* 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.
* BACTERIOPHAGE METAGENOMICS: As discussed by an article from WIRED Online blogs ("Scientists Unearth a Trove of New Bacteria-Killing Viruses" by Shara Tonn, 3 September 2015), biologists have long known about "bacteriophages" AKA "phages", the viruses that infect bacteria -- last mentioned here this summer -- and have a good understanding of them. What biologists haven't had is much of a handle on the diversity of phages. Thanks to modern metagenomic technology, a research group at Ohio State University in Columbus has changed that, performing a metagenomic study of a population of bacteria, and then extracting the phage genomes.
There was, as discussed in earlier articles run here on phages, considerable interest before World War II in using phages to treat bacterial infections. Interest then faded out in the West, though the Soviets continued to make use of them for treatments. With the rise of antibiotic resistance, interest has now revived in the West.
Phages are widespread, and they can have devastating effects on bacterial populations. One particularly deadly set of phages in a bacterial ocean community can kill off half the bacteria in one day. Despite their abundance, phages are hard to study; they have to be grown in bacterial cultures, and most bacteria can't be easily cultured in a lab, meaning no way to culture the phages that infect them, either.
Enter metagenomics. Instead of culturing the bacteria, researchers simply obtain the genomes for an assemblage of them, nailing down the phage genomes in the process. This is a straightforward approach to obtaining the DNA codings; what is hardly straightforward is then sorting them all out. As project researcher Tanja Woyke -- a microbiologist at the Joint Genome Institute of the US Department of Energy -- described it: "It's almost like you took hundreds of different puzzles and threw all the pieces together. Now you have to put those puzzles together and figure out which pieces come from which puzzle."
To make it even more troublesome, phages are inclined to exchange DNA with their bacterial hosts, stealing genes from their hosts, and leave behind genes that are absorbed into a host. One way to help sort out the puzzle is to hunt for sequences that are already known and stored in public genomic databases. That only goes so far, unfortunately; although more than 30,000 microbes have had their genomes sequenced, only about 1,300 viruses have.
Fortunately, phage genomes have a few specific tell-tales. First, they have distinct genes that encode the protein capsule that protects their genetic material; bacteria don't have anything like capsids. Second, their genes are not that much like those seen in bacteria, or anything else for that matter; find an unfamiliar gene that can be linked to a capsid gene, that means it's likely to be part of a phage. According to Simon Roux, a postdoc virologist on the project: "Sixty to 80 percent of the genes look like nothing we have ever seen before."
Roux developed a program named "VirSorter" to spot viral sequences from these two tell-tales, then used it to sift through almost 15,000 public microbe genomes, hunting for "prophages", or phage genomes that had been inserted into bacteria. Although there are other programs that can spot prophage sequences in complete bacterial genomes, VirSorter is the first that can that can accurately pull phage sequences out of a metagenomic assemblage.
The 12,500 phage sequences obtained so far are only a starter; project researchers expect the number to quickly grow by a hundredfold. VirSorter was made accessible and easy to use; any microbiologist with a genome dataset can use it to search for new phages. That leads to another challenge, building the genomes into a taxonomic hierarchy -- a "tree of life" -- that will also require a fair amount of software ingenuity and computing horsepower.
As the big picture becomes clearer, microbiologists and virologists will increasingly be able to track the co-evolution of phages and their hosts, discovering the interesting tricks that phages can play, and the countermeasures bacteria have acquired to fight back. Researchers are starting out from a low level of knowledge, but they're not discouraged; that only means they have a lot they can learn.COMMENT ON ARTICLE
* KEEP COOL (2): Willis Carrier's air conditioning systems were a sales success, but he was still not happy with what he had. He could figure out what kind of an air conditioning installation a facility might need, but it was only by virtue of his considerable experience, and the performance of those systems was not all that predictable. It was an art; it needed to be a science.
From the 1880s, there had been some formal research into the properties of moist air, a field known as "psychrometrics" -- psy-CHRO-metrics, not psy-CHO-metrics -- but not much progress had been made. Carrier saw enough there to build on, however, and worked to create a more effective science of psychrometrics. Carrier devised a comprehensive set of equations, most significantly one that expressed the moisture content of damp air in terms of pressure plus dry-bulb and wet-bulb readings. Using charts, engineers could then predict the performance of an air-conditioning system with some accuracy. Carrier published his results in an influential landmark 1911 paper titled "Rational Psychrometric Formulae".
With his improved grasp of psychrometrics, Carrier could readily control both temperature and humidity. By mixing chilled air with unchilled air that had bypassed the cooling spray, he could achieve any desired setpoint of humidity and temperature. Carrier then decided it was time to move air conditioning on from strictly industrial applications, to providing comfort to the public.
That wasn't quite as straightforward as it might seem in hindsight. An air-conditioning system represented a considerable cost -- both in terms of original outlay and ongoing service -- and a, say, restaurant owner had no way of knowing if it would bring in enough new business to pay for itself. Using ammonia as a coolant was also a problem, since raw ammonia is very nasty, toxic stuff.
However, movie theaters were booming at the time, moving up from auditoriums to entertainment palaces, and owners of top-flight theaters could see the benefits of air condition. In Chicago, two sets of brothers -- Barney and Abe Balaban, Sam and Maurice Katz -- built the ornate Central Park and Riviera Theaters. An engineer named Frederick Wittenmweier installed air-conditioning systems for these two theaters that used carbon dioxide as a working fluid. That technology had been introduced in 1866 by "Professor" Thaddeus Lowe, well-known as a Civil War balloonist; the system tended to leak, but carbon dioxide is odorless and harmless, except in high concentrations.
Obviously, Carrier was interested in cooling movie theaters, working with Sid Grauman of Los Angeles. Grauman had already built the Chinese and Million Dollar Theaters there; when he opened his third theater, the Metropolitan, there in 1923, it featured a Carrier air conditioning system.
Early public air conditioning systems had vents in the floor, like heating vents, but that was forgetting that cold air doesn't rise, with customers freezing their feet. Soon the vents were placed on the ceiling. Carrier also introduced some significant innovations of his own. His original air conditioners had used reciprocating compressors, with pistons moving back and forth, but in 1922 he went to a centrifugal compressor. It was lighter, simpler, more reliable, and easier to keep running.
Carrier also wanted to obtain a better working fluid than ammonia for public air-conditioning systems, settling on a cleaning fluid named dichloroethylene (C2H2Cl2) AKA "dielene". He chose to use it for an air-conditioning system to be installed in New York City's Rivoli Theater, but the city safety commissioner refused to go along. Carrier got an appointment with the commissioner and demonstrated that dielene was safe, even pouring some into a container, then throwing a lit match into it. It burned as gently as a candle, and Carrier got his permit.
The Rivoli was the first air-conditioned theater in New York City, and it was also the first major public installation of an air-conditioning system with a centrifugal compressor and dielene working fluid. The system made its debut in 1925 with Adolph Zukor, boss of Paramount Pictures, in attendance. There was a big crowd; the air conditioning took its time get rolling and Carrier was worried, but soon the theater chilled out, and so did the audience. After the movie, Zukor told Carrier: "The people are going to like it."
The further history of air conditioning would show that was an understatement. By the late 1930s, all but a fraction of US movie theaters had air conditioning. They became a great place to go on hot summer evenings. [TO BE CONTINUED]COMMENT ON ARTICLE
* THE COLD WAR (85): Eisenhower had been feeling pressured by events; he was then pressed to the snapping point. Although he had ordered the MELTING POT stratospheric reconnaissance balloon program killed, the Air Force had continued to work on it anyway. It seems that the Air Force was less concerned about the USSR than the CIA, wanting to have an Air Force strategic reconnaissance capability to counter the CIA's U-2, and not being too concerned as to how credible a capability it was.
Three MELTING POT balloons were launched in July from a small "jeep" carrier from off the east coast of Japan. The balloon reconnaissance payloads had a timer that would cut them loose, to parachute down to lower altitude for recovery. The timers were given settings that were too short, and all three balloons dropped their gondolas while over Red territory. The next thing the president knew, he was getting an angry protest from the Kremlin.
Eisenhower had a very hot temper and he tried to keep it under control, but that was too much. He called up the Pentagon; failing to get Defense Secretary Neil McElroy, he got Deputy Defense Secretary Quarles on the line. The president was furious, saying that if he had been the military officer who had pulled such a stunt, he would have shot himself. Eisenhower suggested that a few heads needed to roll, that people either needed to obey orders or get the hell out of the service.
He cooled off -- slightly -- to then write a stiff memo to Defense Secretary McElroy, saying "there is disturbing evidence of a deterioration in the processes of discipline and responsibility within the armed forces." The president indicated his displeasure with the balloon overflights and also unauthorized U-2 overflights, telling McElroy that he wanted disciplinary action taken "at once".
Exactly what disciplinary actions were actually taken is not clear, but that was the end of American balloon reconnaissance efforts -- or so it seems, since Russian sources claim that balloon reconnaissance overflights of the USSR continued into the 1970s and beyond. The records of encounters between Soviet interceptor aircraft and balloons are detailed and specific, and there's no good reason to doubt they happened; but what were the balloons doing over the Soviet Union?
It seems plausible that the Soviets were excitably chasing after weather and research balloons that had strayed into their airspace, though it is of course difficult to rule out the existence of another "black" reconnaissance balloon program that hasn't been declassified yet. Balloons were a ridiculous approach to aerial reconnaissance, but it is possible they were being used as probes of Soviet air defenses; in other words, they were supposed to detected and intercepted. There are no records of such an effort, and it's difficult to think of a good reason as to why the records would be hidden away, over a half-century later -- thought they might have been simply filed and forgotten. Russian accounts on the balloons are lacking in specifics to help identify their function. In the absence of any solid evidence to the contrary, the most believable conclusion is that they were stray weather balloons.
* The world paid little attention to the balloon overflights; the US government of course said nothing much about them, and the Soviets didn't make a major issue of them. The relatively muted response of the Kremlin had the unfortunate effect of also diminishing Eisenhower's concerns about conducting overflights by other means.
As far the public space frenzy went, it was going full blast, and in fact was continuing to accelerate. In January 1958, Sergei Korolyev wrote a memo to the central committee, proposing the development of an R-7 derivative with an upper stage. The official rationale was to use the improved booster to first send a probe to crash into the Moon, and then to launch a probe to go into orbit around it and take pictures of the unseen lunar farside. Korolyev also emphasized that the new booster would have military applications, such as the launch of heavy reconnaissance satellites.
In parallel, the Americans were also creating a program to "shoot the Moon" under "Project Baker", which was announced at the end of March. The Air Force planned to use a Thor missile fitted with an "Able" second stage, derived from the Vanguard second stage; while the Army planned to use the "Juno II", a Jupiter missile topped with a cluster of solid rockets, like the Redstone modified as the Juno 1 to put Explorer 1 into orbit. ARPA was put in charge of the program, the agency's charter being broad enough to allow the agency to work on space projects of no clear military utility. [TO BE CONTINUED]COMMENT ON ARTICLE
* ANOTHER MONTH: I went over to the Loveland Public Library to find they had put up a display about, of all things, the mechanics of classic pinball machines, with exhibits showing the various subsystems. It was a tribute to the era of electromechanical intelligence, showing what could be done with switches, relays, mechanical numeric indicators, arrays of little light bulbs, and so on, with sequencing performed by notched sets of wheels. It was thoroughly ingenious, though a fully operational pinball machine with a window into the internals showed what a wiring nightmare it all was. These days, we do all that stuff with digital electronics, and use a networking bus.
In more modern technology news, I found a "PC Remote" -- like a TV remote control, but to control a PC -- for cheap on Amazon.com. Since I use a notebook computer hooked up to my TV to play videos, I thought it might come in handy. In any case, it was so inexpensive as to be worth a try, so I ordered it.
It took some time to get to my place, having come from Hong Kong, but I was very pleased with it. It uses infrared wireless, via a USB dongle featuring a cable on a spool to allow the IR sensor to be placed where convenient. It has a little thumb control to move the mouse pointer, along with mouse button equivalents, and various useful PC controls -- NEXT, PREV, PLAY-STOP, VOLUME-UP, VOLUME-DOWN, and so on. I'm not sure it will prove very useful, but it is fun to play with.
* I took my second twice-yearly trip to visit family in Spokane, Washington, this last month. I normally take it in August, but it was delayed by various difficulties -- and the US Northwest was also covered with smoke from wildfires at the time.
I did the outbound trip, 1,770 kilometers (1,115 miles) in a single day, as with the previous in May -- no problems, it's easier to do than I thought it would be. As long as I get regular sleep on the days before and after getting up very early, I can readily soak up the short night. There wasn't much evidence of fires along the route, though I did see a few acres of burned trees along one stretch.
Not much to say about my time in Spokane, it was all just family stuff. I bought some flowers at the Fred Meyers store there; the clerk asked me if I had a Fred Meyers loyalty card, and I said: "I have a King Soopers card, which is another Krogers chain in Colorado -- it might work?"
"It should." She tried it, and it did. I'm really beginning to love loyalty cards.
I did some planespotting while I was in town. I'd been feeling like I was getting into diminishing returns on that hobby, but I found a fair number of interesting aircraft to shoot on the flight lines at both Felts Field, the municipal airport, and Spokane International Airport (SIA). I keep wondering about the "International" in that title, but I know they operate to Canadian cities, so I guess it's barely legal.
I also did some shooting on the approach path. It's easy to do at SIA, there's convenient places to park alongside the road, and so far nobody's ever hassled me. I only got incoming aircraft about once every 15 minutes or so, but I've become more patient. Previously, I'd not been very interested in shooting airliners I'd shot before, but I've come to appreciate that good aerial shots are hard to come by, and I don't care if they're new any more. It's a bit like fishing, I suppose; just get comfortable, read a book or something, and wait for a bite.
For the trip to Loveland, I decided I would visit the fossil museum in Thermopolis in central Wyoming -- it wasn't very far out of my way. I had to take two days driving back in any case, it would have been intolerable and reckless to try to do it one day both ways, so I decided to spend the night in Billings, Montana, about halfway home.
I dropped by the Missoula airport on the way to do more planespotting, again having fairly good luck; and since I had time to spare, visited the Museum of the Rockies in Bozeman. That was something of a bust; the most fun I had with it was running into two little girls in the parking lot who were carrying around long-haired rabbits, wrapped up in towels or such. "Wanna pet him?" "Sure." The big attraction at the museum was a road show of Warner Brother Looney Toons material, which I didn't find very stimulating.
I checked into the Hampton Inn in Billings and did a bit of homework that evening. The next morning, I left Billings for Thermopolis. Trying to navigate along back highways is a good way to get lost, but it was easy, just as long as I knew which towns were along the route. I had to be careful going into the towns, figuring they were speed-trapped, and indeed I often saw a sheriff's car lurking along the road, ready to pounce on the unwary. I still made good time, even stopping at Greybull to take pictures of aircraft on a roadside display. There'd been an air tanker outfit that went bust there, with decrepit old aircraft littering the airport in the distance; they'd hauled up those in best condition out to attract those passing by.
I didn't have any problems finding the museum in Thermopolis. It turned out to be a good news / bad news sort of thing. The good news was that it's one of the best fossil museums I've ever seen. The bad news was that, when I visited it some years back, it had been well-lit; now it was predominantly dark, and it was hard to take good photos, even with the camera's low-light mode. I should have tried the handheld night mode, though that's a very hit-or-miss capability.
Still, I did get some good shots. One that turned out well was a nice pterodactyl (flying reptile) skeleton. They also have an Archaeopteryx (primitive toothed bird) fossil that was found locally, and have a beautiful holographic reconstruction of it. The 3D video starts out with the fossil, "lifts" the bones out of it, assembles them into a proper skeleton, and then covers it with feathers, with the bird flapping its wings. "Just like Disney World!"
There was a crowd of people over in one corner; I didn't pay too much mind to them, until I took a look at one of them, and did a double-take. They were impaired folk, some of them seriously impaired, with their keepers. They were no bother, the keepers were maintaining a close eye on them; I just stayed out of their way. Not as much fun as the gang of high-school kids from the Wind River tribal reservation to the south who were there the last time I visited the Thermopolis museum, some of the little "Indian Princesses" being real cuties.
I didn't spend too much time at the museum, being impatient to get back to Loveland. It was the normal unexciting drive, though going through the Wind River Gorge was interesting -- some impressive geology, I had to stop and take pictures. By chance, there was a convoy of maintenance vehicles running up the railroad tracks on the far side of the river, and I got plenty of shots of them as well. I wish I knew what they did, I'll have to poke around on the internet to see if I can find out more. I also ended up finding a pile of aluminum cans to recycle, still being in penny-pinching mode.
I'm sorting out the pictures now. I'm still several years behind in getting my photo collection straight; indeed, I recently went through the whole thing to find imagery I judged unacceptable, finding about a hundred that either needed fixing or disposal, and am cleaning them up for the moment. I don't think I'll get done before the end of the year. The photos keep piling up; I took about 400 shots on this trip to sort through, which will render down to only maybe 40 or 50 "keepers", but that still takes time.
* Thanks to one reader for a donation to support the websites last month. It is very much appreciated. Notice also that this month's banner is on a Disney motif. It's small, a bit hard to make out, and it will be only be up for a month -- but I still wonder if Disney's lawyers are going to get on my case.COMMENT ON ARTICLE