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07:52 < kanzure> "Whether it works or not is anybody’s guess. If you uncap a frame of honey and hold it upside down, not much happens, so I imagine it is the heat of the hive that makes the honey runny enough to flow. So if you have a cold hive, or especially viscous or partially crystallized honey, I imagine you could have trouble with this."
07:53 < kanzure> why aren't hives transparent
07:53 < chris_99> probably to prevent them getting direct sun i guess, and frying the bees
07:53 < yoleaux> 16 Feb 2015 00:41Z <nmz787> chris_99: cool!
07:58 < kanzure> you could put a piece of cardboard when you don't want to look
07:59 < chris_99> or use fancy LCD glass
08:02 < kanzure> .wik De re metallica
08:02 < yoleaux> "De re metallica (Latin for On the Nature of Metals (Minerals)) is a book cataloguing the state of the art of mining, refining, and smelting metals, published a year posthumously in 1556 due to a delay in preparing woodcuts for the text. The author was Georg Bauer, whose pen name was the Latinized Georgius Agricola." — http://en.wikipedia.org/wiki/De_re_metallica
08:02 < chris_99> i saw a cool documentary on the bbc where they attached RFID tags to bees
08:02 < chris_99> and use a massive rotating radar dish
08:03 < chris_99> to locate them
08:09 < kanzure> paperbot: http://www.cell.com/cell-stem-cell/abstract/S1934-5909%2814%2900195-7
08:09 < kanzure> .title
08:09 < yoleaux> kanzure: Sorry, that doesn't appear to be an HTML page.
08:09 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Reprogramming%20the%20Methylome%3A%20Erasing%20Memory%20and%20Creating%20Diversity.pdf
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09:58 < rigel> what journals does paperbot have access to? i'm thinking IEEE stuff and social science lit
10:02 < kanzure> paperbot tries its hardest to find papers using a varitey of means, including sending angry emails to publishers asking for pdfs
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10:15 < kanzure> "Noticeably, for a small- or medium-sized facility, the rabbit system is ideal to produce up to 50 kg of protein per year, considering both economical and hygienic aspects; rabbits are attractive candidates for the mammary-gland-specific expression of recombinant proteins"
10:15 < kanzure> from http://www.hindawi.com/journals/bmri/2013/580463/
10:17 < kanzure> "However, current methods of generating transgenic animal founders are relatively inefficient and time consuming, and attempts to improve transgenesis by various methods have had limited success. The inefficiency of transgenesis in dairy species, as well as certain innate disadvantages of lactation, has prompted interest in expressing foreign proteins in various tissues of more prolific species. In addition, the purification of ...
10:17 < kanzure> ... recombinant proteins from milk is still a hurdle to be overcome and creates often undefined regulatory issues."
10:18 < kanzure> hmm maybe mammary gland tissue printing is working
10:21 < kanzure> nope.
10:30 < kanzure> "How much sap does a single tree produce in one year, on average?" "The volume of sap produced during one season varies from 10-20 gallons per tap, depending on the tree, weather conditions, length of the sap season, and method of collecting sap. Producers using gravity lines or buckets generally get 10-14 gallons of sap per forest-grown tree. Using buckets on roadside trees or using vacuum tubing yields 15-20 gallons per tap. A single ...
10:30 < kanzure> ... tree can have one, two, or three taps, depending on size and health."
10:31 < kanzure> aww "What size should a tree be before tapping?" "A tree should be 10 to 12 inches in diameter when measured 4.5 feet above ground level."
10:31 < ParahSailin_> use palm tree
10:34 < kanzure> go on?
10:37 < kanzure> i'm not finding much about this.
10:38 < kanzure> what about bamboo sap
10:39 < kanzure> "Water is pumped through the freshly cut culms, forcing out the sap (this method is often used in conjunction with the injection of some form of treatment)."
10:42 < kanzure> "Amphicrossus japonicus is the first known facultatively aquatic nitidulid. The adult beetles breed in bamboo sap and subsequently enter water-filled bamboo culms." http://www.eje.cz/pdfs/eje/2007/03/27.pdf
10:42 < kanzure> what?
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14:09 < fenn> tree sap doesn't contain much protein generally
14:10 < fenn> .wik latex
14:10 < yoleaux> "Latex is the stable dispersion (emulsion) of polymer microparticles in an aqueous medium. Latexes may be natural or synthetic. It can be made synthetically by polymerizing a monomer such as styrene that has been emulsified with surfactants." — http://en.wikipedia.org/wiki/Latex
14:14 < fenn> "Latex as found in nature is a milky fluid found in 10% of all flowering plants (angiosperms).[1] It is a complex emulsion consisting of proteins, alkaloids, starches, sugars, oils, tannins, resins, and gums that coagulate on exposure to air. It is usually exuded after tissue injury. ... It serves mainly as defense against herbivorous insects.[1] Latex is not to be confused with plant sap; it is
14:14 < fenn> a separate substance, separately produced, and with separate functions."
14:14 < fenn> that sounds like a pain
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14:21 < fenn> why is tobacco used for genetic engineering? is there anything special about it?
14:23 < fenn> "The first genetically engineered plant was tobacco, reported in 1983 ... joined an antibiotic resistant gene to the T1 plasmid from Agrobacterium. The tobacco was infected with Agrobacterium transformed with this plasmid resulting in the chimeric gene being inserted into the plant. Through tissue culture techniques a single tobacco cell was selected that contained the gene and a new plant grown
14:23 < fenn> from it." this could have been done with anything
14:26 < chris_99> maybe it was an excuse for the researchers to get cheap smoking tobacco
14:26 < cluckj> ^
14:32 < fenn> i'm reading some stuff about Arthur Hunt and the Kentucky Tobacco Research and Development center and Tobacco Research Institute
14:32 < fenn> "The general production platform for this product – making and purifying the antibody from N. benthamiana – may or may not have been pushed along by the tobacco buy-out of many years ago, but this turn of events did provide an incentive to find alternative uses for tobacco."
14:32 < fenn> not sure what the "buy out" is referring to
14:34 < fenn> meh nevermind
14:34 < cluckj> look it up ;/
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14:38 < fenn> look what up
14:38 < cluckj> tobacco buy out program
14:40 < fenn> "March of 2015 marks the beginning of a new era in genetically modified foods. It’s the first year farmers can plant a generic version of glyphosate-resistant soybeans—the first GMO to be patented by Monsanto in 1996."
14:41 < kanzure> maybe because there was tobacco research money
14:42 < fenn> the tobacco buy-out program was a government subsidy earmarked for specific farming counties, lots of detail here http://fee.org/freeman/detail/the-tobacco-quota-buyout-more-legal-plunder
14:43 < kanzure> silk seems like an inconvenient expression vector
14:44 < kanzure> let's see.. which bugs have useful candidate venoms or stingers.
14:45 < fenn> so a big part of protein compatibility is glycosylation patterns, but i dont know enough about that
14:45 < kanzure> wasps? "One to three generations can develop in a year"
14:46 < fenn> silk is nice because it's just pure protein, you dont have to extract anything
14:46 < kanzure> i always liked scorpions because their tail makes access easy, but no eggs and long lifecycle is problematic
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14:47 < kanzure> perhaps if there is a non-sticky silk
14:47 < fenn> if you're engineering the silk you can make it whatever you want
14:48 < fenn> also there are silk farms with low overhead
14:48 < fenn> not many scorpion farms
14:49 < kanzure> .title https://www.youtube.com/watch?v=f1RTqAWKenM
14:49 < yoleaux> From Cocoon to Silk - Silkworm processing - YouTube
14:49 < fenn> .title http://www.tandfonline.com/doi/abs/10.1271/bbb.70353
14:50 < yoleaux> An Error Occurred Setting Your User Cookie
14:50 < fenn> A New Method for the Modification of Fibroin Heavy Chain Protein in the Transgenic Silkworm
14:50 < fenn> 2007
14:51 < fenn> so i'm thinking you leave the silk mostly the same but attach your protein of interest to it with an easily cut linker
14:51 < kanzure> i was expecting something like "and then you have to spin the silk to separate your protein of interest"
14:51 < kanzure> s/spin/centrifuge
14:52 < fenn> no you just dissolve it into solution
14:52 < kanzure> why would that not dissolve the other proteins?
14:52 < fenn> .wik histidine tag
14:52 < yoleaux> "A polyhistidine-tag is an amino acid motif in proteins that consists of at least six histidine (His) residues, often at the N- or C-terminus of the protein. It is also known as hexa histidine-tag, 6xHis-tag, His6 tag and by the trademarked name His-tag (registered by EMD Biosciences)." — http://en.wikipedia.org/wiki/Histidine_tag
14:53 < kanzure> also, i'm not sure cocoons are useful, you might as well be harvesting blood from something bigger, i dunno
14:54 < fenn> hmm i guess some of the desired protein would end up inside the fiber where it couldn't dissolve
14:55 < fenn> "Polyhistidine-tagging is the option of choice for purifying recombinant proteins in denaturing conditions because its mode of action is dependent only on the primary structure of proteins."
14:56 < kanzure> ParahSailin_: what very obvious thing am i forgetting?
14:56 < fenn> i dont know how you would dissolve silk fibers without damaging the individual protein molecules
14:56 < fenn> oo cool "An intein is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond in a process termed protein splicing"
14:57 < fenn> "Some affinity tags have a dual role as a solubilization agent, such as maltose binding protein, and glutathione-s-transferase"
15:01 < fenn> it would be nice to have a method that doesn't require any purification steps at all
15:01 < kanzure> http://en.wikipedia.org/wiki/Ink_sac
15:01 < fenn> like, a sequence that gets secreted into growth medium, and then you just centrifuge out the cells
15:01 < kanzure> hmm no purification at all.. what would that look like? no other proteins or fluids?
15:02 < ParahSailin_> like silkworm as transgenic protein expression system?
15:02 < ParahSailin_> seems there are much easier things to do
15:03 < kanzure> ParahSailin_: game is "find a good vector that is cheap to scale up and not impossible to extract"
15:03 < kanzure> *expression host
15:03 < fenn> heh i guess if you're growing octopi anyway...
15:04 < kanzure> harvesting from ink in a large body of water is probably more difficult, given contaminants and the large volume
15:05 < fenn> anesthetize them?
15:06 < ParahSailin_> why does it have to be a whole animal
15:06 < ParahSailin_> just do pichia
15:07 < yashgaroth> ^
15:07 < fenn> because cell cultures have to be maintained somewhat sterile and thus are expensive to scale up
15:07 < ParahSailin_> pichia grows in like 30% methanol
15:07 < ParahSailin_> as its carbon source
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15:08 < fenn> well that's interesting. does that kill most everything else?
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15:09 < fenn> also, does that denature proteins in solution?
15:09 < ParahSailin_> its actually more like 1%
15:09 < ParahSailin_> but few things will grow on that
15:09 < ParahSailin_> plus, aseptic technique is not hard in the first place
15:10 < fenn> it's the difference between "hobby craft" and "laboratory technique" though
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15:10 < ParahSailin_> hobby craft like beer?
15:11 < kanzure> fenn: i can't think of any method that wouldn't require centrifugation and hplc
15:11 < fenn> there's no confusing your green cuttlefish with some random cuttlefish you picked up off the sidewalk, but that can happen with yeast, especially if people dont really know what they're doing
15:12 < yashgaroth> who is the intended user here
15:12 < ParahSailin_> pichia produces ridiculous amounts of protein
15:12 < fenn> i'm not really sure the intended use case, but it seems bio engineering needs to be able to live outside the lab
15:12 < ParahSailin_> animal expression is kind of a last resort, and i cant think of any commercial system that uses that
15:13 < fenn> actually moss is kinda cool
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15:14 < yashgaroth> you don't need some hipster expression system, hobbyists grow yeast all the time
15:15 < fenn> why is engineered protein so expensive then?
15:16 < kanzure> s/engineered//
15:16 < yashgaroth> labor, r&d, quality control, capital equipment, economies of scale
15:17 < fenn> why is there no desktop protein maker
15:18 < fenn> i'm pretty sure that's not a dumb question
15:18 < ParahSailin_> human serum albumin is pretty cheap
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17:33 < heath> https://imgur.com/gallery/Gs1Yy
17:33 < heath> cat scanning mummy in 12th century bouddha statue
17:34 < heath> i think it's a cat scan
17:38 < cluckj> yes
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18:16 < kanzure> hmm
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19:01 < kanzure> "Adults (and, as we shall see, even 14-month-old infants) are rather selective in what human action they imitate and under what conditions they do so. In fact, automatically imitating every human action that one is perceptually exposed to is a seriously dysfunctional pathological condition observable in patients with prefrontal lesions who cannot inhibit the tendency to compulsively imitate gestures or even complex actions performed in ...
19:01 < kanzure> ... front of them by an experimenter (Lhermitte et al., 1986)"
19:29 < fenn> today i learned: "The maximum power in a permanent magnet DC motor system occurs at half the maximum speed when the system is loaded with half the maximum torque."
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20:58 < nmz787> .title http://www.nanowerk.com/news2/gadget/newsid=38988.php
20:58 < yoleaux> Lower-cost metal 3D printing solution available
20:58 < nmz787> juri_: ^
20:59 < nmz787> http://diyhpl.us/~nmz787/pdf/Substrate_Release_Mechanisms_for_Gas_Metal_Arc_Weld_3D_Aluminum_Metal_Printing.pdf
21:00 < nmz787> huh, they used openSCAD
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--- Log closed Sun Feb 22 00:00:01 2015