* This weblog provides an "online notebook" to provide comments on current events, interesting items I run across, and the occasional musing. It promotes no particular ideology. Remarks may be left on the site comment board; all sensible feedback is welcome.
* GENOMIC WHODUNITS (4): Studies of ancient pathogens have not exclusively focused on those that infected humans; those that infected human crops could also have historical impacts. Between 1845 and 1852, Ireland suffered an infestation of a blight that destroyed the potato crop, the staple food of the Irish. Roughly a million Irish died in the Great Famine, with at least as many leaving the country to find better fortunes elsewhere. The blight was judged to have been caused by a fungus, but it was actually due to a fungus-like single-celled organism named Phytophthora infestans, an "oomycete".
Using DNA from dried leaves of the "lumper potato" preferred by the Irish that were archived in herbariums, an international team of molecular biologists sequenced the genome of the P. infestans strain that cause the blight. It turns out that it is an extinct strain, one researcher involved in the project commenting: "We found it in all these leaves from Ireland, from England, from France, from Germany. One strain. Then it just disappeared."
The research team had been trying to unravel the history of P. infestans, which of course parallels the history of its potato host. The potato was first domesticated in what is now Peru between 7000 and 10,000 years ago, with the crop plant introduced into Europe by Spanish conquistadors in the 16th century. It became an important food staple that played a major role in the 19th century population boom in Europe. However, Europeans propagated the potato by planting cuttings of potatoes, resulting in huge clone monocultures that were highly vulnerable to pathogens -- and led to staggering disaster in Ireland.
Since the potato still remains an important staple crop, what specific strain caused the Great Famine is a matter of significant current interest. The researchers obtained the genomes of 11 ancient strains of P. infestans found in dried leaves of potatoes -- and tomatoes, closely related to potatoes and similarly vulnerable to the oomycete -- collected from Europe, Great Britain, Ireland, and North America between 1845 and 1896, to be stored at the herbaria of the Botanical State Collection, Munich, and the Royal Botanic Gardens, Kew. The researchers found analysis of the genomes much easier than expected; having obtained them, they compared them to the genomes of 15 modern strains of the pathogen.
While the conventional wisdom had been that the blight was caused by an existing strain named US-1, noted for its international distribution, that wasn't what the researchers found. They found that the strain actually responsible for the famine, which they named HERB-1, emerged in the early 19th century, probably in the US or Mexico. It spread around the globe for another half a century after the famine began, but had vanished by the early 20th century, probably because farmers stopped planting lumpers and began to breed resistant potatoes.
HERB-1 was actually a close relative of US-1, both derived from the same common ancestor, but the split between the two strains apparently took place in the Americas before the first major outbreak in Europe. The research project has been praised for its insight and significance -- as well as its demonstration of how much genomic information is lurking in the world's herbariums. With more tricks being found on a steady basis, the hunt for ancient pathogens is clearly on an upward trend. [TO BE CONTINUED]COMMENT ON ARTICLE
* THE UNITED NATIONS (13): The UN having been created, the Truman Administration focused on clarifying the new order for Europe, and finishing off the war with Japan. The Big Three leadership of Churchill, Stalin, and Truman met in Potsdam, a suburb of Berlin, from 17 July to 2 August 1945, to hash matters out. The meeting proved more significant for its failures than its successes. The Western Allies were not happy at the way the Soviets were incrementally extending control over the lands they had occupied in the East, most notably Poland, nor were they happy at the way the USSR was methodically looting defeated Germany.
Germany was packed with refugees who had been evicted from German-speaking communities in the East, and from the adjustment of Poland's borders. It made no sense for the Western Allies to impose reparations on Germany and then have to pay billions to keep all the refugees from starving. Better to rehabilitate Germany and get its economy going again to ensure that people stayed fed, and to ensure Germany wouldn't be a drag on the economy of Europe. The Soviets, not surprisingly given the rapacious behavior of the Germans in the USSR, demanded reparations from the part of Germany under occupation by the Western Allies -- but it just wasn't going to happen. Although the expectation had been that Germany would be reunited, under the circumstances, it wasn't surprising that it remained partitioned for decades.
The Western Allies did recognize the Polish Lublin government, there not being much else they could do, giving Stalin cause for satisfaction. Stalin in turn agreed to throw his weight against the Japanese after forces could be transferred to Siberia, though the Americans had increasingly mixed feelings about Soviet cooperation in the war against Japan. The Japanese were showing no interest in surrender, US intelligence discovering instead that they were preparing for a last-ditch defense of the Japanese home islands, in hopes of inflicting enough pain on an American invasion force to force a negotiated settlement on terms satisfactory to Japan. In addition, there were Japanese forces scattered through the Far East, most notably in China, and the Americans were dreading the prospect of having to wipe all of them out.
From that point of view, Soviet assistance against Japan was welcome. However, it was becoming obvious that where the Red Army went, Soviet power was likely to become entrenched, and if the Americans could do little to influence what Stalin did, they were increasingly reluctant to give Stalin any more reach. On 16 July, the Americans performed the first test of an atomic bomb, giving Truman what he hoped to be a trump card to eliminate the need for Soviet intervention in the Far East. Truman told Stalin about the Bomb in general terms at Potsdam, to find Stalin oddly disinterested. In reality, the US atomic bomb program had been infiltrated by at least three Red spies, and Stalin had known about it in detail long before Truman did.
On 26 July, the Americans, British, and Chinese issued the "Potsdam Declaration" to Japan, demanding unconditional surrender, providing assurances that the Japanese people would not be enslaved and, after being demilitarized, would be able to select their own form of government. The alternative to surrender, the declaration stated, would be "prompt and utter destruction".
The Japanese government ignored the declaration, and so on 6 August 1945 the Americans leveled the city of Hiroshima with an atomic bomb. On 9 August, the city of Nagasaki was destroyed by an atomic bomb as well, with the Red Army simultaneously jumping off into Manchuria. Overwhelmed, Japan unconditionally surrendered on 15 August. Fighting in Manchuria lingered into September, but Japanese forces in the field accepted, sometimes reluctantly, the Emperor's declaration of surrender. World War II was over.
Stalin had wanted to participate in the occupation of Japan, but the Americans were very cold to the proposal, and indeed only granted their other allies trivial participation in the exercise. Stalin also believed that the primary reason for dropping the two atomic bombs on Japan was to intimidate the Soviet Union -- which was a factor, but they would have been dropped even if it hadn't been. Stalin accelerated work on the Soviet atomic bomb program, with researchers leveraging off stolen American secrets. The postwar environment, generally expected to reflect a global desire for peace, was looking ever more confrontational even before the last shots of World War II were fired. [TO BE CONTINUED]COMMENT ON ARTICLE
* GIMMICKS & GADGETS: BLOOMBERG BUSINESSWEEK had an article on robot sailboats, focusing on the "SD1" from a US startup named Saildrone, out of Alameda, California. The SD1 has a hull like a spindle, 5.8 meters (19 feet) long, with stabilizing outrigger floats to each side and a rectangular "wing", 6 meters (20 feet) tall, sticking up from the back. The craft is made mostly of carbon composites and can be fully submerged. It features solar panels and a battery to supply power for electronics and a rudder steering motor. In the fall of 2013, the SD1 made a trip from San Francisco to Hawaii, 3,760 kilometers (2,336 miles) in 34 days. Average speed was no faster than a brisk walk, though it could get up to sprints for short intervals when winds permitted.
Saildrone was founded by one Richard Jenkins, who decided to build a robot sailboat to circumnavigate the globe in 2012. He sees the SD craft as floating research platforms, carrying instruments and communicating via satellite, with users monitoring them via a Saildrone app. Another firm, Harbor Wing Technologies of Seattle, Washington, has developed the "X-2" drone sailboat, which is being evaluated by the US Navy for ocean surveillance applications, and is working on a 9 meter (30 foot) follow-on that could carry 900 kilograms (2,000 pounds) of cargo. It wouldn't be able to deliver freight very quickly, but operational costs would be very low.
* TIME magazine reports that a startup named OpenTable is now taking another baby step towards a cashless society by allowing diners in restaurants to pay for their meals via smartphone, bypassing the annoying wait for the check. Users log their credit card with OpenTable beforehand; the bill includes tax and (presumably optional) tip, with the receipt emailed to the user. OpenTable is now conducting a pilot program in San Francisco.
As reported by BBC WORLD Online another smartphone app, far more serious in intent, has been developed by a Lebanese student named Sandra Hassan. Violence has been rising in Lebanon as of late; her app allows smartphone users to send the message I AM ALIVE to a predefined list of recipients with the push of a single button. After a bombing or comparable incident, phone traffic gets into a pile-up; the short message can get through much more easily.
* As reported by an article from BBC WORLD Online, one Anirudha Surabhi, a London design student, was zipping down the street when a driver opened up a car door. Anirudha hit the car door, went heels over teakettle, and landed on his head, which was fortunately protected by a helmet. Though it wasn't amusing and the helmet was a loss, he suffered no serious injury, and came up with a brainstorm as a result: why not a paper helmet?
The idea behind a cycle helmet is to provide a "crumple zone" to soften the abrupt deceleration of impact; as the saying goes, it's not the fall that's the problem, it's the sudden stop at the end. Cycle helmets are typically made of plastics, but Anirudha got thinking that paper would do a better job of crumpling. He came up with a multilayer honeycomb sheet that could be cut up and fabricated into a helmet. He said: "What you end up with is with tiny little airbags throughout the helmet. So when you have a crash, what these airbags do is they go pop, pop, pop, pop, pop -- and they go all the way to the bottom, without the helmet cracking. That's what absorbs the energy."
Tests demonstrated that the paper helmet reduced the gee forces of an impact to a third of what they were for a plastic helmet. His design is on the market now. He hopes it will catch on: "I think the public will accept it because if you think about it, stuntmen have been jumping onto cardboard boxes for decades, which are all made out of paper. They risk their lives from five-storey buildings purely because they know that paper actually works."COMMENT ON ARTICLE
* THE SEPSIS CHALLENGE: As reported by an article from SCIENTIFIC AMERICAN Online ("Researchers Struggle To Develop New Treatments For Sepsis" by Maryn McKenna, 27 March 2013), everybody knows what a heart attack or cancer is, but we're mostly oblivious to the notion of "sepsis". A 2011 survey showed only 1 in 5 Americans recognized the word, and the majority of those who did recognize it had no clear idea of what it meant.
Sepsis, which begins with an aggressive immune system response to an infection, kills 18 million people around the world every year, over a quarter of a million of them in the USA. Sepsis -- and its most severe form, septic shock -- has been estimated to be the leading cause of death for intensive care patients in America, and the 10th most common cause of death for everyone else in the country.
Physicians don't have a good handle on it either, often failing to spot the early warning signs because they mimic other problems, and the condition progresses very rapidly from trivial to deadly, meaning it may not be recognized until it's far too late. If sepsis isn't identified quickly, it may be too late to launch the needed interventions -- antibiotics to stop an infection, drugs to deal with a perilous drop in blood pressure, and a mechanical ventilator to raise dangerously low oxygen levels. Progress on better treatment of sepsis has been painfully slow.
Sepsis begins quietly when the immune system targets invading pathogens. Immune cells release signaling proteins known as "cytokines" to stimulate one another and deal with the intruders -- but for reasons not well understood, the response can go off the rails, with the immune cells releasing far more cytokines and other inflammatory molecules than is typical. The overload of immune molecules surging through the bloodstream has the inadvertent effect of making blood vessels slack and permeable, reducing blood pressure and allowing the fluid component of the blood to seep into surrounding tissues. The blood components left behind clot in the smallest vessels, blocking oxygen from major organs.
At this point, someone with sepsis has transitioned from the earliest stage of the condition, known as "systemic inflammatory response syndrome", to the later stages of "severe sepsis" and "septic shock". The patient becomes confused; the heart's activity becomes erratic; the kidneys and other organs fail; blood pressure cannot be raised even with large amounts of intravenous fluids and drugs. It's not the pathogen that the killer: it's the body's own immune system.
Medical researchers have worked on drugs to interrupt the chemical cascade that triggers inflammation and clotting, but so far none of them have proven effective, clinical trials going nowhere. Sepsis, it turns out, is peculiarly difficult to nail down: mice don't seem to be very good models for humans as far as sepsis goes, and its rapid progress makes controlled trials very difficult. Worse, there's a strong suspicion that "sepsis" isn't a single condition, but a range of them, making treatment difficult. Work continues on treatments, but some researchers believe that matters have to be completely rethought -- lest they continue down blind alleys while patients continue to die.COMMENT ON ARTICLE
* TRY TRY AGAIN: The notion of a reusable launch vehicle (RLV) has been around since the beginning of the Space Age. After all, what sense did it make to build a big expensive booster that could only be used once, and then simply discarded? Why not fly it repeatedly like a jetliner? That turned out to be far easier said than done. The only RLV to ever go into service, the US Space Shuttle, was only partly reusable, and it ended being more costly to fly payloads with it than with a one-shot expendable booster.
As reported by an article from AVIATION WEEK ("Reusable Redux" by Graham Warwick, 2 December 2013), the US Defense Advanced Research Projects Agency, the military's "blue sky" program office, wants to try to fly an RLV again, having initiated the "Experimental Spaceplane One (XS-1)" program. The XS-1 is envisioned as a reusable "first stage" vehicle that will carry an upper stage with a payload to the edge of space for launch. Payload is to be from 1,360 to 2,265 kilograms (3,000 to 5,000 pounds) into low Earth orbit (LEO), with a launch cost of $5 million USD per flight on a launch rate of at least ten flights a year. That's compared with about $55 million USD to launch a similar payload on an Orbital Sciences Minotaur IV booster, which is flown only about once a year.
The XS-1 program complements the DARPA "Airborne Launch Assist Space Access (ALASA)" program, mentioned here in 2012. ALASA envisions a small booster launched from an aircraft, notionally a business jet, on short notice to put a 45 kilogram (100 pound) payload into space on short notice. Boeing, Northrop Grumman, and Lockheed Martin were awarded preliminary design contracts for ALASA in 2012, with demonstration flights expected in 2015. NASA is working on similar, and possibly connected, scheme for flight in 2016.
XS-1 is a more ambitious project. DARPA officials admit that the past history of RLV efforts is discouraging, consisting of little but failure:
DARPA officials believe that they can succeed now because the technology is available to do the job:
The US has now flown a reusable space vehicle, if not an RLV, in the form of the USAF X-37B spaceplane, which has been put into orbit three times to date. Boeing, which builds the X-37B, intends to leverage off it in the company's XS-1 proposal. DARPA still regards SSTO as unrealistic, DARPA official Pamela Melroy -- previously a NASA space shuttle commander -- saying: "I banned the word single-stage-to-orbit from any discussion, instantly. We are not going there. We are not talking about it."
DARPA plans to award up to four contracts of up to $4 million USD each in early 2014 for preliminary design concepts, with a single contract of up to $140 million USD awarded a year later to build and fly the XS-1 demonstrator. First flight will be in late 2017, leading to an orbital flight test in 2018. The test program will involve:
DARPA has generated a straw configuration, with a winged RLV first stage about the size of an F-15 Eagle fighter, powered by twin SpaceX Merlin 1D rocket motors. Total take-off weight is 102 tonnes (112 tons), including a upper stage weighing 6.8 tonnes (7.5 tons) with payload. The upper stage is expected to cost no more than $2 million USD. DARPA officials believe that it would be straightforward to scale up the XS-1 design to handle greater payload weights.
One difficulty is that the US now flies no more than five missions a year in the size range envisioned as supported by XS-1. However, DARPA managers believe, with fair cause, that interest in "smallspace" is growing, and that a relatively low-cost launch option would do much to boost it. With that kind of payload capability, it would be possible to put an entire constellation of 100 kilogram (220 pound) tactical support satellites into orbit in a single launch, making it very attractive for military use, while civil users could fly highly capable constellations of satellites as well. However, although DARPA should be wished the best of luck, the sad past history of RLV efforts is hard to ignore.COMMENT ON ARTICLE
* ANOTHER MONTH: As a follow-up to my comments last month on setting up a video download system based on an Acer Aspire One netbook, I've been busy downloading YouTube videos -- for example, the entire COLD WAR series from 1998. They're low resolution, but the price is right and they work fine, being at least comparable to normal video reception from the days of analog broadcast TV. Imagine, in no long period of time the younger generation will respond to tales of multipath "ghosting" in TV transmissions with an incredulous stare. After all, they'll only know about video breaking up into fragments, which though obnoxious isn't as distinctly spooky as ghosting.
I've been stowing the downloads on one of my old USB hard disk drives; it's easier than shuttling them around on wi-fi, and when I go on the road I can take the drive along with for entertainment if I have some dead time. Having got comfortable with downloads from YouTube, I got to thinking about downloading videos from anime sites. I had an app for downloading flash videos from YouTube, but it had difficulties on other video sites. After considerable number of dead ends, I finally found an anime site named "kumby.com", which to my surprise gave me a control for downloading their low-resolution anime videos directly, no tool required.
The "kumby.com" site seems to be supported by online ads to wretched excess; I was a bit startled to find them running two, possibly more, video ads in parallel on a page. It was a shrug, downloading was straightforward, and the downloads contained no clutter. I downloaded all 17 episodes, two gigabytes total, of a series named KILL LA KILL, or KIRU RA KIRU as it's rendered in Japanese. It involves a post-apocalyptic town centered on a high school run by an Orwellian student council, the psychotic council members murderously enforcing their rule by wearing magic uniforms that give them super powers, the uniforms drawing some blood from wearer for sustenance.
They're challenged by Ryuuko, an exchange student, who wields a weapon like one blade of oversized scissors that can defeat the uniforms, and acquires a magic uniform of her own. The series might be appropriately given the alternate title of HIGH SCHOOL DEATH MATCH 2100. Ryuuko's uniform, incidentally, looks more or less like a traditional Japanese schoolgirl sailor suit ("seiraa fuku" or "seifuku") -- except in combat mode, when it alters itself up to the razor-edge threshold of wardrobe malfunction. It's sentient and somewhat perverse, taking a real pleasure in being ironed.
Anyway, enough already, KILL LA KILL isn't something I'd dare recommend. I found it entertaining, but it's wildly over the top, weapons-grade Nipponkitsch on recreational drugs: "This is REALLY, REALLY Japanese!" I was, however, unambiguously pleased to get the entire series conveniently for free, all the more so because I'd be reluctant to pay much money for it. I copied the episodes over to the Aspire One and have been watching them using Windows Media Player -- works perfectly. TV is dead; long live TV.
* In my other cruisings of anime sites, I kept running across images of "Vocaloids", most of them of a "Hatsune Miku", apparently an anime NipponPop idol, with a lip mike and long green hair tied into twintails. I didn't pay the matter much mind, until I got curious, wondering from the name "Vocaloid" -- rendered in Japanese phonetics as "Bokaroido", by the way -- and the fact that Hatsune Miku had a number on the skin of her right shoulder if she was a singing android.
It turned out, only an android to the extent of being able to sing. Vocaloid is not an anime series as such; it's a series of Sony voice synthesis systems, and Hatsune Miku is a mascot of one such Vocaloid product, the voice samples obtained from actress Fujita Saki. Some CG animations have been put together -- "Hatsune Miku Live in Sapporo" for example -- turning Vocaloid tunes into music videos, and she's made appearances in other media, in a few cases from the edge inappropriate for public discussion: "The internet is DIRTY!"
I have to characterize the Vocaloids as really Japanese, too, if not so nearly over the top. It has been commented that the Japanese, coming from an animist Shinto culture, have a stronger inclination to read personalities into machines than do Westerners -- Hatsune Miko makes a pleasant and appealing kami, a Shinto concept translating as something between "spirit" and "petty deity". By the way, the name very roughly renders into "Leading Sound from the Future"; it has a pretty sound in Japanese, "hah-t'soo-neh mee-koh" -- pronounced more or less without emphasis on syllables as per Japanese style.
* I got nicked on a copyright complaint for posting a wallpaper, as has been my custom every month. I had been thinking they were okay because they were in general circulation and my use was casual, but on being given a warning I realized I was on thin ice. I went through the back archives to delete all the wallpapers, and I won't be posting them any more. The top banner is about as legally dodgy, but not only is the top banner unobtrusive, it also only has a lifetime of a month, so the likelihood of a complaint is small -- and it can be immediately changed if I do get a complaint.
I don't recall ever having been nailed on a copyright violation before. I was grateful I got a warning. Legal staffs sometimes shoot first and ask questions later. Other than some logistics, it was no problem to kill off the wallpapers; they were inconsequential to my purposes. I'm hanging on to them, however, since I have a little jigsaw puzzle game program and they make nice jigsaws.COMMENT ON ARTICLE