2011-12-18.log

--- Log opened Sun Dec 18 00:00:33 2011
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strangewarpBelatedly... there has been some transhumanist sentiment in small slices of the furry community over the years. At its best, it was entirely self-aware and creative, and led to lovely inspired storytelling in places like Puzzlebox (my username is an homage to part of that place), which sadly has fallen off the internet largely un-archived..00:23
sylph_makohttp://en.wikifur.com/wiki/Puzzlebox_MUCK00:43
sylph_makostrangewarp smells like someone I know. I'm pretty sure they're not him. We'll see.00:43
strangewarpI'm not. I'm just a guy who arrived to the party late, and already burned out. :00:46
strangewarp:P00:46
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strangewarpTo clarify: I stumbled over that MUCK's wiki (now offline) in 2008 or so, at about the same time I was reading through the posts on OvercomingBias that would spark LessWrong (I know, I know, I've come to dislike their lack of actionable engineering or coherent plans for such), and the two served as representations of conflicting impulses while I was waking up intellectually.01:03
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JayDuggerGood morning, everyone.01:39
Mariuhey, JayDugger01:40
Mariuhow's it going ?01:40
JayDuggerAll well enough.01:40
JayDuggerNo real progress on projects of interest here, but otherwise life goes well.01:41
MariuCool, nice to hear that.01:41
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Lucas_http://www.youtube.com/watch?v=qx72xt0utm411:48
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delinquentmeOMG MISSED YEW AW13:32
delinquentme<313:32
sylph_mako..?13:39
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ybithi delinquentme, sylph_mako15:24
ybithope everyone here is doing well, been awhile since i've talked with anyone15:25
sylph_makoI just hung up a yule bow ^ ^15:25
sylph_makoI wish a joyous yuletide festival from to you all.15:26
ybitgracias y back to you15:26
delinquentme^_^15:27
* ybit ^5s delinquentme 15:27
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sylph_makoWait a second. Yule is a winter celebration.15:40
sylph_makoI live in the southern hemisphere.15:40
sylph_makoIt's summer.15:40
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delinquentmesylph_mako, (christmas_tree)^-115:57
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mrtrousersHello18:11
mrtrousersIs there a diy way to sequence genome?18:11
kanzurehow diy do you want to do it18:14
kanzureyou can buy a dna sequencing machine18:14
kanzureor you can build your own dna sequencing machine18:14
kanzureor you can manually write down fluorescent colors as you see them pass by under a microscope..18:14
klafka1lol18:19
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mrtrousersSo to lets say.. To sequence your own genome you either pay to get it done or buy a sequencer machine?18:34
kanzurewell, it depends on how much coverage you want18:34
kanzureto a certain extent it's more efficient to just use 23andme and get a number of snps and apply that against a knonw-good genome18:35
kanzurebut! getting your own dna sequencer opens up a lot of other possible projects18:35
mrtrousersWhat is 23andme? How much are sequencers running for? Any open source project on it?18:36
kanzurethere's at least one open source sequencer but i think its material cost is 20k18:36
kanzureworking, used dna sequencers from 10 years ago go for maybe 12-15k18:37
kanzurenew dna sequencers will cost 50k-1200k18:37
klafka150k would be pretty cheap18:38
klafka1what would that be?18:38
kanzurei am making shit up18:38
klafka1oh18:38
klafka1lmao18:38
kanzurei know that some "top of the line" models go for 700k18:38
klafka1yeah18:38
klafka1exactly18:38
kanzurebut i'm pretty sure there's some <100k models18:38
mrtrousersOut of my budget.. Theres got to be a cheaper way to do it..18:38
klafka1the church one is like 150k~18:38
klafka1mrtrousers you can pay someone18:38
klafka1what is it like 10k?18:38
kanzuremrtrousers: you can just send in samples to someone18:38
klafka1or so18:38
klafka1still18:38
mrtrousersYup..18:38
kanzurei haven't seen an order form for pgp18:38
kanzuredoes it actually exist yet?18:39
klafka1no idea18:39
klafka1that's what i've heard18:39
kanzurei know they have sequenced some people, but they could have just outsourced that to knome or something18:39
kanzurewhen are you going to be in sf?18:39
klafka1kanzure no i'm talking about their machines18:39
klafka1tomorrow18:39
kanzureok i'm in sf tomorrow18:39
kanzurewhat time?18:39
klafka1polonator18:40
klafka1umm i think i get in around 5pm18:40
kanzureah i'll be gone before then18:40
klafka1ah18:40
kanzureyou have a place to stay?18:40
klafka1the company is putting me up at a hotel18:40
mrtrousersBy the way.. Going around the world sequencing diferent organism genomes could be made into a job?18:40
kanzureyou can take my place at langton labs (where fenn sleeps)18:40
klafka1oh can i stay tehre for a few months?18:41
klafka1:P18:41
kanzuremrtrousers: sure... check out beijing genomics institute18:41
kanzureklafka1: yeah, i think they have some rooms open for rent18:41
klafka1oooooh18:41
klafka1really?18:41
klafka1fenn_ get in here18:41
kanzurepretty chill place too18:41
klafka1tell me about your magic land18:41
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kanzurefenn is currently ignoring irc i think18:41
klafka1i wanna stay some place cheap and hopefully near caltrain if i get this job18:41
kanzurethis is near bart- look it up on google maps ("langton labs")18:42
klafka1for like a month or two then get an apt and have the gf move out18:42
kanzureare they in sf?18:42
mrtrouserskanzure: interesting..18:42
klafka1menlo park18:42
kanzureah lame.. langton might not be best then18:42
klafka1if it's cheap it'll work18:43
klafka1maybe18:43
kanzureyeah i'll pester fenn to get online in a bit18:43
kanzuretry pm'ing him..18:43
klafka1ok18:43
klafka1sweet18:44
mrtrouserskanzure: So lets say one sequences the genome for diferent organisms.. How do you monetize it?18:44
klafka1all kinds of ways18:44
kanzureuhh are you broke18:44
klafka1me?18:44
kanzureno18:44
klafka1oh18:44
klafka1heh18:44
klafka1mrtrousers you don't make money so much from the sequencing18:45
kanzureit's just a little unusual or someone to have to monetize a genome18:45
kanzure*for someone to have to monetize a genome18:45
klafka1typically places that sequence are either gov/grant funded or they do consulting work or they do lab work for hire18:45
klafka1e.g. they have a big ass sequencing lab and other people pay them to sequence shit for them18:45
mrtrousersYou travel the world seguencing rare genomes and monetizing so you can keep doing it..18:45
mrtrousersIm broke too18:46
klafka1well18:46
klafka1if you're craig venter18:46
klafka1and own a company18:46
klafka1and are rich18:46
klafka1then you can do that18:46
mrtrousersDid Craig Venter hit something interesting on that sailing expedition?18:47
kanzurehe published a few papers18:48
kanzureand usually you pay a bucketload to publish a paper (unfortunately)18:48
klafka1yeah18:49
klafka1like 3-4k18:49
kanzureklafka1: my last paper was 2k per coauthor18:49
kanzurethere were 11 coauthors18:49
klafka1wtf18:49
mrtrousersPeople pay to publish a paper? Really?18:49
klafka1kanzure it's usually a per page cost i thought18:49
kanzuremrtrousers: it's all kinds of fucked up18:49
kanzureklafka1: yeah there was that too18:49
klafka1kanzure it's preferable to the alternative18:49
klafka1honestly18:49
klafka1the current alternative18:49
kanzurethis was the "open access fee"18:49
klafka1i maintain it's  still preferable to the alternative currently18:50
mrtrousersIs there a database of currently sequenced organisms, people, etc.. ?18:52
klafka1sure18:52
klafka1check out pubmed.com18:52
klafka1fucking  flac18:52
kanzuremrtrousers: yes you can download genomes via ftp on ncbi18:52
mrtrouserscool18:53
mrtrousersWhat do you think of biobricks? Do you work with the registry of standarized parts?18:53
kanzurebiobricks is a nice concept but there's lots of edge cases that you run into18:54
kanzureplus, i don't think they are mailing biobrick books to non-institutions at the moment18:54
klafka1i haven't looked into synthetic biology18:54
klafka1however i think that there are going to be lots of emergent phenomenon and epiphenomenon that occur when you try and combine a lot of them18:54
mrtrousers...18:55
kanzurelike "taking a random metabolic network from one organism and into another organism" might have conflicting proteomes and shit18:55
mrtrousersSo when you combine the parts to make more complex devices.. It wont work?18:55
klafka1yes18:55
kanzureor "other shit breaks"18:55
klafka1yeah that's slightly more accurate18:55
kanzureand then you're debugging for three or four years..18:55
klafka1the things may do what you want, but they may do OTHER shit that you have no idea about18:56
mrtrousersIm trying to design a biosensor from existin devices..18:56
kanzurego for it18:56
klafka1mrtrousers you have to remember that biological 'programming' isn't like regular programming, the program is also data is also physical18:56
kanzurewhat are ou sensing?18:56
kanzure*you18:56
mrtrousersId like to sens air quality and pollutants from oil, gas, chemicals would trigger a change of colour or phosphorescent light.. I think e. choli chassis..18:57
kanzuresounds like you should just express some surface protein or other object that can bind to air pollutants non-selectively18:58
kanzurethe problem with non-selectively..18:58
mrtrousersis..18:59
kanzureuh? it's non-selective and thus useless if anything can set it off18:59
mrtrousersAnything that is a pollutant?19:00
mrtrousersWell anyway, I need to work on it..19:01
mrtrousersKlafka1: you have to remember that biological 'programming' isn't like regular programming, the program is also data is also physical.. Id like to hear more on that..19:02
kanzureno not just "anything that is a pollutant" more like... anything anything19:03
klafka1well your 'program' ends up being DNA which has actual physical properties and DNA can interact with DNA in various physical ways in addition to containing the basic 'atcg' information19:03
kanzureklafka1: i think protein-protein interactions are more relevant here19:04
klafka1further mRNAs interact with each other, they compete competitively for polymerase translation19:04
kanzureright19:04
klafka1er19:04
klafka1transcription19:04
klafka1adn ribosomal translation19:04
klafka1and THEN the protein end-products are physical things that can interact in emergent phenomena19:04
klafka1which is the big thing i think kanzure  and I agree on19:04
kanzureor other things can happen like.. pH changing drastically and killing your cell19:05
klafka1yeah19:05
kanzuresome of this can be modelled and predicted ahead of time i think,19:05
kanzurelike "Oh, i'm modifying the ph stability stuff, hur dur"19:05
kanzurebut anything else is a guessing game19:06
kanzuremore probabilistic19:06
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klafka1yeah19:06
klafka1basically things aren't impossible but they are fucking hard and they have the ability to really go off the wall19:06
mrtrousersYou guys are hobyists or biology academics?19:07
klafka1i'm no longer in academia but i was involved in comp bio @ in academia19:07
kanzurei'm just a tortoise19:07
kanzurei'm not even human19:07
eudoxiaIs there such a thing as an open manufacturing wiki?19:10
mrtrousersThere is open cource ecology..They do open hardware..19:10
kanzureeudoxia: no, but there's appropedia, gvcs stuff on openfarmtech.org, old hplusroadmap wiki stuf..19:10
eudoxiaOh I know that one, I was just wondering something more broad, though it would be 90% OSE19:11
kanzurethere's also wikipedia19:11
mrtrousersCan I make silly questions?19:14
kanzuresilly questions are the best kind..19:14
klafka1sure19:14
mrtrousersIf in a species every organism has a slightly diferent genome.. How do we decide which genome is the average or the one that defines the specie?19:15
kanzurestatistics19:15
kanzuremost members of a population have the same genome and just have different alleles19:15
mrtrousersSo when they sample bees, they dont just do one, they do lots..19:16
klafka1eh it's more like typically they try and take a 'normal' member of a species19:17
klafka1and sequence it's genome19:17
kanzureeudoxia: feel free to talk in here..19:18
kanzureinstead of separately..19:18
klafka1you have to understand that genome sequencing itself is a very probabilistic thing as well, each base pair is determined typically with some margin of error19:18
klafka199% of a species genome is the same and it's a set of SNPs that separate individuals19:18
kanzureand then there's all sorts of parts of the genome that are too highly repetitive to sequence with any certainty [with current techniques]19:19
klafka1yep19:19
mrtrousersIv seen when sequencing they break the dna into lots of strands to read it.. How do they piece it in the right order afterwards?19:20
ybitfenn_: do you think the ml-class was worth your time?19:20
kanzureybit: i just saw him walk in.. klafka has dibbs on him first19:20
kanzurelet me pester him19:20
klafka1mrtrousers by looking at overlap19:21
klafka1it's a fairly classic substring reconstruction problem19:21
mrtrousersOk19:22
klafka1for de novo sequencing there are two ways of doing it, either they create longer strands using sanger sequencing then using NGS to do 'shotgun sequencing'19:22
klafka1or um you can do denovo sequencing with just NGS but it requires very very high coverage19:22
mrtrousersDo you think laptops will incorporate labonachips to run experiments in the near future?19:23
eudoxiathat would be a mildly expensive adon19:24
eudoxiaaddon*19:24
klafka1er um19:24
klafka1why would a laptop have a lab on a chip?19:24
kanzurefenn is currently ignoring the interwebs19:25
mrtrousersDont know yet..19:25
eudoxiawhile we're at it, we could also add a scanning probe and an electron microscope19:25
mrtrousersSo you could run experiments on the fly, read genomes, etc..19:25
kanzuredirect dna sequencing with electron microscopy is another technique, although not ready for commercial use19:25
mrtrousersOr.. Would there be a day where you code something on a computer and something is grown on a petri?19:26
klafka1kanzure who is doing that?19:26
eudoxiaI wonder if you could sequence DNA with an atomic force microscope...19:26
kanzuremrtrousers: why? do you need that19:26
kanzureklafka1: halcyon molecular19:26
klafka1mrtrousers this is slightly beyond near future19:26
kanzureeudoxia: yeah.. you can19:26
klafka1more like 5+ years at least19:26
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/19:27
klafka1man kanzure  i boought pacbio stock19:27
kanzurehttp://diyhpl.us/~bryan/papers2/AFM/19:27
klafka1i hope they aren't tanking lately19:27
kanzurepacbio will probably end up on top19:27
klafka1i think they had a rough patch19:27
klafka1but they have solid tech19:27
klafka1don't you agree?19:27
klafka1wow halcyon hasn't had an update since Nov 201019:27
klafka1that's not good at all19:28
kanzurethey aren't a website company19:28
kanzurekim jong is dead19:28
kanzureeverybody hide under your desk!19:28
klafka1well i guess they are still around19:29
klafka1they are hiring a help desk admin19:29
klafka1kanzure just growing startups usually have regular news blurbs, are hiring, have jobs posted on their sites, etc...19:29
klafka1but anyway they are still doing well?19:30
klafka1are they sort of flying under the radar atm while they dev?19:30
kanzureuhrm19:30
kanzureit's a long story19:30
klafka1ah19:30
klafka1oh19:30
kanzureand i just got done ranting/complaining about them yesterday, so it will be a few days until i care enough to complain again19:30
klafka1ok19:31
klafka1well when you do let me know19:31
klafka1i want to know their story19:31
kanzureokie dokie19:31
klafka1since i intimately care about the state of sequencing tech19:31
klafka1so let's just remember http://kimjongillookingatthings.tumblr.com/19:33
kanzureoh man that's great19:34
kanzure☑ Kim Jong Il ☑ Khaddafi ☑ Osama Bin Laden ☑ Saddam Hussein ☐ Internet Explorer19:34
mrtrousersfunny19:35
* ybit pokes fenn_ 19:42
kanzureybit: try calling him19:42
* ybit calls fenn_ 19:43
kanzureybit: see pm19:43
ybitsee pm19:43
ybit*eeeevil*19:44
ybitkanzure: can you just hit him with a wadded sheet of paper and tell him that's from me and that he should answer my question?19:46
kanzureno19:46
kanzurehe's behind a door19:46
foucistah, you are sharing the same geolocation19:49
foucistthat explains some pecularities of this channel19:49
ybitnot all of them19:49
kanzurefoucist: most of the time, no19:50
kanzurebut the last week, yes19:50
ybiti still don't understand why kanzure tells fenn_ to roll over sometimes19:50
kanzureroll over?19:50
ybitbad joke?19:50
kanzure"bend over" would be funnier19:50
ybiti would explain the picture in my head, but i'd rather that image not be there19:51
ybithttp://www.r-tutor.com/19:52
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klafka1lol19:52
klafka1foucist it's hard to explain the pecularities of the channel19:52
klafka1ybit this seems interesting19:52
ybitklafka1: the images do19:52
klafka1also why are the images like crazy19:53
ybitthey make you think there's going to be some amazing visuals19:53
ybitmy question too19:53
klafka1i've never seen an ANOVA graph look so cool19:53
klafka1i was curious to see GPU SVM with R though19:53
klafka1anyway19:53
klafka1shower19:53
klafka1bbiaf19:53
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foucistwhat does "X has experience in mobile app, but he mostly does native app development."  mean to you20:04
foucistnative app dev = iOS ?20:04
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ybityeah, sounds like objective-c or java20:08
ybitnot mobile site development20:08
kanzurefoucist: it means he's bad at english20:10
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ybithttps://plus.google.com/108772200278976934119/posts/2xXxs3nMPaU20:31
kanzureyou are obligated to explain obfuscated links20:31
kanzureunless the context is obvious20:31
ybitnew biotech badge20:32
ybitfrom adafruit20:32
klafka1that's cool20:39
klafka1that reminds me that i just bought http://www.spacetribe.com/shop/images/JK54_M30A_XL.jpg20:42
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foucistwhat's the alternatives to phonegap?21:05
ybitmaybe alternativeto.net knows21:05
kanzurefoucist: there is no alternative21:08
kanzurekeep using it21:08
kanzurebut there's also appcelerator/titanium or whatever21:08
kanzurefoucist: if you use phonegap i can help you out bunches21:08
kanzurefoucist: what are you up to21:09
kanzurePOKEMON DIDN'T EVOLVE, GOD MADE POKEMON, DONT BELIEVE THE LIBERAL ATHEIST LIES!21:22
kanzurehttp://i.imgur.com/eXGKy.jpg21:22
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joshcryerreq: Observing the Multiexciton State in Singlet Fission and Ensuing Ultrafast Multielectron Transfer21:25
foucistkanzure: i was just at startup weekend bangkok and my team won21:29
foucistwe get to do the asian ycombinator bootcamp in singapore21:29
foucistycombinator-like21:29
foucistthe biz idea is to let people chat with others that are also watching the same TV show they are21:31
foucistoriginal name was TVeeter (TV twitter)21:31
foucistkanzure: anyways basically need to do a mobile app with twitter integration..  made good progress with jquery mobile/rails during the weekend but time to start looking at doing a proper job of it21:32
foucistdo you think phonegap is suitable for a twitter mobile app?21:32
kanzureuh.. sure21:58
kanzureyeah i don't see a problem doing that21:58
kanzurefoucist: you should meet up with http://www.justin-klein.com/22:01
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ybit#webdev #android #ios www.curl.com23:13
ybithttp://opalang.org/23:16
ybit#note-to-self23:16
* ybit throws a paper airplane at fenn_ and calls it a night23:18
ybitwas wondering if the ml-class was worth it, just in case you didn't see23:19
ybitbye now23:19
kanzureybit: he says "i don't know because i didn't do it but generally no i don't think it's worth it"23:36
kanzure"tell him to just read the book"23:36
kanzure"or better yet just read the lecture notes and look at the wikipedia articles"23:37
kanzure"i mean ml is just statistics"23:37
kanzure"statistics is boring"23:37
kanzure"but it's useful so pffrtt"23:37
kanzurei can't type the sound he made23:37
kanzure"like statistics with optimization"23:37
Utopiahybit: you can get opinions from people who did it on #ml-class23:40
--- Log closed Mon Dec 19 00:00:35 2011

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