My coworker does a WHOLE lot of deep (DNA) sequencing at work, and was tracking down a reference on Pubmed the other day when she came across the article "Is bacteriophage φX174 DNA a message from an extraterrestrial intelligence?". A TL:DR of the abstract indicates that no, it's not a message, "No significant patterns have been observed and other means of constructing pictorial arrays with other phage DNAs are planned". Bryan wisely inquired why the authors might have thought this about that phage. Well, apart from the '70s being a crazy time scientifically and otherwise, that particular phage was the first for a lot of things. It was the first DNA genome to be Sanger-sequenced, as well as the first thing/virus to the synthesized by purified enzymes in a test tube by Arthur Kornberg, and the first thing to be generated in vitro from completely synthesized materials by Craig Venter and company.
I was at a wedding a few weekends past (Congrats, Emily and Mike!) wherein a large number of guests hailed from Ohio. During the dancing portion of the evening, these guests requested the song 'Hang on Sloopy', and proceeded to yell O-H-I-O (with matching arm motions, a la the YMCA) during pauses in the chorus of this, all out there on the dance floor. Given this was in San Antonio, more than a few of us hadn't encountered this practice before, but apparently the song was adopted by Ohio State University, first being played in the football stadium in October of 1965, where it has now become a tradition to play between the 3rd and 4th quarters. Originally, the song was called 'My Girl Sloopy, and recorded by a group called the Vibrations, before going mainstream after being covered by the McCoys. Also, fun fact, until very recently, i thought it was 'Hang on, Snoopy', not Sloopy. It turns out, a snippet of the song with that substitution was used in the song parody 'Snoopy versus the Red Baron', but it was removed under threats related to copyright. Not the origin of my misheard lyric, but nice that someone else hears it, too.
The lovely Kate B. linked (via twitter) these 'virus trading cards' to me. They're really neat, but the whole trading card aspect invites a lot of 'gotta collect 'em all' puns that are a little concerning.
Cold brewed coffee (beans are steeped in cold water, versus iced coffee's hot-water-brewing-then-chill method) can be made in a number of ways. My former protocol (straining grounds which had soaked overnight though a coffee-filter lined mesh strainer) was a little messy/slow, so i went poking around for a new method, eventually settling on filling a nut bag (mesh bag used for making nut milk) with ground coffee, suspended in water in a glass lidded jar. This works okay, though i have to use a coarser grind or filter the whole thing again through a pour-over coffee set-up, which sort-of-defeats the purpose. Anyway, i bring this up because i came across some completely lovely and somewhat impractical/expensive methods of cold-brewing coffee, including this stand, which 'adds a touch of drama to your kitchen', and this crazy lovely Gothic version (all for slightly over $7000). (H/T here.) While we're on the subject, apparently Starbucks is taking up the Nitro tap train, by installing taps dispensing cold brewed coffee infused with nitrogen (kinda like carbonation). i've seen it in a bar or two, but this is an interesting development.
The term 'cultivar' refers to a strain of plant grown/selected/cultivated to have a specific characteristic, like heat tolerance or resistance to a specific pest. This general modification process is covered in a previous post (where i apparently also discussed bacteriophage).
Regarding classification of muskmelons: all cantaloupes are muskmelons, but not all muskmelons are cantaloupes - the 'European' version are green fleshed (including honeydew melons). Cantaloupes are named for the region, Cantalupo, where they are said to have originated, and the region name itself translated to 'singing wolf', for events said to occur as it was being established. Cantaloupes-the-melons are split in to two categories with mainly commercial distinction for the East and West coasts of the US, 'eastern' ( "Eastern cantaloupe varieties feature rounded 5- to 7-pound fruits with sutures, netting, and a large seed cavity" ) and 'western' ( "Western cantaloupe types are oval-shaped 3- to 5-pound fruits without sutures and have coarse netting" ), though each cultivar can be grown in both regions, as stated here. i picked up one specifically labeled at the market this past weekend, and was curious at the distinction, so did some research. The domestication of plants is a fascinating subject (with nod to Michael Pollan and company).
Made a bet with a friend this morning regarding alligators, with my position being that there ARE some in Atlanta. My reasoning was that there are alligators in Houston and San Antonio, albeit, ones that were probably released after growing too big to be cute little aquarium inhabitants (and full disclosure, i grew up running around the lake mentioned for San Antonio). Anyway, regarding the Atlanta alligators, some research indicates that one predicted to be about 8 years old was trapped on the Chattahoochie river in March 2016, and relocated south. The speculation about someone releasing a former-pet as a (pet) theory is applicable in this instance, too.
While we're on the subject of alligators... Here is a nice site regarding the phenotypic differences between American alligators and more southern American crocodiles. (Did you just picture a reptile wearing a flowered hat and speaking with a drawl, 'cause i sure did.) We can now add Nile crocodiles to the mix, which is an issue, because those are much larger, and not shy about eating anything.
Finally, for levity, did you know an easy way to tell the difference between an alligator and a crocodile? One will see you later, and the other will... see you in a while.
Sunday, June 19, 2016
Wednesday, June 1, 2016
musical organs, Lusitana, Nata de coco, quantum and teleportation, Yankee geological products, pergola.
A while back, Nate B. kindly sent along this fascinating clip of M.J.'s song Smooth Criminal played on a barrel (grinder) organ. Anyhow, this song gets a strange amount of play on ATL radio stations (in the normal, non-organ form) as i hear it at least once a week. Barrel organs are distinct from steam organs (calliopes), as the former is a bellows driven primarily by a crank, and the latter by, of course, steam going through whistles, though both instruments can be played by musical rolls. Conversely, a hurdy-gurdy is essentially a fiddle with a crank-driven wheel substituted for the bow, explained/played here. Okay?
Woke up the other day with Stromae's terrific Ave Cesarina in my head, which is a song about Cesarina Evora, a singer from Cape Verde (known also for performing barefoot). Cape Verde, because shamefully i had to look this up, is off the coast of Senegal, and was settled by the Portuguese, which makes a lusophone country. 'Luso-', in this case, is derived from Lusitania, "Hispania Lusitana was an ancient Iberian Roman province including approximately all of modern Portugal south of the Douro river and part of modern Spain", to reference wikipedia. Curiously, the Portuguese Empire is considered the first global empire, stimulated in large part by the efforts of the Portuguese duke aptly named Henry the Navigator and the control of ports in South America and Africa.
Nata de coco is a product made from the fermentation of coconut water with Acetobacter xylinum, resulting in a translucent, chewy/stringy mass that is actually tastier than it sounds (as is the case with most fermented products). It is frequently served sweetened as a dessert, and is apparently high in dietary fiber.
A recent discussion with a co-worker began innocently enough with the question, "Why isn't teleportation a thing yet?" This became philosophical fast, with the breakdown of teleportation basically consisting of being scanned down to the atomic level, then recreated elsewhere (from this, "Samuel Braunstein made this point quite clear when he noted that if teleportation were possible today, the transmission of information about an entire human being would take about 100 million centuries, about the age of the universe. ‘It would be faster to walk,’ he said"), leading to the question regarding the 'divine spark' of human consciousness - things evolved into a discussion of quantum entanglement ("An entangled system is defined to be one whose quantum state cannot be factored as a product of states of its local constituents, that is to say, they are not individual particles but are an inseparable whole. If entangled, one constituent cannot be fully described without considering the other(s). Note that the state of a composite system is always expressible as a sum, or superposition, of products of states of local constituents; it is entangled if this sum necessarily has more than one term", thanks wikipedia), and the idea that to be teleported, one has to essentially die to re-appear elsewhere, or potentially exist in a duplicated state, referencing this interesting discussion. This arced over to another discussion of the situation illustrated by the Ship the Theseus, essentially, how much of something can be replaced before it is another thing entirely? Personally, i've wished before that there was more than one of me (that would share a brain), so i could be in multiple places at once, but acknowledge that this would get pretty confusing after a while. Also, shout out to the Calvin and Hobbes duplicator.
Two things about the curious geological products of the US' upper Northeast. One, Herkimer diamonds are water-clear, faceted, doubly terminated (read, "pointy on both ends") pieces of quartz that are nearly as hard as diamonds, and first found near Herkimer County in New York (and later found in places like Arizona, Afganistan and Tibet). These formed in cavities in dolostones, which accounts for their nice shape. Two, Goshen stone is a varibly-colored mica schist (sheets of stone used for pavers) found primarily in New England. A notable story associated with this is the discovery of 24 million tons on land belonging to former Dodgers' pitcher Matt White. It's a heartwarming story; "in 2003, White purchased 50 acres (200,000 m2) of mountain real estate in Cummington, Massachusetts from his aunt for $50,000, giving her the money she needed to enter a nursing home. His original intention was to build his home, but he found the land to be too hard. When he called a surveyor out to inspect the land, the surveyor found that the land was solid Goshen stone, a type of mica schist estimated to be about 400 million years old. Estimates have placed the low estimate of the find at 24 million tons. At current prices (he has been selling the stone for over $100/ton), it is estimated to be worth around $2.5 billion, minus extraction costs". Way to help out your aunt there, Mr. White.
Finally, my brother and sister-in-law are building a pergola in their backyard. Growing up in South Texas, i was unfamiliar with the term 'pergola' (as is the rest of my family apart from my sibs), and various discussions about the nouns 'pergola' versus 'arbor' ensued. Finally, i took to google. The difference between these two is that an arbor is typically a smaller tunnel, while a pergola is a larger structure incorporating a porch with a roof (not to be confused with a trellis, which can form a wall/top to the other two, but mostly is just a structure on which to support growing plant vines).
Woke up the other day with Stromae's terrific Ave Cesarina in my head, which is a song about Cesarina Evora, a singer from Cape Verde (known also for performing barefoot). Cape Verde, because shamefully i had to look this up, is off the coast of Senegal, and was settled by the Portuguese, which makes a lusophone country. 'Luso-', in this case, is derived from Lusitania, "Hispania Lusitana was an ancient Iberian Roman province including approximately all of modern Portugal south of the Douro river and part of modern Spain", to reference wikipedia. Curiously, the Portuguese Empire is considered the first global empire, stimulated in large part by the efforts of the Portuguese duke aptly named Henry the Navigator and the control of ports in South America and Africa.
Nata de coco is a product made from the fermentation of coconut water with Acetobacter xylinum, resulting in a translucent, chewy/stringy mass that is actually tastier than it sounds (as is the case with most fermented products). It is frequently served sweetened as a dessert, and is apparently high in dietary fiber.
A recent discussion with a co-worker began innocently enough with the question, "Why isn't teleportation a thing yet?" This became philosophical fast, with the breakdown of teleportation basically consisting of being scanned down to the atomic level, then recreated elsewhere (from this, "Samuel Braunstein made this point quite clear when he noted that if teleportation were possible today, the transmission of information about an entire human being would take about 100 million centuries, about the age of the universe. ‘It would be faster to walk,’ he said"), leading to the question regarding the 'divine spark' of human consciousness - things evolved into a discussion of quantum entanglement ("An entangled system is defined to be one whose quantum state cannot be factored as a product of states of its local constituents, that is to say, they are not individual particles but are an inseparable whole. If entangled, one constituent cannot be fully described without considering the other(s). Note that the state of a composite system is always expressible as a sum, or superposition, of products of states of local constituents; it is entangled if this sum necessarily has more than one term", thanks wikipedia), and the idea that to be teleported, one has to essentially die to re-appear elsewhere, or potentially exist in a duplicated state, referencing this interesting discussion. This arced over to another discussion of the situation illustrated by the Ship the Theseus, essentially, how much of something can be replaced before it is another thing entirely? Personally, i've wished before that there was more than one of me (that would share a brain), so i could be in multiple places at once, but acknowledge that this would get pretty confusing after a while. Also, shout out to the Calvin and Hobbes duplicator.
Two things about the curious geological products of the US' upper Northeast. One, Herkimer diamonds are water-clear, faceted, doubly terminated (read, "pointy on both ends") pieces of quartz that are nearly as hard as diamonds, and first found near Herkimer County in New York (and later found in places like Arizona, Afganistan and Tibet). These formed in cavities in dolostones, which accounts for their nice shape. Two, Goshen stone is a varibly-colored mica schist (sheets of stone used for pavers) found primarily in New England. A notable story associated with this is the discovery of 24 million tons on land belonging to former Dodgers' pitcher Matt White. It's a heartwarming story; "in 2003, White purchased 50 acres (200,000 m2) of mountain real estate in Cummington, Massachusetts from his aunt for $50,000, giving her the money she needed to enter a nursing home. His original intention was to build his home, but he found the land to be too hard. When he called a surveyor out to inspect the land, the surveyor found that the land was solid Goshen stone, a type of mica schist estimated to be about 400 million years old. Estimates have placed the low estimate of the find at 24 million tons. At current prices (he has been selling the stone for over $100/ton), it is estimated to be worth around $2.5 billion, minus extraction costs". Way to help out your aunt there, Mr. White.
Finally, my brother and sister-in-law are building a pergola in their backyard. Growing up in South Texas, i was unfamiliar with the term 'pergola' (as is the rest of my family apart from my sibs), and various discussions about the nouns 'pergola' versus 'arbor' ensued. Finally, i took to google. The difference between these two is that an arbor is typically a smaller tunnel, while a pergola is a larger structure incorporating a porch with a roof (not to be confused with a trellis, which can form a wall/top to the other two, but mostly is just a structure on which to support growing plant vines).
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