--- Log opened Sun Dec 18 00:00:33 2011
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00:23 < strangewarp> Belatedly... 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..
00:43 < sylph_mako> http://en.wikifur.com/wiki/Puzzlebox_MUCK
00:43 < sylph_mako> strangewarp smells like someone I know. I'm pretty sure they're not him. We'll see.
00:46 < strangewarp> I'm not. I'm just a guy who arrived to the party late, and already burned out. :
00:46 < strangewarp> :P
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01:03 < strangewarp> To 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.
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01:39 < JayDugger> Good morning, everyone.
01:40 < Mariu> hey, JayDugger
01:40 < Mariu> how's it going ?
01:40 < JayDugger> All well enough.
01:41 < JayDugger> No real progress on projects of interest here, but otherwise life goes well.
01:41 < Mariu> Cool, nice to hear that.
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11:48 < Lucas_> http://www.youtube.com/watch?v=qx72xt0utm4
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13:32 < delinquentme> OMG MISSED YEW AW
13:32 < delinquentme> <3
13:39 < sylph_mako> ..?
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15:24 < ybit> hi delinquentme, sylph_mako
15:25 < ybit> hope everyone here is doing well, been awhile since i've talked with anyone
15:25 < sylph_mako> I just hung up a yule bow ^ ^
15:26 < sylph_mako> I wish a joyous yuletide festival from to you all.
15:26 < ybit> gracias y back to you
15:27 < delinquentme> ^_^
15:27  * ybit ^5s delinquentme 
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15:40 < sylph_mako> Wait a second. Yule is a winter celebration.
15:40 < sylph_mako> I live in the southern hemisphere.
15:40 < sylph_mako> It's summer.
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15:57 < delinquentme> sylph_mako, (christmas_tree)^-1
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18:11 < mrtrousers> Hello
18:11 < mrtrousers> Is there a diy way to sequence genome?
18:14 < kanzure> how diy do you want to do it
18:14 < kanzure> you can buy a dna sequencing machine
18:14 < kanzure> or you can build your own dna sequencing machine
18:14 < kanzure> or you can manually write down fluorescent colors as you see them pass by under a microscope..
18:19 < klafka1> lol
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18:34 < mrtrousers> So to lets say.. To sequence your own genome you either pay to get it done or buy a sequencer machine?
18:34 < kanzure> well, it depends on how much coverage you want
18:35 < kanzure> to a certain extent it's more efficient to just use 23andme and get a number of snps and apply that against a knonw-good genome
18:35 < kanzure> but! getting your own dna sequencer opens up a lot of other possible projects
18:36 < mrtrousers> What is 23andme? How much are sequencers running for? Any open source project on it?
18:36 < kanzure> there's at least one open source sequencer but i think its material cost is 20k
18:37 < kanzure> working, used dna sequencers from 10 years ago go for maybe 12-15k
18:37 < kanzure> new dna sequencers will cost 50k-1200k
18:38 < klafka1> 50k would be pretty cheap
18:38 < klafka1> what would that be?
18:38 < kanzure> i am making shit up
18:38 < klafka1> oh
18:38 < klafka1> lmao
18:38 < kanzure> i know that some "top of the line" models go for 700k
18:38 < klafka1> yeah
18:38 < klafka1> exactly
18:38 < kanzure> but i'm pretty sure there's some <100k models
18:38 < mrtrousers> Out of my budget.. Theres got to be a cheaper way to do it..
18:38 < klafka1> the church one is like 150k~
18:38 < klafka1> mrtrousers you can pay someone
18:38 < klafka1> what is it like 10k?
18:38 < kanzure> mrtrousers: you can just send in samples to someone
18:38 < klafka1> or so
18:38 < klafka1> still
18:38 < mrtrousers> Yup..
18:38 < kanzure> i haven't seen an order form for pgp
18:39 < kanzure> does it actually exist yet?
18:39 < klafka1> no idea
18:39 < klafka1> that's what i've heard
18:39 < kanzure> i know they have sequenced some people, but they could have just outsourced that to knome or something
18:39 < kanzure> when are you going to be in sf?
18:39 < klafka1> kanzure no i'm talking about their machines
18:39 < klafka1> tomorrow
18:39 < kanzure> ok i'm in sf tomorrow
18:39 < kanzure> what time?
18:40 < klafka1> polonator
18:40 < klafka1> umm i think i get in around 5pm
18:40 < kanzure> ah i'll be gone before then
18:40 < klafka1> ah
18:40 < kanzure> you have a place to stay?
18:40 < klafka1> the company is putting me up at a hotel
18:40 < mrtrousers> By the way.. Going around the world sequencing diferent organism genomes could be made into a job?
18:40 < kanzure> you can take my place at langton labs (where fenn sleeps)
18:41 < klafka1> oh can i stay tehre for a few months?
18:41 < klafka1> :P
18:41 < kanzure> mrtrousers: sure... check out beijing genomics institute
18:41 < kanzure> klafka1: yeah, i think they have some rooms open for rent
18:41 < klafka1> oooooh
18:41 < klafka1> really?
18:41 < klafka1> fenn_ get in here
18:41 < kanzure> pretty chill place too
18:41 < klafka1> tell me about your magic land
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18:41 < kanzure> fenn is currently ignoring irc i think
18:41 < klafka1> i wanna stay some place cheap and hopefully near caltrain if i get this job
18:42 < kanzure> this is near bart- look it up on google maps ("langton labs")
18:42 < klafka1> for like a month or two then get an apt and have the gf move out
18:42 < kanzure> are they in sf?
18:42 < mrtrousers> kanzure: interesting..
18:42 < klafka1> menlo park
18:42 < kanzure> ah lame.. langton might not be best then
18:43 < klafka1> if it's cheap it'll work
18:43 < klafka1> maybe
18:43 < kanzure> yeah i'll pester fenn to get online in a bit
18:43 < kanzure> try pm'ing him..
18:43 < klafka1> ok
18:44 < klafka1> sweet
18:44 < mrtrousers> kanzure: So lets say one sequences the genome for diferent organisms.. How do you monetize it?
18:44 < klafka1> all kinds of ways
18:44 < kanzure> uhh are you broke
18:44 < klafka1> me?
18:44 < kanzure> no
18:44 < klafka1> oh
18:44 < klafka1> heh
18:45 < klafka1> mrtrousers you don't make money so much from the sequencing
18:45 < kanzure> it's just a little unusual or someone to have to monetize a genome
18:45 < kanzure> *for someone to have to monetize a genome
18:45 < klafka1> typically places that sequence are either gov/grant funded or they do consulting work or they do lab work for hire
18:45 < klafka1> e.g. they have a big ass sequencing lab and other people pay them to sequence shit for them
18:45 < mrtrousers> You travel the world seguencing rare genomes and monetizing so you can keep doing it..
18:46 < mrtrousers> Im broke too
18:46 < klafka1> well
18:46 < klafka1> if you're craig venter
18:46 < klafka1> and own a company
18:46 < klafka1> and are rich
18:46 < klafka1> then you can do that
18:47 < mrtrousers> Did Craig Venter hit something interesting on that sailing expedition?
18:48 < kanzure> he published a few papers
18:48 < kanzure> and usually you pay a bucketload to publish a paper (unfortunately)
18:49 < klafka1> yeah
18:49 < klafka1> like 3-4k
18:49 < kanzure> klafka1: my last paper was 2k per coauthor
18:49 < kanzure> there were 11 coauthors
18:49 < klafka1> wtf
18:49 < mrtrousers> People pay to publish a paper? Really?
18:49 < klafka1> kanzure it's usually a per page cost i thought
18:49 < kanzure> mrtrousers: it's all kinds of fucked up
18:49 < kanzure> klafka1: yeah there was that too
18:49 < klafka1> kanzure it's preferable to the alternative
18:49 < klafka1> honestly
18:49 < klafka1> the current alternative
18:49 < kanzure> this was the "open access fee"
18:50 < klafka1> i maintain it's  still preferable to the alternative currently
18:52 < mrtrousers> Is there a database of currently sequenced organisms, people, etc.. ?
18:52 < klafka1> sure
18:52 < klafka1> check out pubmed.com
18:52 < klafka1> fucking  flac
18:52 < kanzure> mrtrousers: yes you can download genomes via ftp on ncbi
18:53 < mrtrousers> cool
18:53 < mrtrousers> What do you think of biobricks? Do you work with the registry of standarized parts?
18:54 < kanzure> biobricks is a nice concept but there's lots of edge cases that you run into
18:54 < kanzure> plus, i don't think they are mailing biobrick books to non-institutions at the moment
18:54 < klafka1> i haven't looked into synthetic biology
18:54 < klafka1> however i think that there are going to be lots of emergent phenomenon and epiphenomenon that occur when you try and combine a lot of them
18:55 < mrtrousers> ...
18:55 < kanzure> like "taking a random metabolic network from one organism and into another organism" might have conflicting proteomes and shit
18:55 < mrtrousers> So when you combine the parts to make more complex devices.. It wont work?
18:55 < klafka1> yes
18:55 < kanzure> or "other shit breaks"
18:55 < klafka1> yeah that's slightly more accurate
18:55 < kanzure> and then you're debugging for three or four years..
18:56 < klafka1> the things may do what you want, but they may do OTHER shit that you have no idea about
18:56 < mrtrousers> Im trying to design a biosensor from existin devices..
18:56 < kanzure> go for it
18:56 < klafka1> mrtrousers you have to remember that biological 'programming' isn't like regular programming, the program is also data is also physical
18:56 < kanzure> what are ou sensing?
18:56 < kanzure> *you
18:57 < mrtrousers> Id 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..
18:58 < kanzure> sounds like you should just express some surface protein or other object that can bind to air pollutants non-selectively
18:58 < kanzure> the problem with non-selectively..
18:59 < mrtrousers> is..
18:59 < kanzure> uh? it's non-selective and thus useless if anything can set it off
19:00 < mrtrousers> Anything that is a pollutant?
19:01 < mrtrousers> Well anyway, I need to work on it..
19:02 < mrtrousers> Klafka1: 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..
19:03 < kanzure> no not just "anything that is a pollutant" more like... anything anything
19:03 < klafka1> well 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' information
19:04 < kanzure> klafka1: i think protein-protein interactions are more relevant here
19:04 < klafka1> further mRNAs interact with each other, they compete competitively for polymerase translation
19:04 < kanzure> right
19:04 < klafka1> er
19:04 < klafka1> transcription
19:04 < klafka1> adn ribosomal translation
19:04 < klafka1> and THEN the protein end-products are physical things that can interact in emergent phenomena
19:04 < klafka1> which is the big thing i think kanzure  and I agree on
19:05 < kanzure> or other things can happen like.. pH changing drastically and killing your cell
19:05 < klafka1> yeah
19:05 < kanzure> some of this can be modelled and predicted ahead of time i think,
19:05 < kanzure> like "Oh, i'm modifying the ph stability stuff, hur dur"
19:06 < kanzure> but anything else is a guessing game
19:06 < kanzure> more probabilistic
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19:06 < klafka1> yeah
19:06 < klafka1> basically things aren't impossible but they are fucking hard and they have the ability to really go off the wall
19:07 < mrtrousers> You guys are hobyists or biology academics?
19:07 < klafka1> i'm no longer in academia but i was involved in comp bio @ in academia
19:07 < kanzure> i'm just a tortoise
19:07 < kanzure> i'm not even human
19:10 < eudoxia> Is there such a thing as an open manufacturing wiki?
19:10 < mrtrousers> There is open cource ecology..They do open hardware..
19:10 < kanzure> eudoxia: no, but there's appropedia, gvcs stuff on openfarmtech.org, old hplusroadmap wiki stuf..
19:11 < eudoxia> Oh I know that one, I was just wondering something more broad, though it would be 90% OSE
19:11 < kanzure> there's also wikipedia
19:14 < mrtrousers> Can I make silly questions?
19:14 < kanzure> silly questions are the best kind..
19:14 < klafka1> sure
19:15 < mrtrousers> If 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 < kanzure> statistics
19:15 < kanzure> most members of a population have the same genome and just have different alleles
19:16 < mrtrousers> So when they sample bees, they dont just do one, they do lots..
19:17 < klafka1> eh it's more like typically they try and take a 'normal' member of a species
19:17 < klafka1> and sequence it's genome
19:18 < kanzure> eudoxia: feel free to talk in here..
19:18 < kanzure> instead of separately..
19:18 < klafka1> you have to understand that genome sequencing itself is a very probabilistic thing as well, each base pair is determined typically with some margin of error
19:18 < klafka1> 99% of a species genome is the same and it's a set of SNPs that separate individuals
19:19 < kanzure> and 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 < klafka1> yep
19:20 < mrtrousers> Iv 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 < ybit> fenn_: do you think the ml-class was worth your time?
19:20 < kanzure> ybit: i just saw him walk in.. klafka has dibbs on him first
19:20 < kanzure> let me pester him
19:21 < klafka1> mrtrousers by looking at overlap
19:21 < klafka1> it's a fairly classic substring reconstruction problem
19:22 < mrtrousers> Ok
19:22 < klafka1> for 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 < klafka1> or um you can do denovo sequencing with just NGS but it requires very very high coverage
19:23 < mrtrousers> Do you think laptops will incorporate labonachips to run experiments in the near future?
19:24 < eudoxia> that would be a mildly expensive adon
19:24 < eudoxia> addon*
19:24 < klafka1> er um
19:24 < klafka1> why would a laptop have a lab on a chip?
19:25 < kanzure> fenn is currently ignoring the interwebs
19:25 < mrtrousers> Dont know yet..
19:25 < eudoxia> while we're at it, we could also add a scanning probe and an electron microscope
19:25 < mrtrousers> So you could run experiments on the fly, read genomes, etc..
19:25 < kanzure> direct dna sequencing with electron microscopy is another technique, although not ready for commercial use
19:26 < mrtrousers> Or.. Would there be a day where you code something on a computer and something is grown on a petri?
19:26 < klafka1> kanzure who is doing that?
19:26 < eudoxia> I wonder if you could sequence DNA with an atomic force microscope...
19:26 < kanzure> mrtrousers: why? do you need that
19:26 < kanzure> klafka1: halcyon molecular
19:26 < klafka1> mrtrousers this is slightly beyond near future
19:26 < kanzure> eudoxia: yeah.. you can
19:26 < klafka1> more like 5+ years at least
19:27 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/
19:27 < klafka1> man kanzure  i boought pacbio stock
19:27 < kanzure> http://diyhpl.us/~bryan/papers2/AFM/
19:27 < klafka1> i hope they aren't tanking lately
19:27 < kanzure> pacbio will probably end up on top
19:27 < klafka1> i think they had a rough patch
19:27 < klafka1> but they have solid tech
19:27 < klafka1> don't you agree?
19:27 < klafka1> wow halcyon hasn't had an update since Nov 2010
19:28 < klafka1> that's not good at all
19:28 < kanzure> they aren't a website company
19:28 < kanzure> kim jong is dead
19:28 < kanzure> everybody hide under your desk!
19:29 < klafka1> well i guess they are still around
19:29 < klafka1> they are hiring a help desk admin
19:29 < klafka1> kanzure just growing startups usually have regular news blurbs, are hiring, have jobs posted on their sites, etc...
19:30 < klafka1> but anyway they are still doing well?
19:30 < klafka1> are they sort of flying under the radar atm while they dev?
19:30 < kanzure> uhrm
19:30 < kanzure> it's a long story
19:30 < klafka1> ah
19:30 < klafka1> oh
19:30 < kanzure> and i just got done ranting/complaining about them yesterday, so it will be a few days until i care enough to complain again
19:31 < klafka1> ok
19:31 < klafka1> well when you do let me know
19:31 < klafka1> i want to know their story
19:31 < kanzure> okie dokie
19:31 < klafka1> since i intimately care about the state of sequencing tech
19:33 < klafka1> so let's just remember http://kimjongillookingatthings.tumblr.com/
19:34 < kanzure> oh man that's great
19:34 < kanzure> ☑ Kim Jong Il ☑ Khaddafi ☑ Osama Bin Laden ☑ Saddam Hussein ☐ Internet Explorer
19:35 < mrtrousers> funny
19:42  * ybit pokes fenn_ 
19:42 < kanzure> ybit: try calling him
19:43  * ybit calls fenn_ 
19:43 < kanzure> ybit: see pm
19:43 < ybit> see pm
19:44 < ybit> *eeeevil*
19:46 < ybit> kanzure: 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 < kanzure> no
19:46 < kanzure> he's behind a door
19:49 < foucist> ah, you are sharing the same geolocation
19:49 < foucist> that explains some pecularities of this channel
19:49 < ybit> not all of them
19:50 < kanzure> foucist: most of the time, no
19:50 < kanzure> but the last week, yes
19:50 < ybit> i still don't understand why kanzure tells fenn_ to roll over sometimes
19:50 < kanzure> roll over?
19:50 < ybit> bad joke?
19:50 < kanzure> "bend over" would be funnier
19:51 < ybit> i would explain the picture in my head, but i'd rather that image not be there
19:52 < ybit> http://www.r-tutor.com/
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19:52 < klafka1> lol
19:52 < klafka1> foucist it's hard to explain the pecularities of the channel
19:52 < klafka1> ybit this seems interesting
19:52 < ybit> klafka1: the images do
19:53 < klafka1> also why are the images like crazy
19:53 < ybit> they make you think there's going to be some amazing visuals
19:53 < ybit> my question too
19:53 < klafka1> i've never seen an ANOVA graph look so cool
19:53 < klafka1> i was curious to see GPU SVM with R though
19:53 < klafka1> anyway
19:53 < klafka1> shower
19:53 < klafka1> bbiaf
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20:04 < foucist> what does "X has experience in mobile app, but he mostly does native app development."  mean to you
20:04 < foucist> native app dev = iOS ?
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20:08 < ybit> yeah, sounds like objective-c or java
20:08 < ybit> not mobile site development
20:10 < kanzure> foucist: it means he's bad at english
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20:31 < ybit> https://plus.google.com/108772200278976934119/posts/2xXxs3nMPaU
20:31 < kanzure> you are obligated to explain obfuscated links
20:31 < kanzure> unless the context is obvious
20:32 < ybit> new biotech badge
20:32 < ybit> from adafruit
20:39 < klafka1> that's cool
20:42 < klafka1> that reminds me that i just bought http://www.spacetribe.com/shop/images/JK54_M30A_XL.jpg
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21:05 < foucist> what's the alternatives to phonegap?
21:05 < ybit> maybe alternativeto.net knows
21:08 < kanzure> foucist: there is no alternative
21:08 < kanzure> keep using it
21:08 < kanzure> but there's also appcelerator/titanium or whatever
21:08 < kanzure> foucist: if you use phonegap i can help you out bunches
21:09 < kanzure> foucist: what are you up to
21:22 < kanzure> POKEMON DIDN'T EVOLVE, GOD MADE POKEMON, DONT BELIEVE THE LIBERAL ATHEIST LIES!
21:22 < kanzure> http://i.imgur.com/eXGKy.jpg
21:25 -!- joshcryer [~g@unaffiliated/joshcryer] has joined ##hplusroadmap
21:25 < joshcryer> req: Observing the Multiexciton State in Singlet Fission and Ensuing Ultrafast Multielectron Transfer
21:29 < foucist> kanzure: i was just at startup weekend bangkok and my team won
21:29 < foucist> we get to do the asian ycombinator bootcamp in singapore
21:29 < foucist> ycombinator-like
21:31 < foucist> the biz idea is to let people chat with others that are also watching the same TV show they are
21:31 < foucist> original name was TVeeter (TV twitter)
21:32 < foucist> kanzure: 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 it
21:32 < foucist> do you think phonegap is suitable for a twitter mobile app?
21:58 < kanzure> uh.. sure
21:58 < kanzure> yeah i don't see a problem doing that
22:01 < kanzure> foucist: you should meet up with http://www.justin-klein.com/
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23:13 < ybit> #webdev #android #ios www.curl.com
23:16 < ybit> http://opalang.org/
23:16 < ybit> #note-to-self
23:18  * ybit throws a paper airplane at fenn_ and calls it a night
23:19 < ybit> was wondering if the ml-class was worth it, just in case you didn't see
23:19 < ybit> bye now
23:36 < kanzure> ybit: 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"
23:37 < 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 < kanzure> i can't type the sound he made
23:37 < kanzure> "like statistics with optimization"
23:40 < Utopiah> ybit: you can get opinions from people who did it on #ml-class
--- Log closed Mon Dec 19 00:00:35 2011