems. The imaging system was fitted on a gun-type mount to reduce the need for spacecraft maneuvering. Other surveillance satellites have done the job on occasion -- most particularly the USAF Midcourse Space Experiment (MSX), which was launched in 1996 and continued in operation into 2008 -- but SBSS Block 10 was the first spacecraft to be designed from the ground up for the mission. Boeing has suggested to the military that observation sensors similar to that flown on the SBSS spacecraft could be flown as secondary payloads on comsats and other spacecraft.

Minotaur 4 launch with SBSS satellite

This was the first launch of the Orbital Sciences Minotaur 4 booster, a four-stage solid-fuel vehicle capable of putting 1,360 kilograms (3,000 pounds) into low Earth orbit. The first three stages consisted of "recycled" Peacekeeper ICBM first stages, while the fourth stage was an Orion 38, used on Orbital's other space launch boosters as a upper stage. The Minotaur 4 will only be used for military launches.

-- 30 SEP 10 / COSMOS 2469 (OKO / US-KS) -- A Molniya-M booster was launched from the Russian Plesetsk Northern Cosmodrome to put a secret military payload into high-inclination eccentric "Molniya" orbit. The payload was designated "Cosmos 2469". It was believed to have been an "Oko" AKA "US-KS" type missile early warning satellite, joining two other Oko satellites, Cosmos 2430 and 2446, in orbit.

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[WED 20 OCT 10] BREED A BETTER OYSTER / SPIDER SILK FROM SILKWORMS

* BREED A BETTER OYSTER: Humans have been at the game of domestication of animals and plants for a long time, and have acquired an impressive array of tricks at the game -- as illustrated by an article from THE ECONOMIST ("Shelling Out", 30 January 2010) on the domestication of oysters. Harvesting oysters from the wild is becoming more difficult and so oysters have become a more expensive item on the menu, giving an impetus to the farming of oysters. Unfortunately, wild strains of oysters aren't all that cooperative about being farmed, tending towards the runty and relatively slow to reproduce, and so work is underway to come up with a more cooperative oyster.

Breeders have long known that combining two different strains of an organism can sometimes produce offspring with superior qualities to either of the parent strains, a phenomenon referred to as "hybrid vigor". A few years ago, a team of researchers under Dennis Hedgecock of the University of Southern California (USC) crossbred two inbred small strains of oysters, named simply "oyster6" and "oyster7", to produce a hybrid strain logically named "oyster6x7". Oyster6x7 was almost everything an oyster farmer could want, being large, fast-growing, easy to open, and generous in its production of eggs. Unfortunately, there was a catch: the next generation produced by inbreeding oyster6x7 was runty again, or in other words the strain didn't "breed true". Since oyster6 and oyster7 only generated a few million eggs apiece -- orders of magnitude more are needed for commercial breeding -- and were hard to open to get at the eggs, using oyster6x7 wasn't a sensible business proposition.

However, the USC researchers then crossed two other runty strains, "oyster8" and "oyster9", to produce a "oyster8x9" hybrid that had similar virtues to oyster6x7. Oyster8x9 also didn't breed true -- but it turned out that crossing the two hybrids to produce "oyster6x7x8x9" provided a perfectly satisfactory commercial oyster that was big and fast-growing. This elaborate two-stage process promises to make commercial oyster farming a reality.

Of course, this sort of selective crossbreeding is a brute-force approach to creating a commercial oyster; a more sophisticated approach would be to tweak its genetics. The USC group has been poking around in the oyster genome, and has found 350 of the organism's 23,000 genes that vary between the strains being bred together; the next step is to figure out exactly how these genes work. The ultimate goal is a domesticated large, fast-growing oyster that breeds true. Oyster farming promises to become a big business, with oysters having a particular benefit in that they are filter-feeders that clean up, instead of pollute, the water column. That presents the possibility of raising oysters and less benign farmed aquaculture like salmon together to get the best of both worlds.

* SPIDER SILK FROM SILKWORMS: Spider silk is amazing stuff, with a staggering tensile strength generally rated as equal to kevlar polymer, and in some cases much more than that. There's been considerable interest in schemes to produce the material on a commercial basis, but it turns out to be tricky to chemically synthesize it, and up to now attempts to produce it using bioengineered bacteria or other organisms haven't panned out.

According to WIRED Online, molecular biologist Malcolm Fraser of the University of Notre Dame and his colleagues decided to try a new approach that seems neatly obvious in hindsight: genetically modify silkworms to produce spider silk. Silkworms have a long history of domestication, are easily handled, and are efficient at churning out silk in large quantities -- the silk-producing gland in a caterpillar's body may account for up to a third of its body mass.

The gene for spider silk could be spliced into the genome of silkworm embryos in various locations, resulting in silk with different properties depending on location. Since not all of the silkworms modified ended up expressing the spider silk gene, the researchers included a gene for red fluorescent protein along with the spider silk gene, with caterpillars that could express the spider silk gene featuring glowing red eyes. The resulting silk was actually a hybrid of silkworm and spider silk, but in the best case it was 80% as strong as spider silk. The scheme isn't ready for commercialization yet, but it seen as a very promising step towards large-scale production of spider silk.

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[TUE 19 OCT 10] RETURN OF THE BUBBLE CAR?

* RETURN OF THE BUBBLE CAR? As reported by an article from THE ECONOMIST ("The Bubble Car Is Back", 30 September 2010), as much as the automobile is cursed, almost everyone still wants the freedom of movement that cars offer. With the middle class growing in developing nations like Brazil, China, and India, that means more and more people have the money to buy cars -- but at the rate things are going, most of those autos are likely to end up in monstrous traffic jams. Population is still rising and more people are living in cities; by 2030, an estimated 60% of humanity will live in cities, up from 50% now. Cars demand energy, land for roads and parking, and produce volumes of emissions that can turn big cities into smoggy nightmares.

Some auto designers think the solution will be to reinvent a concept from half a century ago: the "bubble car" of the 1950s. Bubble cars were generally three-wheelers with two seats, intended to provide cheap personal transport; they became particularly popular when fuel prices shot up in 1956, as fallout from the Suez crisis. One of the first was the Italian-made Iso Isetta, but the Germans got into the act, too, with bubble cars being made by Messerschmitt, Heinkel, and BMW -- BMW producing the Isetta fitted with a BMW motorcycle engine.

1957 BMW Isetta

* Fuel prices fell again, incomes rose, and people eventually gave up on the bubble car -- but the challenges presented to the automobile in the 21st century suggest that it might be time to bring it back. Three new-concept bubble cars, formally known as "Electric Networked Vehicles (EN-V)" were on prominent display at Expo 2010 in Shanghai, where they attracted considerable interest. The new bubble cars are not only electrically powered, they are capable of autonomous operation -- driven manually, or unpiloted if the passengers feel they have better things to do -- and they can be fetched to a location with a cellphone call. Most intriguingly, they have only two wheels, set in parallel.

The three EN-Vs all have distinct styles, but they are all built by a collaboration between US auto giant General Motors (GM) and Shanghai Automotive Industry Corporation, one of China's biggest carmakers. If the two-wheel scheme of the EN-Vs suggests a Segway personal transporter, it's not a coincidence, since Segway developed the drive system for the little cars.

A Segway personal transporter has a bidirectional electric motor in each wheel, with a computer control system using inputs from accelerometers and balance sensors to keep the vehicle from falling over. A rider leans forward or back on the handlebars to accelerate or back up. An EN-V is not so different from an oversized Segway, without the handlebars. The body of the EN-V accommodates two passengers and a battery pack; it slides on top of the frame of the drive system, for example moving forward for parking, tipping onto "landing wheels" in the nose. That makes it easier to get in and out, since the body of the EN-V has a clamshell configuration, hinging up from the back, meaning passengers get in and out of the vehicle from the front. When the EN-V powers up, the body slides backward, with the vehicle then balanced on its center of gravity. Of course it's not controlled by leaning, instead being directed by a steering wheel, throttle, and forward-reverse control -- if the riders bother to drive themselves.

Why two wheels? Mainly compactness -- an EN-V is only about 1.5 meters long and 1.4 meters wide (59 x 55 inches) -- though the two wheels also permit maneuverability, with the vehicle able to turn around completely in place. Top speed is only 40 KPH (25 MPH) and range is only 40 kilometers (25 miles), but for getting around a city that's usually all that's needed. The problem with a full-sized car is that, being designed for intercity freeway traffic, it's overdesigned for urban transport; since the EN-V is strictly designed for the urban environment, it can be made built lighter without compromising safety, with bodies constructed from carbon-epoxy composite and doors made of high-impact polycarbonate plastic.

* If the EN-V takes a relaxed attitude towards vehicle construction, it makes up for it with impressive electronic smarts. It uses a Global Positioning System (GPS) receiver to figure out where it is, backed up by a set of sensors:

Wireless communications are useful too, allowing EN-Vs to communicate with an urban traffic-control system, as well as each other. The traffic-control system would automatically guide vehicles along optimum routes to avoid congestion; vehicle-to-vehicle communications would allow two EN-Vs to coordinate their actions to determine, say, how one should pass the other. Wireless communications can also permit "platooning", with one or more EN-Vs tagging along automatically behind a leader -- allowing a large family to travel together in a "train", or allowing a EN-V to be loaded up with heavy baggage and tag along with an EN-V carrying passengers in front. Of course, the vehicles could pass on warnings about accidents and traffic blockages to the traffic-control system and to each other.

In high-density urban environments, it might not make sense to actually own an EN-V, since many people won't have a place to park it. They could either pay per use or sign up for a subscription service, calling for an EN-V on a cellphone; the nearest empty EN-V would respond, with a message sent back to the client indicating the vehicle's estimated time of arrival. Even people who owned EN-Vs would find the vehicle's autonomy and communications useful: if a couple goes to the theater, they could disembark, tell the vehicle to go park itself, and then retrieve it with a cellphone call after the performance.

GM EN-V concept

* Other auto firms are exploring similar concepts. The initial impression of the new bubble car concepts is that they're cute -- but are they practical? There's good reason to think they will be in a decade or two: many of the advanced sensor systems required are already being sold for high-end cars, and others are being put through their paces in the lab. The US Defense Advanced Research Projects Agency (DARPA) has been sponsoring development of autonomous vehicles and, after a slow start, is now making impressive progress. There's good reason to believe vehicles that drive themselves aren't so far away, with autonomy not only promising convenience but also giving people who can't drive -- the blind, the elderly -- a freedom of mobility they don't have now.

Of course, the vision of a city swarming with little automated vehicles isn't going to be achieved without a lot of effort, but the new bubble cars still have plenty going for them even if they have to be driven manually at the outset. Given increasingly packed cities, they actually may be the only way to go anywhere at all.

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[MON 18 OCT 10] SYSTEM UPDATES REVISITED (1)

* SYSTEM UPDATES REVISITED (1): Following my exercise in getting my Windows 7 update stabilized, I documented what I did and then put together a writeup for my website on the use of Windows batch files. It was basically an update of a document I'd written like twenty years ago; it turned out to be more work than I expected, since there were things I didn't know, and Microsoft had actually enhanced batch files for Windows. There was also the issue of documenting how batch files integrated into the Windows environment.

That done, there didn't seem to be any more to be concerned about on my PC -- but then my DSL modem began to go down. At first I thought it was an ISP problem, because I called Qwest and was told they were having troubles. They fixed them and I was back online. Then I started going down again on occasions until I was just plain dead. Qwest told me things were fine at their end; the DSL modem also had a wi-fi hub capability and none of the PCs in my house were communicating with each other, so I concluded the modem was dead.

I didn't know exactly where to get a replacement. Obtaining a new DSL modem in a hurry turned out to be a reminder on how getting things done works in the real world.

Such is life. I bought the modem -- an ActionTek PK5000 -- came back home, and promptly got back online. However, I had never got my various PCs to work all that well together on wi-fi to begin with, and now they were working worse, so I decided to set aside time and get my household wi-fi network working once and for all. The issue was really to get a clear idea of how configuring a wi-fi network under Windows was done. There were a number of "how-to" articles, none of which were very clear, but after some days of writing up notes, I had an outline of what I could do for a start. [TO BE CONTINUED]

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[FRI 15 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (13)

* THE KILLING OF JFK -- THE ASSASSINATION (13): While Lee was being arraigned, Robert Oswald arrived at police headquarters. Robert had heard the news about Lee on the radio that afternoon. He first went home and told his wife to take the kids to the farm owned by her parents outside of Fort Worth, on the basis that crazies might want to take action against Lee's relatives. He then went downtown and spoke with the FBI in the Dallas Federal Building. He couldn't tell them much, not having seen Lee for a year, and the FBI suggested Robert go over to Dallas City Hall if he wanted to see Lee. The place was a madhouse when he arrived; the desk officer didn't pay him Robert too much mind until he explained that he was Lee's brother.

However, although Will Fritz promised to talk with Robert, everything was much too hectic and it didn't happen. Robert ended up in a waiting room with Marguerite, who had also arrived recently. While they were sitting there, Marguerite told Robert to be careful about what he said: "The room is bugged!" Robert was thoroughly familiar with his mother's paranoid games and was annoyed: "I don't care whether the room is bugged or not." He had nothing to hide.

To no surprise, Marguerite continued to rattle on. She'd believed ever since Lee went to the USSR that he was working as some sort of secret US government agent. As his mother rambled, Robert got the uneasy feeling she actually enjoyed being in the spotlight the arrest of her son had thrown on her. They didn't get to see Lee that Friday night.

* People all over the world were hanging on to the news reports to see what would unfold next, and the announcement that Oswald had been identified as a suspect quickly made the global rounds. L. Fletcher Prouty -- the conspiracy theorist previously mentioned in connection with the claim that the Secret Service customarily evacuated all tall buildings along a presidential motorcade route -- later found something sinister in the matter, pointing out that the newspaper the CHRISTCHURCH STAR in New Zealand ran a fairly detailed article on Lee Harvey Oswald only hours after he had been announced as a suspect. How, Prouty asked, could such information have been disseminated so quickly? It was obviously preprepared and released as part of an effort to "frame" Oswald.

In reality, there was nothing about Oswald in the article in the STAR that hadn't already been on file with the newspapers. The article was derived from an Associated Press wire release; articles on Oswald had been published when he defected to the USSR and when he came back again, providing details on his background, and it was neither difficult nor time-consuming to retrieve the articles from the archives and render them into an updated release, adding such information as had appeared in the media later, such as Oswald's Fair Play for Cuba activities. The photo of Oswald that appeared in the STAR article had been taken in Moscow in 1959 and had been run along with articles on his defection. News organizations have long known the importance of covering a hot scoop quickly and they tend to be efficient at doing so.

Along with the facts retrieved from the files, by late that evening speculation was circulating in the press that Oswald might have been part of some Communist plot. Even before the day was out, conspiracy theories were beginning to take shape. [TO BE CONTINUED]

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[THU 14 OCT 10] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: Heart pacemakers, discussed here earlier this year, remain an evolving technology. DISCOVERY CHANNEL Online reports that researchers from Case Western Reserve University and Vanderbilt University have come up with a new concept for pacemaker operation: using laser pulses instead of electric shocks. Current pacemakers simply dump electricity into the heart and have to use wires with metallic contacts to connect to the heart. A laser provides a highly selective pulse and uses a fiber-optic thread to hook up to the heart, with the thread being less prone to corrosion and also not requiring an electrical contact. A laser-based pacemaker would also require less power, meaning the battery would last longer.

The laser beam actually controls the heart by heating up the target area, causing ion channels to open, triggering an electrical impulse. The researchers have only performed a proof of concept demonstration on quail embryos and don't feel they are close to having a practical device. Their work is part of a broader effort to use lasers in implants, with extensive studies having been performed on laser-based cochlear implants, the laser beam providing very sensitive control over nerve stimulation.

* Intel made the tech headlines with the company's new "Sandy Bridge" chip, to be released early in 2011. The major gimmick is integration of a graphics processor unit (GPU) on chip with CPU cores. At the outset, there will be four-core versions, and low-power dual-core versions for mobile applications. Some claim that Sandy Bridge will hit makers of GPUs like Nvidia hard; Nvidia responds that they will be able to come up with more powerful GPUs to stay ahead of the game. What Sandy Bridge will certainly bring to the party is better graphics for low-cost machines; Intel's competitors are also certain to respond, ensuring that prices will be low.

* WIRED Online reports that Britvic, a UK firm that sells flavored spring water under the brand name "Juicy Drench", has introduced vending machines with a touch-based interface that allows a customer to play games. The games are simple puzzles and the like -- pick which one of several similar objects is different from the rest, remember the sequence in which colored lights go on, count the number of bouncing balls -- and if the customer scores high, the machine hands out a freebie Juicy Drench. Britvic offers the puzzles on their website for the curious.

* THE ECONOMIST had a note on Warren Brush, who operates a farm in Cuyama, California that features buildings made of straw. Local authorities have not been pleased with the idea, but have been hobbled in taking action because California's building codes don't have a problem with straw buildings -- since the building codes don't say anything about the matter.

Besides, Brush has his sympathizers, who point out that straw has its merits as a building material. It's a great insulator; it's effectively waste material and so is cheap; and significantly, buildings made of it stand up well to earthquakes, a big issue in California in general and to Brush in particular, since his farm is near the notorious San Andreas fault. Studies by the University of Nevada show straw buildings can stand up to quakes that would tumble down conventional structures.

straw house in construction

In reality, the straw buildings are hardly crude in appearance, though they certainly are low-tech. They're built on a foundation of gravel covered with a soil mortar, with walls built of tightly-packed bales of hay, held together with fishnets and bamboo pins, then set up on the foundation. The walls are finally sealed over with a clay-based plaster. The end result resembles adobe or stucco in appearance. All the elements have a lot of "give" to them and so such a building rides out a quake fairly well.

Of course, buildings in California are built to ride out quakes anyway and straw honestly isn't suited to large structures, but the economy of straw houses makes them more generally attractive in poorer places, such as Pakistan, where straw houses are now springing up. The authorities in California are starting to warm to the concept, having gradually lost the idea that a straw house necessarily reflects the flimsy structure depicted in the classic fairy tale THE THREE LITTLE PIGS. Says a straw sympathizer: "The lesson of THE THREE LITTLE PIGS isn't to avoid straw. It's that you don't let a pig build your house."

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[WED 13 OCT 10] DIGITAL BIOPSIES

* DIGITAL BIOPSIES: As discussed by an article from SCIENTIFIC AMERICAN ("A Better Lens On Disease" by Mike May, May 2010), modern medical practice, despite its use of advanced tech, sometimes seems far behind the times. For a particularly significant example, consider the hundreds of millions of pathology slides prepared every year. The procedure for "biopsies" is much the same as it has been for more than a century: a tissue sample is cut into paper-thin sections and stained to bring out specific features, then examined under a microscope for anomalies. For example, in a breast cancer biopsy, a pathologist examines the slide for the type and quantity of tumor cells. It can take two or three days to between the time the sample is taken and the analysis is complete.

In the late 1990s Dirk Soenksen, a medical business manager began to tinker with the notion of digitizing biopsies, leading to the establishment of a startup company named Aperio, in Vista, California. The concept is to take digital images of tissue samples for examination by pathologists and, eventually, analysis by computer. Digitized biopsies promise to reduce labor, provide much faster turnaround, and permit more detailed examinations. Pathologists will still need to examine and interpret the results, but once the samples are in digital form, they'll be easy to inspect in detail, and the digitize format will provide pathologists at different locations immediate access to a common archive of samples, stored on a secure website.

The concept sounds straightforward from the point of view of 21st-century technology, but there are obstacles. First, while a relatively high-end consumer digital camera might have 12 million pixels -- 12 megapixels -- a biopsy slide needs 900 megapixels to for adequate resolution. Although there are military and astronomical cameras that have resolution of that order, at present they're much too expensive for other uses, and so a line scanner system has to be used instead. That would seem like a perfectly adequate solution, except for the fact that scanning may take several minutes per slide. Given that a medical center prepares hundreds of thousands or millions of biopsy slides a year, a single scanner system couldn't keep up with the demand. Improved scanning methods are required.

Second, developing effective computer image analysis techniques to inspect digitized biosamples isn't a trivial task, and at the outset the digital imagery will still be examined by pathologists. Of course a 900 megapixel image can't fit on a computer display at full resolution, but there's no problem in displaying a low-resolution image and then "zooming" in on details as needed. We do the same with satellite imagery on Google Earth, and building a system for digital biopsy imagery with capabilities along the lines of Google Earth is, if not trivial, certainly practical, with work underway to that end. As far as computer analysis of the imagery goes, work is being done towards that end as well, though much remains to done.

A digital biopsy system would be an important element in a digital medical system, but that goal remains the most troublesome of all. Medical practice is difficult to digitize due to the complexity of the tasks and the lack of interoperability standards between different medical organizations. As discussed here in 2007, work towards a unified medical information system has proven slow and painful, and even given the clear benefits of "going digital", there's no guarantee that we're going to get there soon. Still, even without a comprehensive medical information system, the notion of the digital biopsy has a lot going for it, and development is certain to continue.

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[TUE 12 OCT 10] OBAMA SPACE PLAN FINALIZED

* OBAMA SPACE PLAN FINALIZED: The Obama Administration's plans for changing the direction of the US National Aeronautics & Space Administration (NASA), outlined here early this year, drew a good deal of flak, mostly on the perception that the idea was to abandon human spaceflight. After considerable wrangling, however, in late September, the House of Representatives passed a compromise bill that seems to have a chance of making everyone more or less happy.

The House, in a 304-to-118 vote on 29 September, approved a Senate-written bill authorizing $58 billion USD for NASA over the next three years and setting priorities for the agency. The Senate had passed the bill in August; now it goes on to President Obama for his signature. As the administration had wanted originally, the compromise bill funds work on developing a commercial spacelift capability for putting crews and cargoes into orbit, primarily for support of the International Space Station (ISS); supports use of the ISS to 2020; stretches funding of the space shuttle into 2011 to support the last flight of the system; and most significantly kills the Constellation program, a program with a long-range plan to return to the Moon that had turned out to be unaffordable.

The bill does retain some parts of Constellation, confirming the continued development of the Orion space capsule, capable of supporting human deep-space missions, and directing NASA to develop a heavy-lift booster that could put a payload of at least 64 tonnes (70 tons) into low Earth orbit (LEO). NASA was required to submit a plan for a heavy-lift booster within 90 days. Obama has stated he wants to begin development of the heavy-lift booster by 2015, and envisions a crewed mission to an asteroid by 2025, followed by a crewed Mars flyby in the 2030s.

Even after Obama signs the bill into law, NASA cannot yet begin working in earnest on its new mission since funding actually hasn't been allocated yet. Some sources claim Congress may well balk at adequately funding the plan even after approving it. We shall see.

* The heavy-lift booster was a particular sore point in the debate over the space bill. As reported by an article from AVIATION WEEK ("Crunch Time" by Frank Morring JR, 13 September 2010), NASA had already been considering what should be done. The agency's "Human Exploration Framework Team (HEFT)", organized for planning future US human spaceflight efforts, has come up with a concept for a shuttle-derived booster that can be developed on a fast track and then enhanced in phases:

shuttle-derived boosters

Of course other options could be considered over the longer run, such as liquid-fuel boosters replacing the SRBs, NASA having already performed studies of such technology. This development path -- starting with a shuttle-derived booster with the minimum possible changes, to then be incrementally enhanced -- seems so obvious that it's hard to understand why it would be particular controversial. Congress still has to give the nod, however, so again, we'll have to wait and see what happens.

* The Obama Administration's goal of sending astronauts to an asteroid by 2025 seems to be drawing considerable interest. As reported by another article from AVIATION WEEK ("Space Rocks" by Mark Carreau & Frank Morring JR, 6 September 2010), Lockheed Martin is pushing a mission under its "Plymouth Rock" plan that would use two Orion capsules to fly two astronauts to an asteroid as early as 2016 or 2019. The astronauts would conduct a six-month mission to pay a visit to an asteroid, with candidates ranging from 9 to 73 meters (30 to 240 feet) in diameter.

Plymouth Rock mission to an asteroid

Plymouth Rock envisions launch of a crewed Orion capsule on a Delta IV or comparable booster, accompanied by a launch of an uncrewed Orion and an Earth departure stage on a heavylift booster. Once in space, the two assemblies would mate up and depart Earth orbit for a three-month trip to an asteroid. The 2016 candidate target is 2008 HU4, about ten meters in diameter; the 2019 candidate target is 2008 EA 9, which is roughly the same size. Astronauts would tether the spacecraft to the asteroid and then conduct five days of investigations. One of the Orions would then return home in three months with 90 kilograms (200 pounds) of samples. Of course, any such mission would require a robot precursor to perform advance scouting of the target asteroid.

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[MON 11 OCT 10] TRAIN WRECK (2)

* TRAIN WRECK (2): American rail freight is among the cheapest in the world, with costs less than half as much as in Japan or Europe, even cheaper than China. The freights have also been beneficiaries of congestion on freeways and well as the increasing disrepair of the US interstate highway system. Ironically, the trucking industry itself has turned to the rails for relief, hauling truck trailers by rail over long distance, with local delivery and pickup on the roads. It turns out to be cheaper, and besides the number of people interested in the truck driving life is on the decline, accelerated by tougher drunk-driving laws. Trucking companies have very high turnover.

Although America's freight railways are a modern success story, there still has been some dissatisfaction with things. Since 2003, capacity limits and rising fuel costs have driven shipping costs steadily upward, with some coal companies feeling trapped because they have no alternative means of shipping product. Although most American rail corridors involve two railroads covering the same origin and destination points, in reality competition is limited: usually one route is more direct than the other, and if a mining company has sidings and a branch line linked to one railroad, it can't quickly and easily switch to another.

Congestion is becoming a real problem. The US Department of Transportation (DOT) believes that many rail freight companies are already operating at the limits of their capacity. The DOT says capacity will have to increase by almost 90% to meet forecasted demand in 2035, implying a hefty bill for investment in infrastructure. Once the update of the Panama Canal -- discussed here in 2007 -- is complete, there will also be a shift of sea transport to Gulf of Mexico and East Coast ports that will demand a shift in rail connections as well.

On top of all this, the freight railroads face a $15 billion USD bill for a new safety system to control trains on lines that also carry passengers or dangerous chemical cargoes. This system, "Positive Train Control (PTC)", is intended to stop or slow a train automatically if a driver goes too fast or passes a red signal. The bill mandating PTC was signed by George Bush in 2008 a month after a crash between a Metrolink commuter train and a Union Pacific freight train in California, resulting in 25 deaths and 135 injuries. The railway companies are not happy about being force-fed PTC, pointing out that only 3% of crashes are caused by the sort of human error that PTC is designed to deal with, and that there is no real basis for believing it will make the rails safer or more efficient. The railways feel they are being unreasonably handed the short end of the stick, and are seeking tax breaks and other subsidies to reduce the cost of compliance.

* The PTC issue is merely a component of what the freight railroads see as re-regulation and a return to the bad old days. Customers -- notably chemical, coal, agribusiness and utility companies -- are rebelling as over rising freight rates, and accusing the railroads of abusing their market power. The railroads reply that their profit margins are not generous, and that rising fuel costs have hit the transport industry across the board, with truck shipping costs rising in pace with rail shipping costs. However, a faction in Congress is trying to push through a bill to reimpose regulation on the rails; it doesn't seem likely to pass, but it is making the railroad companies nervous.

The Obama Administration's push for intercity express passenger lines is making them even more nervous. The difficulty is not the creation of new corridors with trains rattling along at 240 KPH (150 MPH). Such lines, like those proposed in California or between Tampa and Orlando in Florida, would have their own track, separated from existing lines, though on the same strip of land as a freight railway. The technology for building such lines is mature, with firms in Europe and Japan having plenty of experience in implementing them.

The difficulty for the freight railways is that most of the planned new fast intercity services will run on their tracks, and mixing slow freight and fast passenger trains on common tracks is difficult. With some exceptions on Amtrak's Acela and North East corridor tracks, as mentioned the status quo is a maximum speed of 80 KPH (50 MPH) for freights and 128 KPH (80 MPH) for passenger trains. In the new order, the passenger trains will run at up to 175 KPH (110 MPH), which complicates traffic management on the tracks -- it's complicated to begin with, because freight lines don't typically run on regular schedules.

The railroads have learned to live with the status quo, but they say that one Amtrak passenger train flying down the tracks at 175 KPH will displace the capacity for six freight trains in any corridor, and that the claim that PTC will permit higher capacity by allowing closer spacing of trains is hard to buy. Given that the freight railroads are already faced with a massive bill to increase capacity, they're not happy to be presented with the prospect of having to accommodate new lines of fast passenger trains as well.

freight train on the roll

Federal and state grants will flow to the freight railroads to help them upgrade their lines for more and faster passenger trains, but the railroads have noted the money already budgeted for the work includes funds for sidings where freight trains can be idled while intercity express trains speed by. In addition, the intrusion of the government into the rails implies government regulation and control over the effort to modernize the rails. Railroad officials also believe the FRA is not very interested in their inputs, and there have been hot discussions between the two camps. Fast passenger rails may be the way of the future; hopefully, America can acquire them without slipping back into some of the bad ways of the past. [END OF SERIES]

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[FRI 08 OCT 10] THE KILLING OF JFK -- THE ASSASSINATION (12)

* THE KILLING OF JFK -- THE ASSASSINATION (12): Just before 4:00 PM on 22 November, national TV news identified Oswald as a suspect in the killing of the president. Later that hour, Oswald was finally given a thorough personal search -- it seems the police who arrested him did no more than make sure he was unarmed and get his ID -- with the police finding five rounds of 0.38 caliber ammunition in his pocket, as well as a transfer ticket stub for the bus ride Oswald had taken that afternoon. He then stood in a lineup to be identified by Helen Markham as the man who had gunned down Officer Tippit. Markham was in a very shaky state, almost in need of medical attention, but she pointed Oswald out, taking care to examine him from different angles to make certain he was the man.

Oswald complained about being the only one in the lineup with a tee shirt and insisted that he be given a jacket so the lineup would be more fair. However, the killer had been wearing a jacket when Tippit was shot, which had been dropped at the service station later. The police actually had some problems finding men roughly Oswald's size for the lineup. They normally used prisoners, but feeling was running so high over the shooting of JFK that it might not have been prudent to let them get too close to Oswald. Captain Fritz found off-duty officers to stand in the lineup, telling them to take off their jackets and muss up their clothing.

* A second interrogation session followed. Oswald indicated that he wanted to obtain John Abt -- a Leftist lawyer who had participated in a number of high-profile cases involving Communists -- for his defense. Oswald then told more demonstrable lies, claiming that he hadn't actually used the alias "O.H. Lee", but that his landlady had got his name wrong -- a particularly unbelievable statement, considering Oswald deliberately waffled on his "Hidell" alias when he was arrested. Oswald said he had bought the pistol in Fort Worth; that he didn't have the money to buy a rifle. The police found him cool, evasive, and arrogant.

There was a second lineup at 6:30 PM, with Oswald shouting to reporters: "I didn't shoot anyone!" He was identified by Ted Callaway, the gung-ho ex-Marine from the car lot who had gone hunting for him after the killing of Tippit, as well as Callaway's work colleague Sam Guinyard -- now three witnesses had identified him as Tippet's killer. Bus driver Cecil McWatters was also there -- the police had traced him thanks to the transfer stub in Oswald's pocket -- but he wasn't so sure Oswald was the man he had picked up. After the lineup, Callaway and Guinyard were taken upstairs to be shown the jacket dropped at the service station, and they said it matched the jacket worn by the killer.

At 7:10 PM, Oswald was arraigned by the State of Texas in Captain Fritz's office by a judge for the murder of Tippit. The Dallas police wanted to make sure that Oswald was theirs, not merely because they had reservations about the FBI, but because they had cause to believe he had killed a cop -- one of their own, making it personal. Oswald was indignant, believing that an arraignment could only be performed in a formal courtroom setting. Maybe elsewhere -- but in Texas a judge made the decision and could make it any time or in any place. The police told him: "Shut up and listen!" Since Oswald was accused of a capital crime, he was denied bail. [TO BE CONTINUED]

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[THU 07 OCT 10] SCIENCE NOTES

* SCIENCE NOTES: A study published early this year on the morphologies -- shapes and structure -- of dog skulls came to some startling conclusions. Dogs, thanks to the willingness of humans to exploit changes that have naturally occurred in the dog genome, have accelerated the diversification of dogs to a massive extent in a few thousand years. This wild diversity in form is actually linked to very small genetic changes, most dogs having nearly identical genomes that closely match the genome of their wolf ancestor.

What is startling in the paper's conclusions is that measurements of the variation in dog skulls not only show their variation exceeds that of all the other canines -- wolves, foxes, jackals, and such -- but of all other members of the mammalian carnivore order -- cats, bears, badgers, otters, weasels, raccoons, and so on. It would be difficult to provide any more impressive evidence of the plasticity of organisms.

* As reported by SCIENTIFIC AMERICAN Online, while it is well known that indiscriminate use of antibiotics can select for antibiotic-resistant bacteria, the rise of such resistant bacteria actually ends up promoting their non-resistant siblings. A few resistant bacteria in a culture can actually enhance the resistance of the rest, it appears by secreting chemical signals named "indoles" that help the non-resistant bacteria ride out an antibiotic attack. The study demonstrates how colonies of seemingly independent microorganisms may have collaborative mechanisms; more practically, obtaining a better understanding of the resistance phenomenon may help in figuring out how to defeat it.

* As discussed here a few months back, researchers were surprised to find the genetic remains of a "bornavirus" in the human genome. It was a surprise because, although broken viral codes are common in the human genome, making up an estimated 8% of the total, they traditionally were all recognized as "RNA retroviruses", which have a habit of inserting their genomes into the genomes of a host cell. The bornavirus is a non-retroviral "RNA virus" and it doesn't normally do such things.

That finding turned out to be no more than the tip of the iceberg. As reported in the science blogosphere, further research has revealed that the genetic fossils of bornaviruses and also "filoviruses" -- a group that includes the deadly Ebola virus -- are common in humans and a wide range of other animals. Having heard news about bornavirus fossils in genomes, researcher Anna Skalka of the Fox Chase Cancer Center in Philadelphia and her colleagues scanned through the archives of the vertebrate genomes available, 48 in all, and looked for traces of 5,666 RNA viral sequences from 38 known families of RNA viruses and nine genera that are presently unclassified. Skalka's study found that squirrels, guinea pigs, zebrafish, and many other species besides us showed remnants of RNA viruses in their genomes. Furthermore, the research showed that the RNA viral fossils consisted almost entirely of bornaviruses and filoviruses. Why them, and not other RNA virus groups?

Skalka isn't sure of the answer, but she suspects that the viral genomes were transcribed into host cell genomes by malfunctioning cellular replication machinery. She also suspects that such processes could have carried on the genomes of any RNA viruses, but that all genomes except those of bornaviruses and filoviruses were weeded out over time. The bornavirus and filovirus fossil sequences have been embedded in the genome for about 40 million years; they may have been retained for so long because there was some selective advantage to keeping them.

Others suggest, since Skalka's team scanned for the sequences of known RNA viruses, that the heavy representation of bornaviruses and filoviruses is due to the fact that these viruses have had relatively stable genomes for tens of millions of years -- that is, there may be far more RNA virus fossils in animal genomes, but we can't spot the others because the genomes of modern representatives have changed too much. Skalka acknowledges this: "There may be some ancient ghosts in there, but the surviving viruses have evolved so far that we can't recognize them anymore."

* The notorious Ig Nobel prizes were awarded on 1 October. There was the usual list of "science of the strange", but one that caught my eye was a study done by Japanese researchers using swarm intelligence algorithms -- discussed here last month -- based on the swarm activity of slime molds as a model for the optimization of the layout of railroad tracks. Seems sensible enough to me, but it does admittedly sound a little bizarre.

Another one of the awards that got my attention was a computer simulation performed by a group of Italian researchers that suggested organizations would work about as well if they promoted people at random. The appalling thing is that I have a strong sense they're correct. I suspect people tend to underestimate the importance of accident in our normal ways of getting things done.

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[WED 06 OCT 10] DINING IN SPACE

* DINING IN SPACE: As reported by an article from DISCOVERY CHANNEL Online ("What Do Astronauts Eat?" by Robert Lamb, 2 July 2010), keeping astronauts fed is a challenge, both in terms of providing them with a enjoyable and nutritious menu, and in terms of the handling required to get the food to orbit and maintain it there.

The stereotype of astronaut food is that it's prefabricated and bland. That has some truth to it, but if the logistics of spaceflight force mean prefabrication of meals, those responsible for the job do all they can to keep the food tasty. Says Vickie Kloeris, who manages spaceflight food preparation for the US National Aeronautics & Space Administration (NASA): "We're able to provide a wide variety of products in thermal-stabilized or freeze-dried form. And we can provide some in natural form, such as cookies or crackers."

NASA space food

Astronauts don't like bland. Under zero gee, fluid tends to accumulate in the sinuses, dulling smell and taste, and so spicy foods are welcome. One long-standing favorite is shrimp cocktail, with freeze-dried shrimp and powdered cocktail sauce. Add water and it's a very tasty snack; some astronauts have even eaten it for breakfast. Hot sauces are also very popular.

Although not all foods work for space -- Kloeris says that pizza remains out of reach, and carbonated drinks cause instant indigestion in zero-gee -- NASA can provide about 180 different foods and beverages for astronauts on the International Space Station (ISS). The other partners on the station have their own menus as well; as Kloeris says: "The Russians have about 100 different food and beverage items on the ISS, and we have a few from the Japanese agency and a few from the European Space Agency as well. So we have around 300 different foods and beverages in orbit at the ISS that the crew members can choose from."

There's not much ordering off the menu, though NASA has been careful to offer vegetarian or kosher foods for some short term visits. ISS crew members also can haul personal "preference items" to orbit, amounting to about 100 cubic centimeters (a cubic foot) per month in space, including favorite snacks compatible with spaceflight.

That notion of "compatibility" relates to issues such as shelf life and bulk. That's why space food tends toward the freeze-dried or the heat-treated. NASA specs a two-year shelf-life for freeze-dried foods and three years for thermostabilized foods; given that the cargo spacecraft used to deliver supplies to the ISS have limited capacity and, by the standards of any other food delivery vehicle, are insanely expensive, there's every incentive to make the foods as compact as possible.

Kloeris says that preparing and packaging the food isn't even really the hardest part of the job -- it's scheduling: "The biggest challenge is getting the food where it needs to be, figuring out which vehicle to put it on, when the vehicles are going to launch and when they're going to get to the station so we can supply a consistent supply of food aboard the station. Launch schedules change, and it's difficult to keep up with that."

Now that the ISS has a water recycling system, dehydrated foods are preferred, helping to deal with the bulk issue. However, food packaging remains troublesome; as Kloeris explains: "It takes a lot of packaging to get the kind of shelf life we need on these products. Plus the crew members really want the items to be packaged in single servings. They don't want to have to deal with opening and re-closing things, because it's difficult to deal with bulk storage in microgravity." The discarded packaging has to be packed into docked cargo spacecraft along with other trash, with the spacecraft eventually undocked and deorbited, to burn up in the Earth's atmosphere.

As far as nutrition goes, the guidelines are pretty much the same in space as they are on the ground, though with some slight differences. For example, not as much iron is needed since there's a lower turnover in red blood cells. The lack of gravity means food tends to sit high in the stomach, making astronauts feel full quickly, leading to a preference for small meals and snacks. NASA continues to tweak the menu for best effect; Kloeris says: "Consuming too much salt isn't healthy, and that's especially true for our astronauts. We know that high sodium contributes to bone loss, and all astronauts experience at least some degree of bone loss when they're in orbit. So we're working right now to try to bring down the overall sodium content of the menu to help mitigate some of the medical issues that have begun to show up in our long-duration crew members."

* A video accompanying the article interviewed NASA astronaut Leroy Chiao, who commented that space food that tasted okay during ground training sessions would become, for whatever reasons, absolutely delicious after a few weeks in space. There was also a fair amount of food swapping between American astronauts and Russian cosmonauts, both sides enjoying the variety in the diet -- Chiao said he really liked the Russian veal and potatoes, as well as their onion mashed potatoes. He also commented that, while NASA preferred plastic wrapped foods, the Russians tended more towards tinned foods.

According to sidebars to the article, tortillas are preferred to bread, since tortillas have a longer shelf life and don't produce crumbs; crumbly foods like potato chips or graham crackers are very troublesome in space. Since bone mass loss is a problem in zero gravity, calcium-rich yogurt is another popular item on the NASA menu, though the Russians prefer tangy cheeses. Astronauts also get special treats in their meals every now and then -- celebrity chef Rachel Ray cooked up Swedish meatballs, a Thai chicken dish, and a vegetable curry for a 2006 shuttle flight, and other big-name chefs have done their bit on occasion as well.

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[TUE 05 OCT 10] HARD BARGAIN? / EVOLVING FOR THE CITY

* HARD BARGAIN? It's well known that humans who live in malarial regions have acquired adaptations to help defend against the disease. The most familiar is the genetic mutation that causes sickle-cell anemia if a subject obtains the gene from both parents; if the subject only obtains it from one, the result is red blood cells that help stymie the attacks of the protozoan parasite that causes malaria. As reported by an article from AAAS SCIENCE ("Kidney Disease Is Parasite-Slaying Protein's Downside" by Mitch Leslie, 16 July 2010), some populations of Africans may have ended up with a similarly dodgy defense against another protozoan parasite, the trypanosome that causes lethal African sleeping sickness, spread by the bite of the tsetse fly.

The research group, led by Martin Pollak -- a nephrologist (kidney specialist) and human geneticist at the Harvard Medical School in Boston -- wasn't really looking for the resistance mechanisms against sleeping sickness at the outset. They were instead investigating genetic "risk factors" for two kidney conditions, "focal segmental glomerulo-sclerosis (FSGS)" and "hypertension-attributed end-stage kidney disease (H-ESKD)", that are four to five times more common among black Americans than white Americans. It was known the diseases were linked to human chromosome 22, but nobody had investigated them much more closely than that.

The researchers focused on a gene named APOL1 on chromosome 22 that codes for a blood protein named "apolipoproteing L-1 (ApoL1)". They searched through genetic data provided by the "1000 Genomes Project", an effort to obtain genomes from people around the world, to see if they could find mutations in APOL1 that were much more common in Africans than in Europeans. The researchers then examined the APOL1 gene variants among black Americans with FSGS or H-ESKD, and came up with two gene variants that correlated to kidney disease:

An analysis showed that if both of a subject's APOL1 genes were the G1 or G2 variant, the risk of developing H-ESKD went up by a factor of seven. What makes this puzzling is that G1 and G2 are very common in Africa. Among the Yoruba of Nigeria, G2's frequency in the population is 8%, while G1's is a massive 38%. Since the gene variants seriously raised the risk of kidney disease, the conclusion was that they had some positive effect that counterbalanced the drawback. Backing up this notion was the fact that comparative population genetics suggested that G1's prevalence is a relatively recent phenomenon, tracing back about 10,000 years.

It is known that the normal ApoL1 protein will protect against the parasite subspecies Trypanosoma brucei brucei but not against the similar subspecies T. brucei rhodesiense, which produces a protein named "SRA" that neutralizes ApoL1. Pollak and his colleagues believe that the G1 and G2 proteins are a counter-countermeasure to T. brucei rhodensiense, reconfiguring ApoL1 so that it is no longer neutralized. In experiments, blood plasma from people with the G1 or G2 mutations, or Apol1 proteins synthesized using the mutant pattern, was highly effective in killing T. brucei rhodensiense.

It looks on the face of it like an example of an evolutionary arms race between human and parasite, but others aren't so sure. T. brucei rhodensiense is found in East Africa but not in West Africa, where the Yoruba live and where the threatening trypanosome strain is actually T. brucei gambiense, which the mutations don't touch. The researchers are expanding their statistical study over Africa to see if they can figure out what's going on. While they haven't made much progress on helping people with FSGS or H-ESKD, they may have found a more effective treatment for sleeping sickness -- traditionally, drugs used to treat the disease were so drastic that they had a fair chance of killing the patient -- and they believe that a better understanding of the genetic basis of the two kidney diseases should help improve treatment down the road.

* EVOLVING FOR THE CITY: In related news, as reported by an article from BBC WORLD Online ("City Life Boosts Bug Resistance", 25 September 2010), a genetic survey performed by a team of University of London researchers shows that a human gene variant providing resistance to leprosy and tuberculosis (TB) is more common among populations with a long history of urbanization than in other populations.

The scientists analyzed DNA samples drawn from 17 different human populations living across Europe, Asia and Africa. The results were cross-checked against historical and archaeological data on the date of the first city or urban settlement in each region. The protective gene variant was found in nearly all subjects from the Middle East to India and in parts of Europe where cities have been established for thousands of years. It was less common in regions with a shorter history of urbanization, such as Africa. One of the researchers, Dr. Ian Barnes, said of the work: "It flags up the importance of a very recent aspect of our evolution as a species, the development of cities as a selective force. It could also help explain some of the differences we observe in disease resistance around the world."

Professor Brian Spratt, chair of molecular microbiology at the Imperial College London School of Public Health, commented: "Individuals who are more resistant to a pathogen that causes a disease with substantial mortality, such as malaria or TB, will survive better and will contribute more offspring to the next generation. As many of their children will have inherited increased resistance to the pathogen, they also will survive better. Thus frequencies of these genetic sequences that provide increased protection to a disease will be far more common in areas where the disease has been killing people for centuries or even millennia than those where the disease has never been endemic. The same effect should occur for some diseases with populations who have lived for centuries within dense cities because diseases such as cholera and TB will have always been a problem in cities due to overcrowding and poor sanitation, compared to people living nomadic lives."

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[MON 04 OCT 10] TRAIN WRECK (1)

* TRAIN WRECK (1): The Obama Administration has been pushing a plan to bring high-speed rail networks to the USA -- but as reported by an article from THE ECONOMIST ("High-Speed Railroading", 22 July 2010), the government's high-speed rail plans may be on a collision course with America's freight railways.

In 2009, the Obama Administration's stimulus package included a lump sum of $8 billion USD, plus a billion dollars a year, to promote construction of fast rail corridors in high-population areas of the USA. Fast passenger rail is common in Europe, Japan, and increasingly China, but the USA currently has only one fast passenger rail line -- Amtrak's "Acela" service from Boston via New York to Washington DC. The Acela line isn't particularly impressive by global fast rail standards, capable of a relatively modest top speed of 240 KPH (150 MPH), and for much of the route only half that because the track system won't handle high speeds. Acela, like virtually all trains run by publicly owned Amtrak, uses tracks belonging to freight railways, whose trains roll along at 80 KPH (50 MPH); passenger trains must stay below 128 KPH (80 MPH) when they share the tracks with freights. For the most part, the "high speed train" future of the USA corresponds to a modest number of diesel-electric intercity trains at going 175 KPH (110 MPH), not European-style electric expresses going nearly twice as fast.

Amtrak Acela line

However, even this modest change threatens the freight lines. Their owners worry that the plans will demand expensive train-control technology that freight traffic, in itself, doesn't need. They worry that passenger trains will reduce the track capacity available to carry freight. Most of all, they worry that the Federal money being spent on upgrading the rails will bring the Federal Railroad Administration (FRA), the government's industry watchdog, down on their backs, in effect re-introducing regulation. Congress has already been twisting the screws on the industry over rising freight rates.

* There's a tendency to see America's railroads as backwards in contrast to Europe's, but that's an oversimplified view. Europe indeed has an extensive network of modern high-speed electric passenger trains linking the major cities of the continent. The USA has nothing to compare -- but in general, the USA generally doesn't have the high population densities and relatively short distances that make fast passenger rail profitable. The well-developed US freeway system does the job generally well for short-range travel, while the airline network handles long-range travel efficiently. Critics also point out that, though the balance sheet of European fast rail does show a clear profit, it doesn't factor in the huge costs of building track, which the critics claim is equivalent to a subsidy of billions of dollars a year.

In contrast, except for Germany and Switzerland, Europe's freight rail services are a disaster, fragmented and bleeding money. Repeated attempts to break down the technical and bureaucratic barriers imposed by national frontiers have gone nowhere. The USA's freight railways are wildly successful, regarded as the world's best.

The freight railroads took off in the wake of deregulation at the end of Jimmy Carter's administration. Two years after deregulation of aviation gave rise to budget carriers and cheap fares, the deregulation of rail freight, under the Staggers Rail Act of 1980, started a wave of consolidation and improvement. The Staggers Act gave railways freedom to charge market rates, enter confidential contracts with shippers, and run trains as they pleased. Operators could close passenger and branch lines -- as long as they preserved access for Amtrak services -- and were allowed to sell lossmaking lines to new short-haul railroads. Regulation of freight rates by the Interstate Commerce Commission was abandoned for most cargoes, provided such cargoes could also be hauled by road.

Before deregulation, America's railways were sinking, declining steadily from the 1940s to the 1960s, culminating in the disastrous collapse of industry giant Penn Central in 1970. In 1980, a fifth of rail mileage was owned by bankrupt firms; rail's share of intercity freight had fallen from 75% in the 1920s to 35%, with tracks and service deteriorating. Regulation was part of the problem: services and rates were heavily controlled, and companies were forced to operate unprofitable passenger services. Another problem for the railroads was the rise of the interstate highway system in the 1950s, which gave a huge boost to trucking, underwritten by what railroaders saw as government subsidies in the form of highway construction funds. Deregulation turned everything around; productivity skyrocketed while rates dropped, and rail's share of the interstate freight market is now 43% -- not in a league with prewar days, but the highest in any developed country.

* Coal is the biggest single cargo, accounting for 45% by volume and 23% by value, with more than 70% of coal transport by rail. As demand grows for the lower-sulphur coal from the Powder River Basin in Wyoming, it has to travel farther, and so railroads have invested in more powerful locomotives to haul longer coal trains. Energy efficiency improved as well, thanks to more fuel-efficient locomotives, lighter freight cars made of aluminum, and double-decker freight cars.

However, the fastest-growing component of of US rail freight is "intermodal" traffic: truck trailers or shipping containers loaded on to flatcars. The number of such shipments rose from 3 million in 1980 to 12.3 million in 2006, though the economic downturn has scaled back the volume a bit. Driving intermodal traffic is the flood of imports from across the Pacific, coming into the West Coast ports of Long Beach and Los Angeles.

A special rail expressway for freight, the "Alameda Corridor", was opened in 2002 to link the ports to the big national rail routes, bypassing the 200 grade crossings on the original branch lines that used to cause huge traffic jams on the roads as mile-long freight trains rumbled across. The corridor, one of the biggest infrastructure projects in modern America, was completed on time and on budget for $2.4 billion USD by a public-private partnership seen by many to be a model for other rail schemes, such as California's proposed high-speed passenger line. [TO BE CONTINUED]

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[FRI 01 OCT 10] ANOTHER MONTH

* ANOTHER MONTH: There was an ad in the freebie local newspaper for a national radio-controlled model aircraft meet at Drake field, a rural airfield about a half-hour's drive from where I live. I debated going, but since I haven't been getting out of the house much lately, I decided I might as well.

Actually, it turned out to be good fun. I got out to the airfield about 11:15 AM and checked out the models sitting around. They tended towards the elaborate, single-engine machines being on the order of a meter in length, multi-engine machines running about twice that. Having done that, I watched the aircraft being put through their paces. I've never flown RC aircraft, but it clearly requires skill, particularly for aerobatics. Landings were also a problem, with a number of aircraft veering off the runway, though they were done little harm -- however, one pancaked in hard and lost its landing gear.

B-17 RC model

Multi-engine models appeared to be the trickiest to keep flying because of their complexity; an oversized B-29 Superfortress bomber model with four engines got off the runway, made a loop, and came back down again immediately. One of the more impressive demonstrations was of an F-18 Hornet with a tiny jet engine, moving along at a very fast clip. I spent some there, enjoying the sun, but at 1:00 PM I figured I'd had enough, to then go back home to get something to eat. I got over 140 pictures; by the time I winnowed through the worthless junk, I only had about 40, and when I got down to the "keepers" I had eight. That's about typical -- with a digital camera, there's no problem with taking duplicates of every shot that seems worth taking.

* On the tale of the Chinook helicopter from last month that flew over in the dark ... now I'm not so sure it was a Chinook. There was a big brush fire to the west of Loveland this last month, with a few homes destroyed though nobody got hurt; pictures in the local newsrag showed Sikorsky S-64 Skycrane helicopters participating in the fire-fighting effort.

The Skycrane is an unusual machine, literally a flying crane, with a cabin but no fuselage to speak of -- just an airframe that can straddle various payloads, like a water tank for fighting fires. They were built during the Vietnam War for the military and weren't produced in big numbers; an outfit named Ericson Skycrane up in Oregon has bought up surplus machines and refurbished them for use as fire-fighters. They are big helicopters and no doubt they are as noisy as a Chinook. I'd never seen one up close and I was tempted to drive out to the area of the fire in hopes of getting a shot of one, but I knew immediately that getting underfoot in an emergency response exercise was a really bad idea. I did have one, probably the same machine, fly over my neighborhood in daylight a few weeks later, but I didn't get a shot of it.

S-64 Skycrane

* In local news for the Loveland, Colorado, area, a citizen busted on felony fraud charges said he shouldn't be held in jail, that he should be "judged only by God." To which, after a moment's thought, the reply would be: "God hasn't requested extradition -- and besides, if He did, the only means we have of handing you over to His custody is something you REALLY wouldn't like. You REALLY wouldn't like it."

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