Sunday, June 19, 2016

bacteriophage firsts, Sloopy Ohio, cold brewed coffee etc, cantaloupe, Southern Alligators and Crocodiles

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.

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