--- Log opened Thu Feb 09 00:00:02 2012
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00:55 < delinquentme> i think steve vai is going down hill
00:56 < delinquentme> i take it back!
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06:27 <@kanzure> Katherine Lugo, et al., Remote switching of cellular activity and cell signaling using light in conjunction with quantum dots, Biomedical Optics Express, 2012; [DOI:10.1364/BOE.3.000447]
06:27 <@kanzure> http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-3-3-447
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06:29 <@kanzure> "Remote switching of cellular activity by optical QD excitation is demonstrated by integrating QDs with cells: CdTe QD films with prostate cancer (LnCap) cells, and CdSe QD films and probes with cortical neurons. Changes in membrane potential and ionic currents are recorded by using the patch-clamp method. Upon excitation, the ion channels in the cell membrane were activated, resulting in hyperpolarization or depolarization of the cell."
06:29 <@kanzure> CdTe QD films? how is that remote
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06:31 <@kanzure> Nanthia Suthana, et al., Memory Enhancement and Deep-Brain Stimulation of the Entorhinal Area, New England Journal of Medicine, 2012; 366 (6): 502 [DOI:10.1056/NEJMoa1107212]
06:31 <@kanzure> http://www.nejm.org/doi/full/10.1056/NEJMoa1107212
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06:48 < JayDugger> Good morning, everyone.
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07:30 <@kanzure> gah 'warfarin' is an awful drug name
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08:35 < Lucas_> http://transhumani.com/topic29.html?sid=11b6e5018737b382a18f345e2445761e
08:39 <@kanzure> what an awful url
08:39 <@kanzure> what is it?
08:40 < strages_work> diy electroporation
08:41 < Lucas_> diy electroporation
08:42 <@kanzure> out of curiosity, why are you linking to that over the other diy electroporation posts out there
08:44 < Lucas_> I had no idea that DIY electroporation even existed.  At least in the way that we intend to use it
08:44 <@kanzure> -_- of course it does, look up the posts on diybio
08:46 < Lucas_> thank you
08:47 < Lucas_> another thing that you may be interested in: http://gizmodo.com/5882725/the-miraculous-nasa-breakthrough-that-could-save-millions-of-lives
08:47 <@kanzure> nope, not interested in news sites
08:50 <@kanzure> what is it?
08:50 <@kanzure> ermererqekrjqioe
08:50 <@kanzure> i meant to send:
08:50 <@kanzure> just saw your skype message.
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09:33 <@kanzure> what is "application/x-Research-Info-Systems"
09:34 <@kanzure> bleh
09:34 <@kanzure> http://en.wikipedia.org/wiki/RIS_(file_format)
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09:37 <@kanzure> hi Guest11431
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09:40 <@kanzure> hi jmil, delinquentme
09:40 < delinquentme> hoy!
09:40 < jmil> o/ kanzure
09:41 < jmil> o/ delinquentme
09:41 < delinquentme> how many gits are there?
09:41 < delinquentme> jmil, \/\/\o/\/\/
09:41 < jmil> lol
09:42 <@kanzure> gits?
09:44 < Mokbortolan_> british word for "jerk"
09:53 < delinquentme> Ghost in the shell :D
09:53 < delinquentme> like my FAV
09:53 < delinquentme> 2nd
09:54 < delinquentme> no 3rd fav anime
09:55 < Molybdenum> Depends on if you're talking about the actual comic or animations.
09:57 < Mokbortolan_> I didn't like the dialogue in the movie
09:57 < delinquentme> do we know if 23 and me actively collaborates with google?
09:57 < delinquentme> Molybdenum, howdy :D
09:57 < Molybdenum> The original GitS movie was garbage, compared to the book.
09:57 < delinquentme> havn't read the manga
09:58 < delinquentme> but i was a fan of the movie
09:58 < Molybdenum> heylo delinquentme
09:58 < delinquentme> the hacker sentience scene
09:58 < Molybdenum> You should read the manga.
09:58 < delinquentme> LUV
09:58 < delinquentme> you didn't like that DNA as the maintainer of humans discourse ?
09:59 < Molybdenum> The comic is much, much more involved as far as the plot line and tech/science aspects of the GitS world in the comic.
09:59 < Molybdenum> ugh, reduntant sentence.
10:01 < Mokbortolan_> I just liked the tank fight
10:02 < Molybdenum> the tachikoma's are awesome
10:03 < delinquentme> Oh and the dude with the extension of chargraffs DNA grammar wrote me back
10:03 < delinquentme> seemed confident in the math....
10:03 < delinquentme> im a little confused as to why this isn't bigger than it is
10:09 <@kanzure> delinquentme: 23andme doesn't collaborate with google as far as i know
10:11 < delinquentme> not at all?
10:11 < delinquentme> even though brin is married to one of the board members
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10:28 <@kanzure> delinquentme: yes, to my knowledge there's no public program in place
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10:39 < yashgaroth> kanzure, i should stress that the electroporator in that thread earlier is much different than the diybio posts
10:40 < yashgaroth> as i'm targeting muscle tissue rather than bacteria, the parameters are much different
10:40 <@kanzure> alright
10:41 < yashgaroth> just fyi :V
10:41 <@kanzure> yashgaroth: i'm wondering about how i'd create more demand to buy dna synthesizers
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10:41 < yashgaroth> tell the terrorists they can make smallpox with it, they have some cash
10:41 <@kanzure> hi nmz787
10:41 < nmz787> hola
10:42 <@kanzure> maybe you could tell the hippies they can experiment with rational protein design for garbage/oil bacteria
10:42 <@kanzure> but i gotta be honest, that's a boring application out of the possibilities
10:42 < nmz787> nootropics could be expressed in bacteria or yeast at home, and secreted... yogurt is a great example media for this
10:43 < nmz787> hippies grow yogurt
10:43 <@kanzure> custom beers maybe
10:43 < nmz787> so if they could easily at home reprogram it
10:43 < nmz787> bam, market
10:43 < strangewarp> I would fucking love some nootropic yogurt, flavored with jam
10:43 < nmz787> see
10:43 < nmz787> a new customer
10:43 < nmz787> step right up
10:43 <@kanzure> but that's more of an argument for a custom yogurt company..
10:43 < Molybdenum> Mmm, burnt plastic flavor :|
10:44 < strangewarp> very strong jam, ten
10:44 < Molybdenum> piracetam powder still ranks as one of the foulest tasting things I've ever eaten.
10:44 < strangewarp> then
10:45 < yashgaroth> erm you're not gonna biosynthesize racetams, they're synthetic
10:46 < nmz787> with some genetic algorithms you could
10:46 < yashgaroth> what
10:47 < Molybdenum> ...you have my attention now.
10:47 <@kanzure> he's suggesting a long and drawn out directed evolution process
10:47 <@kanzure> that would eventually make a molecule that looks like your target
10:47 < nmz787> with inputs to the algorithm being yes or no from an on-chip TLC or something (validator), and the output being randomized DNA sequence for your target enzymes
10:48 < nmz787> yeah
10:48 <@kanzure> metaboli network -> various synthetic outputs -> sequencing -> figure out which sequence caused that, throw that data into your GA
10:48 < yashgaroth> that's far beyond anything possible now, much less DIY
10:48 <@kanzure> not quite what i was expecting.
10:48 < nmz787> so if you could synth and sequence DNA on chip, you could then go on and say to express that DNA in bacteria, and yeah do directed evolution
10:48 <@kanzure> yashgaroth: it's definitely a long process
10:49 < nmz787> ok well thats my version then
10:49 < nmz787> the hippy version would have a working pathway database
10:49 < nmz787> so you just download, then synth
10:49 < nmz787> and it electroprates your host on chip
10:49 < nmz787> or that could even be separate
10:49 <@kanzure> a sequencer is an easy sell.. "see what weird creatures are all around you" "and potentially find new/useful genes somehow"
10:50 < nmz787> its been shown that nasally administered GFP DNA in mice made their liver grow
10:50 < nmz787> glow*
10:51 <@kanzure> what about something like.. drosophila farming
10:51 < nmz787> umm
10:51 <@kanzure> hrm, no
10:51 < roksprok> what would you do with the drosophila?
10:51 < yashgaroth> the technical term is 'ranching'
10:52 < roksprok> eat them?
10:52 <@kanzure> nope not drosophila, let's say "random microbes" instead
10:52 <@kanzure> like from your water supply
10:52 <@kanzure> and just do random electroporation/transformation. i don't know, that doesn't sound that fantastic to me
10:52 < nmz787> and seq?
10:52 <@kanzure> right.. i guess
10:52 <@kanzure> that would require a full genome or to splice in genes
10:52 < nmz787> @home sequencer is an easy sell i think
10:52 < nmz787> tell what your kids infection is
10:53 < nmz787> etc
10:53 <@kanzure> maybe focusing on protein production in 'some culture' is better
10:53 < nmz787> foreseeable to even start faxing that data to your doctor, and let them tell you whether you need to get to the hospital, etc
10:54 < nmz787> yogurt man
10:54 < nmz787> milk media is found everywhere
10:54 <@kanzure> i think protein production/purification is a separate target, besides just normal cell culturing / transformation
10:54 <@kanzure> both require new dna
10:55 <@kanzure> 'make stuff that you put into your body' might not be an acceptable approach
10:55 < nmz787> there's nothing wrong with keeping some toys for ourselves, we could offer a 'lead time' on the fancier ones
10:55 < nmz787> no its not
10:56 < nmz787> well
10:56 <@kanzure> but it's the coolest.
10:56 < nmz787> it might be OK
10:56 < nmz787> yogurt and said organisms are  GRAS
10:57 <@kanzure> there's all sorts of things made possible, but i don't see that being obvious to potential customers
10:57 <@kanzure> like, oh you're a polymer scientist.. well guess what can help you make interesting polymers
10:57 <@kanzure> the educational side is pretty easy to sell
10:58 < nmz787> you wouldnt sell to the polymer guy, you'd sell to his biochem lab partner
10:58 <@kanzure> labs don't buy dna synthesizers, but maybe this could change
10:58 < nmz787> oh?
10:58 <@kanzure> if they are going to write it into the grant budget, they might as well just write in the costs for ordering something online
10:58 < nmz787> i assumed they did, since my school has one
10:59 <@kanzure> i guess you could argue that high-throughput, sequence-specific dna generation opens up new possibilities in the lab
10:59 <@kanzure> your school has *one*
10:59 <@kanzure> and like 200 bio labs
10:59 < nmz787> not that many labs!
10:59 <@kanzure> hmm
10:59 < nmz787> maybe 60-100
11:00 < nmz787> courses
11:00 < nmz787> physical rooms prob more like 40-50
11:00 < roksprok> kanzure: could you make a case that it would be a ton quicker?
11:01 < roksprok> instead of sending something out
11:01 < roksprok> and waiting a few days to get it back
11:01 <@kanzure> the design i'm thinking of could do multiple simultaneous different oligos
11:01 < yashgaroth> i keep telling you, DHS keeps tabs on all registered dna synthesizers
11:01 < roksprok> you could have it by the time you got back from lunch
11:01 <@kanzure> not quite
11:01 <@kanzure> (re: timing)
11:01 <@kanzure> i believe the dhs thing though
11:01 <@kanzure> the timing is more like, maybe it will take a few days
11:02 <@kanzure> but it won't cost you $5,000 for that single molecule
11:02 < roksprok> i still think that would be pretty compelling
11:02 <@kanzure> well, what would you make?
11:02 <@kanzure> you're not going to just buy a $5k synthesizer for fun
11:03 < roksprok> i was still thinking of labs
11:03 < roksprok> that use dna synthesis a bit
11:04 < roksprok> but are limited by the fact that they have to go through a whole process of ordering, waiting, paying a decent chunk of change
11:04 < roksprok> so don't do highly parallel things
11:05 < roksprok> they could now move from 'make sure you know exactly what you need and absolutely need it" to "try a bunch of shit out"
11:06 < roksprok> it seems like it would open up a bunch of low hanging fruit
11:06 < yashgaroth> library generation for panning is a major user of dna synthesis
11:06 <@kanzure> there's already dna library generation techniques, though you don't usually control the entire sequence (you just choose site-specific areas to mutate)
11:06 <@kanzure> (and the mutations aren't under your control, in most of those methods)
11:06 <@kanzure> panning?
11:07 < yashgaroth> well, site-specific regions of maybe 20 residues
11:07 < yashgaroth> yes, panning i'm not gonna describe cuz i'm on my phone keyboard
11:07 <@kanzure> the common example is if you try out a million different versions of a polymerase, you might find one that is a million times better than the others, etc.
11:08 < yashgaroth> well pol is pretty optimized, but a lot of biosynthesis pathways prob. have room for improvement
11:08 <@kanzure> good point
11:09 <@kanzure> so with 3d printers, the business model is "buy or make your open source 3d printer, then start a business around it and rent out time, or make custom parts for people"
11:09 <@kanzure> "custom organisms" aren't quite going to be made possible with just a synthesizer (or even a synthesizer that can do some limited forms of transformation/incubation)
11:10 < yashgaroth> it's like people who want to improve rubisco, not gonna happen, but many commercial pathways are still wild-type
11:10 < strages_work> kanzure: or print and sell printers for others
11:11 < yashgaroth> "custom" organisms as in adding a few genes is easy, just not a whole synthetic genome
11:11 <@kanzure> well, i've always had this ludicrous idea that people would make custom dinoflagellates or weirdly-shaped bacteria
11:11 <@kanzure> and then sell these as designer pets :P
11:12 < yashgaroth> ehh the market for transgenic mammals that stay as neonates
11:12 < yashgaroth> much bigger
11:13 <@kanzure> then get a giant wall-mount lcd screen with a microscope hooked up to the screen, and it's a wall-mounted picture frame showing your strange microbial world
11:13 < yashgaroth> you know you want a baby panda that stays that way
11:13 <@kanzure> stay as neonates?
11:13 < yashgaroth> perma-puppies
11:13 < roksprok> what about replacing the bacteria in your mouth, with ones that don't reek
11:13 < roksprok> as in, selling a kit to do it at home
11:13 < roksprok> with bacteria you discovered and isolated with the help of the dna synthesizer
11:13 <@kanzure> eh
11:14 <@kanzure> why would the synthesizer help with that?
11:14 <@kanzure> that's a very expensive kit..
11:14 < strages_work> altering the bacteria in your gut to allow for better digestion of things we don't usually digest properly
11:14 < roksprok> wouldn't the synthesizer help in the development of the bacteria?
11:14 < yashgaroth> gut is more near-term, esp. since e.coli is the most studied organisms ever
11:15  * delinquentme inserts your momma joke here
11:15 < delinquentme> sorry innapprope
11:15 < delinquentme> <3
11:15 <@kanzure> yes except i don't think that's sellable on the market
11:15 <@kanzure> Mr. VC: so you want people to buy your product.. so they can perform medical experiments?
11:15 <@kanzure> designer microbes would go over better :P
11:15 < delinquentme> well its marketable in the way that marinated cardboard is chinese chicken
11:16 < roksprok> as in customizing it to out compete other mouth flora
11:17 < roksprok> would it be possible to use the synthesizer to change algaes or plants?
11:17 < roksprok> insert a gene or two?
11:17 <@kanzure> sure..
11:18 < roksprok> maybe other hobbyist groups then
11:18 < roksprok> like garderners or aquarium people
11:18 < roksprok> some would have a lot of disposable income
11:18 < yashgaroth> glowing plants for your aquarium or lawn
11:19 < roksprok> and a few already spend shittons of money going on orchid hunting expeditions or something
11:19 <@kanzure> yashgaroth: do you know how transformation works with seeds?
11:19 <@kanzure> i'm familiar with agrobacterium as a method of transfection to a target plant
11:19 <@kanzure> but i haven't looked at seed modification or if that's a thing
11:19 < roksprok> or 'adapt this pretty plant to grow in your climate' then sell it to other gardeners
11:20 < roksprok> that would at least be a bit of a business
11:20 < roksprok> and hobbyists are used to spending tons of money on stuff other people see as a waste of time
11:20 <@kanzure> yup, but to a large extent they don't currently do this (except maybe by crossing plants on their own)
11:20 < roksprok> so i think their economics are a bit different than the usual consumers
11:21 < yashgaroth> you don't need seed modding, you can grow a plant from a transformed cell
11:21 <@kanzure> and there's barely any companies doing "designer microbes" except on a scale where they don't care about the high cost of dna synthesis mail ordering
11:21 <@kanzure> sooo anything i throw together, would have to also help people along on that process
11:21 <@kanzure> or something. not sure.
11:22 < roksprok> are any companies doing designer microbes as pets/art/ not useful stuff yet?
11:23 <@kanzure> not to my knowledge
11:23 < yashgaroth> that guy who made a gfp rabbit for an art project, but not commercially
11:23 <@kanzure> gardners don't exactly have biology labs, so i'd have to throw together a kit for that too
11:23 < yashgaroth> oh, microbes, no
11:24 <@kanzure> biofuel microbe design companies seem to exist, but it's sorta hush-hush because the oil companies don't want each other to know which strands they have been building
11:25 < roksprok> could an igem like competition start for independent diybio people?
11:26 < roksprok> or if more labs popped up you could get each one to buy a synthesizer or two
11:27 <@kanzure> a competition might work..
11:31 < roksprok> if the costs came down maybe custom microbes could be a general part of industrial chemical research
11:31 < roksprok> like, lets find something that works better than teflon or kevlar or whatever
11:32 < roksprok> instead of just places where huge money is involved like energy
11:33 < roksprok> and aren't there a couple medical products made with microbes?
11:37 < yashgaroth> not many medical, but a lot of industrial enzymes
11:37 <@kanzure> i'm not sure how many chemical plants are buying custom enzymes
11:38 < yashgaroth> almost all biopharma prodxn is done in eukaryotes
11:38 < yashgaroth> they'd buy if it works better
11:38 <@kanzure> true, but the development timeline in pharma is decades not months
11:38 <@kanzure> decades because of regulations etc
11:39 < yashgaroth> yes, but not industrial enzymes, long as it's not going in your body
11:40 < yashgaroth> pharma products are waaay out of our league to begin with
11:41 <@kanzure> i'm just trying to imagine a scenario where there's a demand for 20,000 microbe designers
11:41 <@kanzure> or 100,000 people with a dna synthesizer
11:41 <@kanzure> *or enzyme designers
11:43 <@kanzure> biofuels, drugs, bioplastics, biosensors, agriculture
11:43 < yashgaroth> i can't imagine there's 20,000 unique projects to begin with, much less 100k
11:44 <@kanzure> there's certainly more than 20,000 currently active biology projects in the US
11:45 <@kanzure> antibodies.
11:45 <@kanzure> you could scaremonger something about making new antibodies
11:45 <@kanzure> (as long as the antibodies don't kill you)
11:46 <@kanzure> "hey look, i'm fucking immune to mustard gas!"
11:46 <@kanzure> dunno if that would work
11:46 < yashgaroth> it's a bit too small, but a musard gas sequestering protein could work
11:47 <@kanzure> btw if you don't think 20k, can you run me through what a good estimate would look like to you?
11:47 <@kanzure> esp. of currently active research projects or biotech projects
11:49 < yashgaroth> i mean, it's closer to 20k than 200, but that's all biotech, not just dna-synthesis-requiring projects
11:51 <@kanzure> so you could say, great, buy this synthesizer if you want, make up some enzyme to help in some chemical factory process,
11:51 <@kanzure> then start a chemical factory.. yeah um..
11:52 < yashgaroth> you can "plug in" a new enzyme to existing factory relatively easily, esp. with bacteria
11:53 <@kanzure> oh dope i'm a dork
11:53 < yashgaroth> ...if you have access to said factory, that is
11:53 <@kanzure> there's already a lot of economic incentives related to carbon credits
11:53 <@kanzure> and carbon offsetting.
11:59 <@kanzure> es low. I highly recommend the Omnivore's Dilemma. It's generally trucked by the millions of tons to fatten up cows and generating tons of carbon waste. This is the form of carbon sequestering that is causing lots of problems in America and lots of other places.
11:59 <@kanzure> bleh
11:59 <@kanzure> i meant
11:59 <@kanzure> http://diyhpl.us/wiki/transcripts/hplus-summit-2010/d1s1-3-andrew-hessel
12:00 <@kanzure> so anyway.. i could see that as an argument for why there's lots of non-academic people that would buy synthesizers
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12:03 < yashgaroth> heh "you don't have to leave facebook to do this"
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12:04 <@kanzure> hi durth__
12:04 <@kanzure> yashgaroth: yeah :/
12:05 < durth__> Hey
12:05 < Mokbortolan_> I for one welcome the grey goo.
12:05 < durth__> What goo?
12:06 < eudoxia> I played a game yesterday where you were a gray goo particulate that grows and expands and consumes the entire e
12:06 < eudoxia> universe
12:08 < yashgaroth> like, left click to consume matter?
12:08 < eudoxia> yeah
12:08 < eudoxia> well, actually you just move it with the mouse, matter was consumed automatically, though I did spend the first ten minutes thinking I had to click
12:14 < Mokbortolan_> that sounds pretty boring
12:15 < eudoxia> it was actually very addictive
12:15 < Mokbortolan_> in a minecraft sort of way?
12:15 < Mokbortolan_> or bejewelled
12:16 < eudoxia> I guess it was the series of tiny little rewards that kept you going
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13:42 <@kanzure> huh, "a monkey's uncle" refers to darwin's work
13:42 <@kanzure> for once a phrase makes sense?
13:44 < Mokbortolan_1> wouldn't the monkey be your uncle?
13:44 < Mokbortolan_1> you being the monkey's uncle would be devolution
13:44 < Mokbortolan_1> de-evolution?
13:51 < Molybdenum> well, the disconnect with the term makes sense considering the kinds of people who get offended by Darwin's work. (And I'm hazarding the term started out as an insult)
13:56 < roksprok> is there a webstore like sparkfun or dfrobot for the diybio community?
13:56 <@kanzure> roksprok: not really
13:56 <@kanzure> all of the chem suppliers are "too big to fail"
13:57 < Mokbortolan_1> "Well I'll be a Monkey's Uncle" = "I did not believe this was possible, but apparently it is."
13:58 <@kanzure> Mokbortolan_1: yes but apparently it started to become a saying because of darwin's work
13:58 < Mokbortolan_1> but yeah, if they don't recognize its validity it's probably because they don't understand it, so the saying makes sense from that perspective :p
13:58 <@kanzure> remember, for the longest time, people have always thought they were somehow superior or better than other lifeforms
13:58 <@kanzure> so you'd be the "uncle" since you're better.. or something
13:59 < Mokbortolan_1> value judgements always get you in trouble
13:59 <@kanzure> I AM BETTER THAN YOUR MOM
13:59 <@kanzure> there, i said it..
14:04 <@kanzure> roksprok: equipment is usually expensive, so keeping stock is even more expensive
14:04 <@kanzure> most people just hunt for pipettes on ebay
14:04 <@kanzure> chemicals and reagants are a weird story
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14:19 <@kanzure> god this is awful programming
14:19 <@kanzure> http://research.microsoft.com/en-us/um/india/projects/biocoder/tutorial/section4.html
14:19 < delinquentme> anyone know of publishing companies who will push your shit out for free?
14:19 < roksprok> kanzure: the chemicals and reagants aren't controlled, are they?
14:19 <@kanzure> measure_fluid(te, vol(20, UL), sterile_microfuge_tube2);
14:19 <@kanzure> store_until(sterile_mirofuge_tube2, RT, ETHANOL_EVAP);
14:19 <@kanzure> resuspend(sterile_microfuge_tube2);
14:20 <@kanzure> roksprok: sometimes they are. the companies are definitely voluntarily controlling who they sell to, sometimes
14:20 < roksprok> do you think there would be enough demand to kind of make a middle company?
14:21 <@kanzure> based on my understanding of the economies of scale involved, no
14:21 < roksprok> bummer
14:21 <@kanzure> it's my understanding that sigma/aldrich, merck and otherso nly manufacture some of their chemicals
14:22 <@kanzure> others are brought in from other companies on exclusive deals or whatever
14:22 <@kanzure> if you want to build giant chemical factories that's cool, but i don't see this as being scalable
14:22 <@kanzure> i mean, that's large investment stuff
14:23 < roksprok> i was more thinking, order from merck or someone and repackage to sell to individuals or something
14:23 < roksprok> so like, if you wanted to do a diy bacterial transformation you could get everything form one place
14:23 < roksprok> *from
14:24 < roksprok> and lower the barrier of entry
14:24 <@kanzure> redistribution hrmm
14:24 < roksprok> and maybe make kits
14:24 <@kanzure> well that also depends on whether or not they will sell to you ;)
14:25 < roksprok> well i was thinking if you set up a business, had proper zoning, etc.
14:25 < roksprok> maybe present yourself as an education company?
14:26 < roksprok> or a biotech startup?
14:26 < roksprok> and were ordering in somewhat larger quantities
14:27 <@kanzure> education company.. no thanks
14:28 <@kanzure> well, kits are all the rage these days. so you'll pass the social acceptance test
14:28 < roksprok> well it would more be to just explain it in a way that is less 'we are reselling your stuff to hobbyists we have no control over' and more 'we supply small colleges and startups'
14:30 < roksprok> like i know there are a few kits out there already, but it seems there is a gulf between 'follow these exact steps' and 'do actual science'
14:30 < roksprok> unlike say arduino, where sparkfun sells kits but also has a bunch of components and ideas for making your own stuff
14:32 < roksprok> and a place to share them
14:32 < roksprok> like its still a lot of work to get involved in diybio in a meaningful way
14:32 < roksprok> it would be cool to smooth that process
14:33 <@kanzure> have you see the process smoothed before, ever/
14:33 <@kanzure> like what do you mean- no testing required?
14:35 < roksprok> well more like make it possible to go from 'wow synthetic biology is cool' to 'cool i made glow in the dark bacteria' to 'i'm actually being a bit innovative'
14:35 < roksprok> like if i think robots are cool
14:35 < roksprok> i can go get a kit to build a simple one
14:35 < roksprok> see it follow a line or something
14:36 <@kanzure> biology isn't like that, really
14:36 <@kanzure> yes, you can follow steps in a kit to make bacteria glow
14:36 <@kanzure> but oops, you touched your pipette tip to a surface and now you have to start over with your culture ;)
14:37 <@kanzure> except you didn't realize it, and it didn't work "for some reason" even though you followed all steps
14:37 <@kanzure> anyway, i think it's great if you want to make kits
14:38 < roksprok> i guess its the "for some reason" thats the problem
14:39 < roksprok> like in electronics if you short something out you can tell with a multimeter
14:39 <@kanzure> you can test all the way through your experiment, but it's complicated
14:39 <@kanzure> like there's no "dna contamination" multimeter
14:40 < roksprok> yea and thats only one of the things that can go wrong
14:40 < roksprok> i guess it would be easy to get discouraged
14:41 < roksprok> moving away from that a bit, what about little test kits for fish?
14:41 < roksprok> like, am i actually eating sea bass
14:41 < roksprok> or did i just get ripped off
14:44 < roksprok> would it be possible to make those cheaply?
14:45 < roksprok> just a simple thing like a red or green led gets lit
14:45 <@kanzure> i think macowell is making those at the moment
14:45 <@kanzure> http://seqify.com/
14:47 < delinquentme> barcode fungi huh?
14:48 < roksprok> but those you have to mail it off
14:48 < roksprok> and they check it against a bunch of different species
14:49 < roksprok> could you just use unamplified dna to do a single test?
14:49 <@kanzure> so you want to do non-pcr-based testing?
14:49 < roksprok> if possible
14:50 <@kanzure> what mechanism will you use for dna barcoding then?
14:50 < roksprok> could you have the desired dna strand
14:51 < roksprok> and see if the sample binds to it?
14:52 <@kanzure> http://scholar.google.com/scholar?q=hybridization+dna+barcoding
14:53 < roksprok> ok scratch  that then
14:53 < roksprok> thanks
14:53 <@kanzure> might be possible. you'll have to experiment and find out..
14:54 < roksprok> well it seems like segify's way is the best
14:54 < roksprok> targeted at businesses
14:54 <@kanzure> check out dna hybridization assays or something
14:55 < roksprok> k
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15:14 <@kanzure> hrm these guys do sequencer repair http://seqgen.com/
15:16 < delinquentme> kanzure, are you in #biology?
15:16 < delinquentme> i asked a systems bio question and no one can derp on about it
15:17 <@kanzure> are you asking about how to find out the kinetic equations for individual proteins/enzymes?
15:18 < delinquentme> what im *REALLY after* is just machine learning w the internet as my datasource
15:18 <@kanzure> what does that even mean
15:18 < delinquentme> so like i go hunt down open journals
15:19 < delinquentme> sort them by which has free associated data
15:19 < delinquentme> gather multiples resources in this manner
15:19 < delinquentme> XYZ
15:19 <@kanzure> why..
15:19 < delinquentme> 4) profit!
15:19 <@kanzure> are you trying to do whole cell simulation?
15:19 < delinquentme> no im trying to figure out something to stick into this API so I can actually publish a paper
15:20 <@kanzure> what api?
15:20 <@kanzure> you can publish a paper about anything.. pick some crap from your blog, turn it into a paper
15:20 < delinquentme> like a tutorial is cool but ive got a better chance at getting published with some sort of novel data
15:20 < delinquentme> the one I was working on the the last few days
15:20 < delinquentme> https://github.com/delinquentme/sapi
15:20 <@kanzure> why do you want to publish a random paper?
15:21 <@kanzure> wut.. why is this a dna api
15:21 <@kanzure> why not just use fastaa files
15:26 < delinquentme> so the paper is an example of how to do it properly
15:26 <@kanzure> https://github.com/levskaya/BioJSON
15:27 <@kanzure> delinquentme: i don't think that makes sense, there's already tons of tutorials on REST and wsdl and other crap
15:27 < delinquentme> hmm that could be cool
15:27 < delinquentme> make an API that you push up one file and it spits it back out as another file?
15:27 <@kanzure> this is pretty nice:
15:27 <@kanzure> https://github.com/levskaya/BioJSON/blob/master/genbank_parser.py
15:27 <@kanzure> delinquentme: why
15:27 <@kanzure> delinquentme: what are you doing??
15:28 < delinquentme> kanzure, I want to make a API that does something novel
15:28 < delinquentme> in order to present it as a research paper
15:28 < delinquentme> So end goal would be something like
15:29 < delinquentme> " An example tutorial and presentation for XYZ "
15:29 < delinquentme> " An example tutorial on restful API implementation and presentation for XYZ biological function"
15:31 <@kanzure> restful sequence alignment would be nice
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15:37 < delinquentme> kanzure, do you know a "Daniel Wilkerson" ?
15:38 < delinquentme> micheal rae connected me with him .. and hes kinda wigging out on me
15:41 < roksprok> what does wigging out mean?
15:42 < roksprok> is that a british thing?
15:44 < delinquentme> getting angry like call caps typing
15:44 < delinquentme> over asking him questions
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15:52 < roksprok> delinquentme: i like that term i'd never heard it before thanks
15:55 <@kanzure> caps or cops
15:55 <@kanzure> i know a rouillie wilkerson who's into diybio
15:55 <@kanzure> and a shawn wilkerson who's into transhumanism
16:01 < Mokbortolan_1> I wouldn't say that I'm into transhumanism
16:01 < Mokbortolan_1> I mean, I don't have anything against them
16:01 < Mokbortolan_1> if you wanna turn from a girl to a boy or vice versa, who am I to criticize?
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16:15 < Molybdenum> err.
16:17 < Mokbortolan_1> (it was a joke)
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16:38 < Stee|> job acquired
16:55 <@kanzure> "For those of you who don't get the github messages, the C++ generated for AP235TC and AP242 n2813 now compiles. All we need now are exchange files to test with!"
16:55 <@kanzure> "This leaves AP209 as the only schema that fedex_plus fails on, and AP210e2/e3 as the only schemas that gcc won't compile."
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17:19 < delinquentme> whats that Steel?
17:19 < delinquentme> Stee|, ^
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17:28 < ybit> video recommendations for while i'm eating?
17:29 <@kanzure> team fourstar
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17:34 < ybit> heh :)
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17:49 < JayDugger> Great Scapel Mistakes on the Home Surgery Channel.
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18:18 < delinquentme> so what do we get from studying grass
18:18 < delinquentme> like is this the same thing as algae? that we want ot understand it to modify it to create chemicals?
18:19 < delinquentme> or is this only going to net us better grass for football stadiums?
18:19  * delinquentme doesnt get it
18:19 < yashgaroth> you mean, general research on grass biology?
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18:29 < delinquentme> yeah
18:30 < delinquentme> like im looking at a 1mil grant from the NIH for a group to study tomatoes ...  when someone working on a highspeed computer network for genomic transfers .. got 200k ?
18:30 < delinquentme> like how? why?
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18:31 < JayDugger> Given the result, imagine the motivations of the funding agency's decision makers.
18:31 < yashgaroth> because programming only requires stimulants and a terminal, while bio research has a lot of expensive consumables
18:32 < JayDugger> And that's an even better answer.
18:32 < yashgaroth> unless you mean the physical network for large data transfer, in which case I don't see why it's specific to genomes
18:33 < delinquentme> yash its for some big research groups to make a highspeed network
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18:33 < delinquentme> so that they're not mailing hard drives
18:33 < delinquentme> but JayDugger I just have no idea what could come out of indepth study of grass
18:34 < JayDugger> Think about what might motivate people.
18:34 < delinquentme> to research grass?
18:34 < delinquentme> cattle feed...
18:35 < delinquentme> maybe something with cloroplasts
18:35 < JayDugger> No, you still think about grass. Why would people make that decision.
18:35 < delinquentme> sun >> energy?
18:35 < JayDugger> Banal and quotidian reasons matter more than the merits.
18:35 < delinquentme> converting particular soil chemicals?
18:35 < yashgaroth> do you have a link to the grant posting?
18:36 < delinquentme> JayDugger, so you're saying its the NIH buddy system?
18:36 < delinquentme> bc that was my first guess
18:36 < yashgaroth> I'm sure suburbanites wouldn't mind if their lawn sequesters pollutants, if they're gonna mow it anyway
18:36 < delinquentme> http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1125620
18:37 < JayDugger> I don't know. Cynical answers can prove wrong, but when they do it comes as a pleasant surprise.
18:37 < yashgaroth> also rice is a grass
18:37 < delinquentme> but regular old normal grass doesnt sequester pollutants... soooo why are we trying to fix this?
18:38 < yashgaroth> because if we could make it do that, it'd be useful
18:38 < yashgaroth> also that grant is about studying corn, which apparently is also a grass, TIL
18:39 < delinquentme> ah
18:39 < delinquentme> so the american corn growers association or some shit is involved ?
18:39 < delinquentme> that i can see
18:39 < yashgaroth> I think corn is the #1 crop in the US by acres planted, at least #2
18:40 < yashgaroth> oh yeah it's #1 by about >3x acres the #2, soy
18:41 < yashgaroth> a 1% improvement in yield or nutrition from that would be huuuge
18:47 < delinquentme> "internet 1 "
18:48 < delinquentme> "internet 2 " !!!
18:49 < delinquentme> see
18:49 < delinquentme> THIS
18:49 < delinquentme> http://www.nics.tennessee.edu/computing-resources/kraken
18:50 < delinquentme> this i useful
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19:19 < industromatic> hey Bryan
19:20 < industromatic> What do you think about Quinonez, Carlo
19:24 < industromatic> Seems like a non-friend of open hardware.
19:24 < industromatic> Gotta go.
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19:26 < yashgaroth> caralo quinonez is a dick! oh he left
19:32 <@kanzure> yashgaroth: why is he a dick?
19:32 < yashgaroth> I have no idea who he is
19:32 <@kanzure> yashgaroth: http://groups.google.com/group/diybio/t/11855037508b9774
19:33 <@kanzure> sciencedirect makes me angry. they set a new cookie each time you load a page, apparently
19:35 < yashgaroth> so do you mostly use IDs from that ezproxy page? and if so do you have a currently working one
19:36 <@kanzure> i ssh into a few servers that are inside good networks
19:37 <@kanzure> let me see about a good one.. uhh i don't suppose an ezproxy login for ncbi.nih.gov would be ok
19:39 < yashgaroth> hopefully a uni library with decent subscriptions
19:44 <@kanzure> right.. i had one in mind
19:44 <@kanzure> that's why it's taking me a few moments..
19:44 < yashgaroth> at least until Stee| shows up for me to annoy about articles
19:46 <@kanzure> yashgaroth: bradfordcollege
19:46 <@kanzure> ezproxy.free-webmaster-resourcsmies.org/201201/shibboleth-bradfordcollege-ac-uk-library-ezproxy-username-and-password-20120114/
19:46 <@kanzure> this isn't the one i was thinking of though :(
20:19 <@kanzure> delinquentme: pm
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20:58 < delinquentme> http://www.iscb.org/index.php?option=com_content&view=article&id=342&lqm_uid=45  << wish they offered this for free =[
20:59 <@kanzure> well that looks like joomla
20:59 <@kanzure> so just use a joomla exploit
20:59 <@kanzure> oh it's a class.
21:06 < delinquentme> dat cert
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22:13 < n_bentha> yashgaroth: it werks!
22:13 < yashgaroth> congrats!
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22:14 < yashgaroth> so, the reason you didn't need a functional gene is that you're doing gene repression with a the fragment in that plasmid? or what
22:15 < n_bentha> yeah
22:15 < yashgaroth> don't worry, I haven't guesssed which gene you're knocking down
22:16 < yashgaroth> can you tell me what plant it's in, or will that give away too much?
22:17 <@kanzure> don't say cannabis don't say cannabis
22:17 < n_bentha> omg i wish i could do some work on cannabis
22:17 < yashgaroth> man, putting the THC synthesis genes into hops would be so easy, they're almost the same species
22:18 < yashgaroth> practically the same biosynthetic pathway already, it's only a few extra genes and bam
22:18 <@kanzure> yashgaroth: funny story.. it's not much of a story actually
22:18 <@kanzure> but the mol bio professors at ut were talking once and i overheard them,
22:18 <@kanzure> apparently every other student talks about doing just that
22:19 < yashgaroth> haha I'm not surprised
22:19 <@kanzure> and they're cool with it, but after like 30 years one of them have followed through
22:19 <@kanzure> *none of them
22:19 < yashgaroth> well, the full pathway only got published a couple years ago
22:19 < delinquentme> so i guess it makes sense ... but theres is serious complexity implications when inserting genes
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22:19 < delinquentme> so the closer the organisms are the easier it is?
22:19 < yashgaroth> generally
22:20 < yashgaroth> there's no complexity implied when you can copy over the gene and its regulatory sequence straight over
22:20 < delinquentme> r/trees would love to know how close those two things are
22:20 < n_bentha> and omg who doesn't love hops?
22:20 < delinquentme> how beer is totally acceptable
22:20 < delinquentme> ^^^^^^^^^^^^
22:20 < n_bentha> weed-beer
22:20 < delinquentme> what he said
22:20 < klafka> hey
22:20 < klafka> ?
22:20 < klafka> what are you guys talking about
22:21 < yashgaroth> >_>
22:21 <@kanzure> delinquentme fucked up and added a cannabis biosynthesis gene network to his fuckin' gut
22:21  * delinquentme wants some methon throat spray
22:21 <@kanzure> now he's high all the time.
22:21 < klafka> aah
22:21 < yashgaroth> it's a positive feedback loop, the genes are activated by cheetos
22:21 < delinquentme> http://www.youtube.com/watch?v=RsfPFsN_z2U
22:22 < delinquentme> oh! so yeah that sequencing tech based off video compression .. thats the kinda thing you'd use to sequence the gut microbes huh?
22:22 < yashgaroth> is this the one for finding minority species in a mixture and getting their genomes? then yes
22:24 < n_bentha> i'd love to have some guy microbes w/ certain genes that i could kill easily
22:24 < delinquentme> I got MY computational bioinformatics PHD at devry university for FI dollar!
22:24 < n_bentha> or at least turn off their expression by eating something
22:24 < delinquentme> n_bentha, i think that happens all the time
22:24 < delinquentme> no. wait
22:25 < yashgaroth> inducible suicide genes tend to get selected out pretty quick
22:25 < delinquentme> the stuff you eat changes the expressions within genes within 24 hours
22:25 < delinquentme> but im not sure if it said anything about killing off microbes
22:25 < yashgaroth> unless you mean killing gene expression
22:26 < n_bentha> well i want a system where i can throw some genes into bacteria, make a pie, sprinkle them on top, and then eat it, have the microbes produce my proteins of interest, and then die when i eat some spice, or something?
22:27 < delinquentme> FDA-approved drug rapidly clears amyloid from the brain, reverses Alzheimer's symptoms in mice
22:27 < delinquentme> http://medicalxpress.com/news/2012-02-fda-approved-drug-rapidly-amyloid-brain.html
22:27 < yashgaroth> why not keep the bacteria around and just have the spice activate protein expression?
22:28 < n_bentha> yes or that, yashgaroth. some form of control.
22:29 < yashgaroth> it's always nice to have the option to kill them, true
22:29 < n_bentha> what is this black magic, delinquentme? the work of witches i say! burn them all!
22:30 < delinquentme> n_bentha, its much like that claimed "chemistry" whitchcraftery
22:30 < delinquentme> they dont wear burkas so we better burn them to be safe
22:30 < delinquentme> hail jeebus
22:31 < delinquentme> oh! and i've been posting the fuck out of a passage in numbers which lays out the directions to curse a child concieved outside of wedlock
22:31 < n_bentha> lolol
22:32 < yashgaroth> pretty sure the bible already says to stone everyone to death for something or other
22:32 < delinquentme> my primary anti-theistic argument?  You'd think an omnicient being would have the capacity to create a bit more scalable teachings
22:32 < delinquentme> then they say " he wants us to decipher right from left"
22:32 < delinquentme> then why say anything at all jeebus?
22:35 < n_bentha> "Megadoses produced a 50% reduction in plaque in the brains of those mice in 72 hours." --wikipedia on the drug Bexarotene
22:35 < delinquentme> <3
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22:41  * n_bentha makes a run for it
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23:12 < kanzure_> argh freenode
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23:32 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware http://gnusha.org/logs/ http://bit.ly/diybionews2 http://gadaprize.org/ http://groups.google.com/group/openmanufacturing
23:32 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Sun Jan  8 13:52:13 2012]
23:32 [Users ##hplusroadmap]
23:32 [ AlonzoTG] [ epitron        ] [ kanzure_     ] [ SolG        ] 
23:32 [ archels ] [ fenn           ] [ klafka       ] [ Stee|       ] 
23:32 [ audy    ] [ ferrousw1eel   ] [ kvltist      ] [ strages_home] 
23:32 [ audy-   ] [ foucist        ] [ Mokbortolan_1] [ strages_work] 
23:32 [ augur   ] [ gedankenstuecke] [ nchaimov     ] [ strangewarp ] 
23:32 [ bkero   ] [ gnusha         ] [ nuba         ] [ superkuh    ] 
23:32 [ Charlie_] [ gnusha_        ] [ Omega        ] [ uniqanomaly ] 
23:32 [ CIA-9   ] [ Guest427       ] [ pasky        ] [ Urchin      ] 
23:32 [ Coornail] [ Guest46680     ] [ qnm          ] [ utopiah_    ] 
23:32 [ drazak  ] [ Helleshin      ] [ quannum      ] [ yashgaroth  ] 
23:32 [ dsp__   ] [ ivan`          ] [ roksprok     ] [ ybit        ] 
23:32 [ elmom   ] [ jrayhawk       ] [ saurik       ] [ ziyadb      ] 
23:32 -!- Irssi: ##hplusroadmap: Total of 48 nicks [0 ops, 0 halfops, 0 voices, 48 normal]
23:32 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010
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23:33 < yashgaroth> I really don't get who would DOS freenode
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--- Log closed Fri Feb 10 00:00:03 2012