2010-05-21.log

--- Day changed Fri May 21 2010
klafkano it's shipping00:00
klafkaatm00:00
klafkaheh i saw george church talk earlier this year00:00
kanzurefenn: how can i fix that00:00
kanzureis paypal too terrible?00:00
klafkahe's all about being "open" without being really open00:00
kanzureso he's fo-open00:00
kanzurehe's bropen, or broken00:00
klafkahaha00:00
neobiifauxpen00:00
klafkalike he's doing this http://www.personalgenomes.org/00:00
fenn"so how do you pay the bills?" "oh i work for a secret romanian countess desiring of immortality, who i've never met or know anything at all about"00:00
kanzureamong other things00:01
kanzurewhat's your point?00:01
neobiihey look00:01
neobiiare you a rail developer?00:01
klafkawow really?00:01
kanzureno go away00:01
fennwell, a budget would be a start00:01
klafkakanzure that's kind of awesome00:01
neobiihaha it says it on thatp age00:01
kanzureklafka: thanks, at least one of us thinks so00:01
klafkabut like that site is church's, he wants to sequence 100,000 people's genomes00:02
klafkaand has started already00:02
klafkabut notice, none of the data is out there00:02
klafkawhere the fuck is your open data00:02
klafkageorge00:02
kanzureklafka: it's a well known fact that the incumbents are full of it00:02
fennkanzure also, while i appreciate the money, it's not anywhere close to any other option in terms of sheer numbers00:02
kanzurehm00:03
fennguh. i hate talking about this kind of thing00:03
kanzureso does it need a few more digits?00:03
fennyeah00:03
kanzureok. how many.00:03
kanzure(in total)00:03
fenndepends on the time period00:03
kanzureklafka: so yeah, i have funding for crazy projects00:03
klafkaoh wow00:04
klafkaso i take it back00:04
kanzurei'm not allowed to pay for food or stuff for just me like that00:04
klafkahe is in fact making the data public00:04
klafkahttp://www.personalgenomes.org/public/3.html00:04
klafkahttp://www.personalgenomes.org/public/00:04
fennopportunity cost: I can make $40k/yr at minimum on like any "real" job out there00:04
kanzurereality check: you won't00:04
fennO RLY00:04
klafkaone of them is steven pinker too00:04
kanzureor shouldn't :/00:04
fennalso i dont understand why (if?) hackerspace membership dues "don't count"00:05
kanzurewhy are they charging you anyway?00:06
klafkakanzure i want to make an open NGS bio repository that aims to package bio data in ways that ML people can easily use and facilitate cross-communicatoin and collaboration between ML and BIO people00:06
klafkayou can fund that if you wan00:06
klafkat00:06
klafka:)00:06
fennrent.. stuff.00:06
klafkayeah00:06
fennwhy does anything cost anything?00:06
kanzureOR free rent with me? but i'm boring ;)00:06
kanzureoh wait you mean the hackerspace00:06
klafkano rent for the hackerspace00:06
fenntbh i could probably just show up every day and not pay dues and nobody would notice00:07
kanzurei hate recurring payments00:07
klafkaAs a result of system improvements, the current sell price is 170,000 USD.00:07
kanzureor recurring costs or whatever you call them00:07
fennor move to SF and go to noisebridge which is hostile to the concept of dues00:07
klafkacome on a polonator is only 170 grand00:07
klafkanoisebridge doesn't have dues?00:07
klafkajust donations?00:07
kanzurelike at $100/mo, in 50 years that's $60k00:08
fennbut the talent of people you run into at the dojo is higher than random person in noisebridge00:08
fenn50 years is a long time00:08
klafkawhat's wrong with that kanzure 00:08
kanzurei am still thinking like a broke guy00:08
klafkathey are going to have to pay rent every month of those 50 years00:08
kanzureit's weird00:08
fennnoisebridge dues are $80/mo but there's no obligation to be a member00:09
fennrent is stupid, there's no answer00:09
fennif it's not rent it's taxes00:09
fennrent is basically taxes, that's how i think of it00:09
kanzureare they going to tax the string in your pocket00:09
fennyeah00:09
fennused to be you had to pay x amount of grain or whatever, regardless if you had any growing in your field00:10
fennif not you got beat up or something00:10
kanzureand now you get .. confused?00:10
fenni'm confused00:11
kanzurehave i shown you project projector yet?00:12
kanzurehttp://adl.serveftp.org:8091/projector/projects/ (DON'T click "run" because it really sends out text messages)00:12
fennmaybe, i get the idea00:12
fennit's like "manna"00:12
fennbut with cellphones00:12
kanzureit's kind of like my startup pyramid scheme00:12
kanzurebasically i get 10 people excited00:12
kanzureand they get 10 other people excited00:12
kanzurethere's no exit strategy or monetization yet, but i'm super excited about it00:12
fenndid you read "manna"? http://marshallbrain.com/manna1.htm00:13
kanzureno. is it a short story or a novel?00:13
fenni think you need to make gantt charts00:13
kanzurewhy00:13
kanzureoh you mean on the site00:13
kanzureyes00:13
fennmanna is like 10 short chapters00:13
fenngantt charts would force you to explicitly state the dependencies of each task so they can be parallelized.. that's what gantt charts are for00:14
kanzurei bought up promisepyramid.com today for this project actually00:14
fennew00:14
kanzure"i'll do x if 2 of my friends do y"00:14
kanzurehttp://getupandmove.me/00:15
klafkainteresting00:15
kanzureyay for pyramid schemes00:15
fenndouble ew00:15
kanzure:/00:15
kanzurethat's what all this ycombinator / capital factory startup stuff is about00:15
kanzurepyramids of excitement00:15
fennycombinator funds some cool stuff00:15
kanzureyep00:15
kanzuregetupandmove.me is one of their latest00:15
fennoh.00:15
klafkaalll of this web 2.0 stuff does just feel a bit like the internet wanking itself off00:17
kanzureyep00:17
kanzurehttp://capitalfactory.com/ is dumping some money into a startup i'm a part of for an iphone app00:18
kanzurewe have like 50 competitors00:18
fennevery time you dis on ycombinator, a cute young white boy with a macbook dies00:18
kanzurehackers don't use mac00:18
kanzureor.. oh no00:18
neobiithey use rails00:19
kanzurewho does00:19
fenni'm so sick of hearing about "startups"00:20
fenncan't you just say "i'm working at a small business"00:20
kanzurenvm00:20
fenn"i'm running a website"00:20
klafkalol00:20
kanzurewell, actually, a small business is more accurate here00:20
kanzurethese guys haven't a clue about startups00:20
fennwtf is a startup00:20
kanzurei mean.. i keep pointing them to paul graham's articles00:20
kanzurefenn: usually something that is venture backed00:20
klafkalol00:20
fennguh00:21
kanzureat first they wanted to spend all of the capfac money on salaries00:21
kanzureand you DON'T do that with a startup00:21
fennits not like people dont invest in businesses00:21
klafkaLOL00:21
neobiiyeah it's easy for webstartups too00:21
neobiibecause almost 0 overhead00:21
kanzureneobii: are you foreign?00:21
neobiino dude I live in dallas00:21
kanzurewtf00:21
fennhe's a txtr00:22
kanzureare you high?00:22
neobiiwhat?00:22
Utopiahnice conf on startups btw http://steveblank.com/2010/04/15/why-accountants-dont-run-startups/ (yes, just to be annoying)00:22
neobiiI told you I went canoeing in austin haha00:22
kanzurefenn: i feel kind of bad that i've been running around doing all this random programming that isn't directly related to what i actually want to be doing00:22
kanzuredoes this make me a sellout?00:22
fennno it makes you a whore00:23
fennit's subtly different00:23
neobiiI'm a sellout :-(00:25
neobiiI made a bible verse memory flash app for one crazy religious dude00:25
kanzurei don't like how my email rate has gone down the past two months00:26
neobiiwe linked him to csszengarden00:26
kanzurelike, actual content00:26
kanzureand #hplusroadmap has been somewhat quiet00:26
neobiiand he said he wouldn't go because of the "zen" part00:26
klafkahahaha00:26
kanzurecsszengarden is over rated00:26
neobiiyeah it's a common place to show peeps00:27
fenni've been busy making Actual Hardware (tm)00:27
kanzurei saw dave's "actual hardware"00:27
fenndid i mention i had the reprap moving (sorta)00:27
kanzureit's basically just a few bikes laying around next to a bridgeport00:27
fennhey now! thems fightin words00:27
kanzurewhere did lepton go?00:28
klafkahaha00:28
fenneverybody expects some discovery channel robotic factory00:28
fennklafka: are you high? :P00:28
klafkaalso can you make led embedded devices w/ a reprap?00:28
klafkanot really00:29
klafkathat would be neat00:29
kanzureklafka is just an academician00:29
kanzurea grad student i think?00:29
klafkayeah00:29
kanzureyeah, so that should explain it00:29
fenni need to make a bike blinky, i think i'm going to do that as the next non-reprap printed part00:29
kanzurebut actually you're not so bad as far as grad students go00:29
kanzureor at least as they tend to go00:29
klafkahaha howso?00:29
neobiido you have a reprap kanzure?00:30
kanzureneobii: no00:30
kanzurei don't know if i want one or not00:30
fennyou do00:30
kanzurei don't want a makerbot, i know that much00:30
fennit's so much easier than figuring out how to clamp shit on the cnc00:31
kanzureso hey, we have all this equipment laying around00:31
kanzurebetween dave and me00:31
kanzurelaser cutters, cnc machines, drill presses, the mechmate (ok ok it hasn't been worked on in forever)00:31
kanzureand free access to a waterjet cutter00:31
kanzureand a few SLS machines too00:31
fennk, now what00:31
kanzureso why isn't anything happening00:31
kanzurewhy ain't designs for open source dna synthesizers flowing out my ass00:32
fennwell?00:32
-!- genehacker [~genehacke@pool-173-57-40-144.dllstx.fios.verizon.net] has joined #hplusroadmap00:32
fenndont need access to tools to make designs00:32
fennwhy arent you hiring chinese grad students00:32
neobiihey dallas texas00:32
kanzurei don't know any chinese grad students00:32
kanzureso.. that's why i guess?00:32
genehackerhey00:33
kanzurei can't think of any other reason00:33
genehackerwhat?00:33
kanzuregenehacker: what about you00:33
fennhow about indians in call centers00:33
kanzurewhy aren't you making me designs00:33
klafkayeah come on00:33
klafkaopen source dna sequencers00:33
fennheh genehacker has no excuse00:33
klafkalet's get to it00:33
genehackerI'm making one kanzure00:33
kanzureklafka: out of curiosity, have you read the channel logs?00:33
klafkano00:33
kanzurefenn: on second thought, genehacker is notoriously bad at documenting designs00:34
klafkareading channel logs is a lot of work00:34
kanzuretrue that00:34
fenni havent seen him design anything00:34
fennsome pig catapult, if that counts00:34
genehackerok then you want my fluidic sound amplifier that can probably be laser cut?00:34
fenndon't we have a list of word frequency?00:34
kanzurefenn: you have one on fennetic.net00:35
kanzureit turns up in my search results all the time00:35
fennoh right, the pneumatic stepper was pretty cool00:35
genehackerI need to know what bolt sizes you have on hand before I can send it to you00:35
genehackerit's not finished yet00:35
genehackerI stopped development when the gada prize came out00:35
fennah so i do: http://fennetic.net/pub/irc/histo300:35
genehackerwith their 60 watt power limit00:35
kanzureklafka: this might be interesting: http://designfiles.org/~bryan/youtube_videos_from_irc_channel/00:35
fennjust google the first thing you think of and you've probably already said it/done something with it00:36
genehackerI'm working on something secret00:36
klafkainteresting00:36
kanzurefenn: does that make me a keyword squatter?00:36
neobiikeywords would be: rails00:36
genehackeralso I'll hopefully do some research with the SLS people here00:36
fennhm need to filter out ip hostnames from that list00:36
kanzuregenehacker: i'm doing a "startup" with two of the SLS grad students working for dr. beaman00:37
genehackerkanzure do you have any limits to what I can put on design files?00:37
kanzureso if you want it, you should meet with tim silverman and vikram dearajan00:37
kanzure*vikram devarajan00:37
kanzureput on design files? what do you mean.. on?00:37
kanzureoh you mean the server00:38
kanzurenot on files that contain designs00:38
kanzure*sigh*00:38
fennwow, "origami" was mentioned 42 times, versus 35 for "fuck" 00:38
kanzureyeah there's limits. no porn.00:38
kanzurefuck fuck fuck fuck fuck00:38
kanzurefuck fuck fuck fuck fuck00:38
fennok now they're even00:38
genehackersomething that'd get thingiverse in big trouble, no porn00:38
genehackera working SILEX device that can be built by an amateur00:38
klafka    241 DNA00:39
fenngenehacker: make a hello kitty handgun00:39
fennreprappable*00:39
genehackerYOUR WISH IS MY COMMAND00:39
genehackerbut seriously a SILEX device for refining uranium in your home00:39
genehackerSILEX works now00:39
gnusha_origami origami origami origami origami00:39
gnusha_origami origami origami origami origami00:39
-!- You're now known as gnusha00:40
genehackerorigami hand gun that shoots papercranes?00:40
fennhttp://onastick.net/sitz/images/00:40
klafkatimtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi ti00:40
klafkamtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi timtowtdi 00:40
genehackerit's impossible to print a hand gun fenn, not even printable ceramics can hold the pressures00:40
klafkawhy can't you print metal yet?00:41
genehackerreprap can't00:41
klafka:(00:41
fenngenehacker: that's an untested assumption00:41
klafkaalso can reprap do heterogenous materials yet?00:41
fennthe "cant hold pressures" thing anyway00:41
fennthey used to make cannons out of brass for fuck's sake00:41
genehackererr... I have moral problems with making pistols for reprap, it might get reprap in trouble and I can't allow that00:42
fennanyway i've seen designs for crappy homemade pistols out of 1/4" water pipe00:42
fenngenehacker: hence why i suggested it00:42
fennin the meantime, you may peruse http://glassdildome.com/00:43
klafkalol00:43
genehackerbut a SILEX device can also be used for plenty of moral things like bootstrapping nuclear power development, and since SILEX works we're all screwed anyway00:43
fenner, what is SILEX?00:44
fennoh, uranium enrichment00:44
fennpff00:45
genehackera uranium enrichment process that is magnitudes more efficient than other methods00:45
kanzureso anyway00:45
kanzurefenn: any other ideas for where to source designers00:45
kanzurei really want someone (or even me) to do an openscad solid geometry output plugin00:45
fenniceland00:45
genehackerhome CO2 lasers and a special excitable medium might allow one to do it in ones home00:45
kanzurethen maybe i'll pay a few of the makerbot/openscad (ab)users to do design stuff? i don't know00:45
fennand other nordic countries00:46
kanzureit's not like i can't do it, but00:46
kanzureblah00:46
fennplaces where they still teach math00:46
kanzuremy sense of development cycles for hardware is all out of whack00:46
kanzurewhy the fuck has mechmate taken more than 1.5 years00:46
kanzureis this.. normal?00:46
fennbecause paying work keeps getting in the way00:46
fennyes, unfortunately00:46
fennwhy the fuck has hextatic taken >5 years00:47
kanzuredepression?00:47
kanzurei can do software prototyping fairly quickly00:47
kanzurebut hardware prototyping seems to take me much longer00:47
fennit's that damned reality loop00:47
genehackerbecause hardware prototyping takes longer00:47
kanzurei don't think it necessarily has to, though00:47
genehackeralso it's the real world00:47
kanzurei mean, technically, the cnc machines only take a few minutes to run00:47
fennand only hours to set up00:48
genehackercutting what?00:48
kanzurehours to setup is fine in comparison to 1.5 years00:48
fenni actually have a bit of data on this00:48
kanzurei don't know why i am fixating on the mechmate example, but it seems releant00:48
kanzure*relevant00:48
genehackerlast I heard, ultrafast aerospace CNC machines sometimes run for weeks on end cutting one part00:48
kanzurewhat are the tolerances they are doing?00:48
fenn1325 1424 project mini-mendel-cad-idler-brackets00:48
fenn1424 1446 net reprap-irc00:48
fenn1446 1534 project mini-mendel-cad-idler-brackets00:48
fenn1534 1600 project mini-mendel-cam-idler-brackets00:48
fenn1600 1716 fight mach3, stupid tool-table-error, project mini-mendel-cnc-idler-brackets00:48
fenn1716 1844 project mini-mendel-cnc-idler-brackets00:49
genehackerprobably fairly high in titanium00:49
genehackerI know my friend runs his CNC machine over night cutting aluminum00:49
kanzurei honeslty don't think the cutting time is the issue, genehacker 00:49
genehackererr not his00:49
kanzureif it takes all night to bake, that's fine, let it bake00:49
genehackerof course not00:49
fennif i had had an openscad model of the part, and a makerbot, would have been < 5 minutes human attention and <25 minutes total00:49
kanzurei wish i could get over my aversion to stl00:50
kanzurewait, no i don't00:50
genehackeryou could go back in time and force the man who created stl for his research project in one night to actually make it not suck00:51
genehackeryou could also get in on the development of .stl200:51
kanzurewhy not just use solid geometry model formats00:51
kanzurei know that their formats are largely undocumented, but that's no excuse for avoiding the issue entirely00:52
kanzureundocumented in an accessible way00:52
kanzureer, un(documented in an accessible way)00:52
fenna bit of explanation of above: 2.25hr reverse engineering, 0.5hr clicking lots with a mouse, 1.25hr debugging the toolchain, 1.5hr actually cutting parts and figuring out clamping and stuff, 15 minutes to actually cut the parts00:52
genehackerI don't know, because some stuff that get's stereolithographed is too complex for that00:52
kanzurestl is just triangles, sorry00:52
fennnothing wrong with stl00:53
fennit's just not what we want00:53
fenneven step kinda sucks for modification00:53
kanzure:/00:53
fennno parametric anything, no geometric primitives00:53
fenncan't undo a subtraction operation00:53
* kanzure is still confused about the parametric issues re: step00:53
kanzurebut my questions will probably never find themselves answers00:53
fennafaik it's just a boundary representation with trimmed surfaces00:54
fenni could be wrong00:54
kanzureat this point i'd be happy with a csg format00:54
fennyeah csg + fillet modifiers00:54
fennopenscad is not bad00:55
fenni wish it had a geometry explorer like opencascade00:55
kanzureit's a format lock-in00:55
genehackeranyway kanzure you would host a methlab on chip on design files right00:55
kanzuretim schmidt was in here the other day saying that you could just manually read .scad files and repeat the actions in a CAD app00:55
kanzurebut frankly that's terrible00:55
genehackeractually I don't mean methlab I mean microscale adderol factory00:56
kanzuregenehacker: yes00:56
genehackerok then00:56
fennnot really.. as long as you have an understandable format to port to, you can just link the openscad functions to whatever bindings for your format00:56
fenni dont mean by hand00:56
kanzuresure00:56
kanzurebut why hasn't this been done yet?00:56
fenni was thinking about how to convert openscad to step the other day00:56
fennthere arent many people working with openscad in the first place00:57
kanzureopencascade's source code, sadly, has the most complete spec of STEP available00:57
genehackerhmmmm... we still need a special plasma reactor thing to make such complex microreactors though...00:57
fennfrankly i think it'd be better to use POV-RAY and figure out how to export to STL00:57
kanzurefenn: there's a good number of them there makerbot people00:57
fennbut maybe openscad has an advantage in simplicity00:57
kanzurethe makerbot/make people are just eating openscad up like crazies00:57
fennthey are?00:57
kanzurePaola Di Maio, Britton Kerin, Jerry Isdale, Marius Kintel, Zach Smith, Bre Pettis, Aaron Shaw, Steve Talent, Giles Bathgate, Clifford Wolf, the list goes on and on00:58
klafkawhat is the makerbot vs. reprap?00:58
fennmakerbot is a laser cut reprap00:58
kanzuremakerbot is a commercial product based on some modified designs of the cupcakecnc version of reprap00:58
klafkaaah00:58
fennthere was some drama involved00:58
klafkalol why?00:58
klafkabecause they commercialified it00:59
kanzureno00:59
fennabsconding with rrrf donations00:59
klafkaaaaaah00:59
kanzurewait really?00:59
genehackerso could you make some way to manipulate openscad files so openscad has true smart dimensions like other cad software00:59
fennbeing generally dickheaded in decisions leading up to commercialization00:59
genehackerRAGE!00:59
fenni.e. the whole sanguino/smt stepper driver thing00:59
klafkawow 1000 bucks for a reprap seems cheap01:00
fennreprap project has some leadership issues01:00
genehackerdoes sebastien know about this?01:00
fennklafka wanna buy one? :P01:00
klafkaseems small though01:00
klafkanot really01:00
fenni am going to be selling REAL repraps for <$1k01:00
klafkai really don't have time to do maker things01:00
klafkawhat's the diff between a reprap and makerbot?01:00
klafkamuch bigger?01:00
fenn(not that there's any functional difference)01:00
fennit's easier to hack on a reprap because you can modify any part01:01
genehackerfenn are they not going suck like techzonestore's ripoff reprap?01:01
klafkaaah01:01
fennomg no01:01
klafkagrad schoo lreally kills all my time to do fun maker things01:01
genehackerthey used the wrong chips...01:01
fenni so want to delete that "electronics modifications" wiki page01:01
klafkai haven't even been to the hackerspace here01:01
kanzurei still think this might be a good start at parsing step: http://designfiles.org/~bryan/step_importer.py01:01
kanzurebarring that, there are some generic EXPRESS parsers out there IIRC (at least one)01:01
fennyeah the nist stuff01:02
fenngood luck figuring that out01:02
kanzurealso here was my attempt at what a good csg library for python would feel like: http://designfiles.org/~bryan/csg.py01:02
klafkaalthough i'd be interested if there were interesting machine learning problems in the maker community01:02
fenni think EXPRESS is basically XML before there was such a thing01:02
kanzureklafka: sure! tons re: open source hardware compatibility, design, etc.01:02
-!- wolfspraul [~wolfsprau@lucia.q-ag.de] has joined #hplusroadmap01:02
klafkacan they be phrased in such  a way i don01:02
klafkaer01:02
klafkaok let me start over, can they be phrased in such a way i don't have to dig too deep into the field to find the answer01:03
fennyea i dont think it'd be hard to make python bindings for openscad01:03
klafkalike if you can give me a well defined problem maybe i could solve01:03
klafkaor problem my advisor would be interested in01:03
klafkathat would be super keen actually01:03
kanzureklafka: does your advisor have any interest in microfluidics?01:03
kanzurewait, who is your advisor? can you let me stlak him for a bit01:04
klafkanot really, he works a lot in imaging, more generally we both like high tree-width/high dimensional graphical models01:04
fennklafka: it's not machine learning but optimization of geometry for minimum amount of plastic for maximum rigidity01:04
klafkahttp://people.rit.edu/jcdicsa/01:04
neobiikanzure: could you print out something if someone gave you a stl?01:04
fenngiven a few interfaces and forces on them01:04
kanzureneobii: yes but i'd have to use someone else's machine01:05
klafkafenn are they optimization problems you have to solve numerous times?01:05
klafkalike real time optimization solving01:05
klafkait seems like a min max problem eh?01:05
kanzureklafka: that sounds more like the problem domain that CAM tries to solve01:05
neobiiwhat's keeping you from making a reprap machine?01:05
fenni saw something with level set but i didnt really understand it01:05
klafkais it linear? convex? 01:05
genehackeroh man this is hilarious, everyone in the media's flipping out over Craig Venter's let's synthesize a genome that's found in nature, slap some watermarks on it, and put it in an organism and boot it up01:07
klafkai know genehacker 01:07
klafkait's a bit ridiculous01:07
klafkathey did a bit more than that though didn't they?01:07
neobiihehe I read that article and that's how I ended up here01:07
kanzureklafka: yeah they had some neat techniques01:07
genehackernope01:07
klafkadidn't they cut a bunch of extraneous genes out of it?01:07
kanzureklafka: 01:07
kanzureklafka: - one-step, isothermal assembly of DNA in vitro:01:07
kanzurehttp://www.ncbi.nlm.nih.gov/pubmed/19363495?dopt=Citation01:07
genehackernope01:07
klafkatheir point was to make the minimum necessary genome for life01:07
kanzure- whole assembly of oligo-tiles into genes in yeast spheroplasts:01:08
kanzurehttp://www.ncbi.nlm.nih.gov/pubmed/19745056?dopt=Citation01:08
genehackeronly one on accident01:08
klafkahttp://en.wikipedia.org/wiki/Mycoplasma_laboratorium01:08
genehackercool stuff though01:08
genehackernope01:08
kanzureno this wasn't the minimal genome project01:08
klafkaoh it's not htat guy01:08
klafkawow that's even less impressive01:08
genehackerthey haven't booted up Mycoplasma laboratorium01:08
genehackerit is that guy01:08
genehackerif you mean venter01:08
klafkano i mean it's not mycoplasma laboratorium01:08
klafkai know it's venter01:08
klafkaventer likes to plaster his name on everything01:08
genehackeryup even in the genomes of bacteria01:09
kanzureyou would too if the media portrayed you as some sort of demigod of synthetic biology01:09
genehackerwell apparently I have to go to bed, because I have to get on a "normal" sleep schedule01:09
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kanzurefor some reason drew endy always seemed to have the same "hype sense" that i get from ycombinator crowds :/01:10
zoolhi01:10
kanzurehave you guys noticed how drew hasn't had as much media attention?01:10
kanzurei think his lab was sent to stanford because of some ah, issues01:10
klafkaycombinator message boards are  a pit kind of01:10
kanzurehttp://allyourstartuparebelongto.us/01:10
genehackerPLEASE RESUME NORMAL CONVERSATION01:10
klafkalol01:10
klafkafenn i'm still interested in this thing " <fenn> klafka: it's not machine learning but optimization of geometry for minimum amount of plastic for maximum rigidity " got any more info on it? 01:11
neobiiwere you part of the reprap machine display at maker fair last year?01:12
fennyes i'm searching for the page01:12
klafkabecause one thing we're thinking of working on is a way to work on a project that is a way of optimizing optimization problems so that they are more effeective for stuff like real time optimizations01:12
klafkaok01:12
kanzureyo dawg i heard you like optimization so i'm optimizing your optimization optimization algorithm so you can optimize while you optimize your optimized optimizations01:12
fennklafka google for calculix optimization01:13
klafkayo dawg i heard you liked optimization so i'm optimizing your optimization so you can optimize while you optimize01:13
fennand look at http://www.onlinefeasolver.com/load_path.php01:13
fenni dont remember the level set paper but it yielded 3d meshes looking sort of like those diagrams01:13
klafkaoh so it's finite element analysis01:14
genehackerI'll post some research related to this01:14
klafkathere are all these posters on this shit in the applied science and technology peoples stuff01:14
genehackerthere's a researcher here doing exactly that fenn01:14
fennok well add "how to actually make it" on top of that01:15
klafkaso you want the optimal geometric structure that minimizes i guess volume while maximizing rigidty01:16
genehackerROBUST DESIGN OF CELLULAR MATERIALS WITH01:16
genehackerTOPOLOGICAL AND DIMENSIONAL IMPERFECTIONS01:16
fennyep and also satisfy various other constraints01:16
genehackergoogle scholar that 01:16
klafkahmm and you give what as inputs? the dimensions you want it to be? and rigidity in a given dimension/dimensions?01:16
fennoh seepersad finally decided to do something worthwhile?01:17
genehackeryou know seepersad?01:17
fennthe name got stuck in my head at one point so i investigated01:17
fennit's right down the hall from ADL01:18
kanzure"due diligence"01:18
kanzurei need to find some chinese solidworks users to hire and abuse01:18
genehackerfar better idea than openscad people01:18
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kanzurewtf is up with his part message anyway01:19
fenni dont think the cellular materials thing is what i'm talking about01:19
kanzurei am also interested in somehow fixing the temporal discrepancy in hardware construction that i've been observing.. fixing it seems, uh, valuable01:20
fenni mean stuff like http://www.nextnature.net/2007/10/bone-chair/01:20
klafkai think if you could give me the optimization problem a bit more abstractly as opposed to learn about dimensional analysis, rigidity, etc... then it would be workable, or is the problem in developing the optimization problem itself?01:21
fennmore abstractly? that's the first time i've heard that excuse01:21
klafkareally? talk with more mathematicians01:22
klafka:P01:22
fenni have a set of interfaces, i want to connect them together without wasting material01:22
fennautomatically generate plausible geometry that doesn't suck01:22
kanzurei've been working with a mathematician recently on some, uh, web development.. and he wants to do all these latex whitepapers on tag clouds before implementing a simple weighted tag cloud01:22
fenni dont really know how to make this more abstract01:22
* kanzure doesn't get it01:22
klafkaok, do you have the actual physics equations you would need to optimize for that though fenn? 01:23
klafkalike ok let's take a chair01:23
fenn"implement a robust graph structure with edge weights proportional to their expected usage"01:23
klafkayou need to have maximum rigidity in certain vdirections01:23
kanzurefenn: be careful, you might end up locked into thinking like that01:23
fennINTEGRATE01:24
kanzurenight01:24
fennklafka: there's beam bending equations, it's much simpler to use finite element method with just tension and compression though01:25
klafkathere is probably some newtonian formula for calculating rigidity eh?  so you need to input in what directions you need the rigidity to go, the dimensions of the interfaces, how much rigidity you need, and the equations for rigidity with the constants for the material and stuff01:25
klafkaeh01:25
klafkabut it seems like this isn't really all that hard of an optimization problem, it seems it's more of a problem of designing the optimization problems 01:26
fennyou can represent a beam with a mesh of triangles and get the same result01:26
klafkainteresting01:26
fennyeah i mean everything is simple when you understand it01:26
fennbut it always takes longer than you think01:26
fennit's not really a hard problem01:26
fennjust something that comes up all the time that nobody seems to give a shit about for some reason01:26
fenn"oh this problem isnt hard enough, fuck it"01:27
fennHUH?01:27
fenndo you see the reason i want this procedure in the first place?01:27
klafkawell it sort of straddles the line where it's important to the domain but not interesting to the person who wants to develop new techniques to solve problems 01:27
klafkai do see01:27
fennso then i can simply vary the interface locations and everything else magically falls into place01:28
klafkayep01:28
klafkado you think you  can just modify an existing FEA system to do this?01:28
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fennFEA just evaluates the "cost function" (if i'm using the term right)01:28
fennactually figuring out what to do next is outside of the scope of FEA01:29
klafkaso you want to minimize the cost function right?01:29
fennyep01:29
fenncost = flex + amount of material used + complexity01:29
klafkaok so now we're getting somewhere, so we have a cost-space, i'm going to guess this is an incredibly non-convex space huh?01:30
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fennhmm.. for just mechanical parts, no, it's rather straightforward01:30
fennif we start adding other functions to the geometry then it gets more interesting01:31
klafkafenn do you know what i mean by non-convex? 01:31
fenni think so.. you can vary parameters continuously in a convex space01:31
fennthis was something i was supposed to read about yesterday and didnt have time01:31
klafkano, a convex space, is well in 2d it's one that curves upwards basically and is continuous too yes01:32
klafkabasically the thing abotu convex spaces are they are the things we are really good at optimizing because findinga local optima implies you've found a global optima01:33
fennconvex just means one global minimum or maximum?01:33
klafkathat's strictly convex01:33
klafkaa convex space is that any local minima is a global minima01:33
fennthat's what i just said01:34
klafkano, there is a difference between one local minima and multiple local minima01:34
fennif there's only one local minimum then it's the global minimum, no?01:34
klafkayou can have multiple solutions with a convex function, you can have only one solution with a strictly convex01:34
fennyes so a trough vs a bowl01:35
klafkaright01:35
fennok so why do i care?01:35
klafkaoh you don't particularly ,i was just making the comment that it was probably a really non-convex space, because it seems like you're probably solving lots of weird compled PDEs numerically 01:36
klafkait just requires different tools to solve the problem01:37
fennso simulated annealing instead of gradient descent01:37
klafkayeah maybe, hopefully something better than that 01:37
fennsometimes i wonder why people don't just start out with "the big guns"01:38
klafkawhat are the big guns? simulated annealing? Because it's really really slow01:38
fennmeta meta optimizer optimizer01:38
klafkaand no guarantee on finding a good solution01:38
fennbut really really slow doesn't fucking matter if you're running lots of different experiments at low resolution01:38
fenni see people running extremely detailed simulations for days at a time to get the answer that they set up the simulation wrong01:39
klafkahahaha01:39
klafkaugh i've done that so much :(01:39
klafkaw/ Gradient descent nonetheless01:39
fennmost of this stuff should be done at such a low resolutoin you can interact with it in real time01:39
klafkawell your problem yeah perhaps01:40
fennany problem01:40
fennno data set is this complex01:40
klafkahahaha01:40
klafkai disagree01:40
fennif you think you need to analyze all 9 million data points at once you're doing it wrong01:40
fennthe universe behaves in a rational predictable manner (except for where it doesnt)01:41
klafkai dont' think you can accurately say that without context, it depends on the scope of the problem you're trying to solve01:41
klafkaand the nature of the problem itself01:41
fenni just want the computer to work out the answer on its own01:42
klafkafor instance take image classification at a certain level that involves classifying individual pixels, a 100x100 image (pretty low res) has 100,000 classifications that needs to be done01:42
fennwithout me holding its hand every step of the way01:42
fenn"does gradient descent converge? no? try the next magic trick"01:42
klafkawell the thing is, does gradient descent not converge because of a theoretical or an implementation reason01:42
fennimplementation meaning the optimization parameters?01:43
fennlike step size, convergence threshold01:43
klafkayeah, like step size01:43
klafkamainly01:43
fennwell, that seems fairly easy for a computer to fiddle01:43
fenn(two for loops)01:43
fenna couple timeouts01:44
klafkayeah but what if doing one run of GD takes one day01:44
fenndon't do it that way01:44
fennwtf01:44
fennwhy would it take a day?01:44
fenn"yer doin it wrong"01:44
klafkaoftentimes because you have to approximate parts of the gradient01:45
klafkausually via MCMC01:45
fenncan i have an example problem where you'd use MCMC?01:45
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klafkasure,  you want to learn a markov random field via gradient descent for whatever reason (imaging, bionetwork inference, etc...) but the gradient requires you to calculate the derivative of the partition function, now the partition function is the logsumexp of the function over the entire space, the derivative is not calculable, but you can estimate it by taking an average of the sample01:48
fennan average of the sample... (cut off)01:49
fennor perhaps i'm just not understanding01:50
fennit's probably time for bed01:50
klafkayeah most likely01:50
klafkai'm trying to extrapolate from my specific instance and make it general, all we had to actually do is take the difference of the mean of the training data vs. the mean of the samples 01:51
klafkaconvergence happened when that difference became 001:52
fennmaybe you forgot to add a constant01:53
klafkasorry?01:54
fennoh, another geometry thing that's probably more up your alley: reverse engineering mesh (STL) files to CSG01:59
fennand various "3D scanning" 02:00
klafkahmm02:00
klafkathe STL I know is standard template library02:00
klafkathey are various like cad formats?02:01
klafkaah i see02:01
klafkahmm that's an interesting problem02:02
fennstl stands for 'stereolithography format' which basically means 'bag of triangles'02:04
* fenn sleeps02:05
* fenn dreams of spam and bacn02:05
fennif you can make a program to sort diybio by interest to me, i'd pay you a million dollars02:06
klafkalol02:07
klafkai tell you open design sequencer that can be largely made via a reprap02:07
klafkathat'd be fucking useful02:07
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fennok first things first, gotta get the reprap working02:08
klafkabut really about the other thing w/ the interfaces, has anyone tried doing something like simulated annealing or an evolutionary algorithm to do that?02:09
klafkaor greedy hill climbing perhaps02:09
klafkathat'd be a lot faster 02:10
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thesnarkits too bad we can't all have a huge party about the cell being created08:19
thesnarkI mean, that's like08:19
thesnarktoday is a great day08:19
kanzurethesnark: it's not as important as the media is making it out to be08:21
thesnarko rly08:23
thesnarkI mean08:23
thesnarkI can sort out through most of the fluff but I guess it seemed like a big milestone to me since I haven't been following it08:23
Utopiahabout Craig Venture?08:24
thesnarkyeah08:24
Utopiahto me that's pretty much 10 years he's repeating the same thing so maybe Im not following enough to be in awe08:28
thesnarkthat he made a living cell?08:30
thesnarkhe has said it before?08:30
Utopiahhe made a living cell from scratch? guess I need to re-read the articles08:30
thesnarkyeah08:31
thesnarkthat is his claim08:31
Utopiahhttp://www.nature.com/news/2010/100520/full/news.2010.253.html08:34
Utopiah "'reboot' a cell from a different species of bacterium" + "The custom-built genome is a near-exact replica of its natural counterpart" + etc so I think "from scratch" is rather exagerated anyway08:36
kanzurei thought it was a chromosome assembly technique08:37
kanzureand then they inserted the chromosome into the cell08:37
Utopiahthesnark: so Im not saying it's not great and I could do the same but to me it sounds like Stephen Wolfram saying (again) that he nearly invented copmutation... it's great marketing though08:38
Utopiahmy related page btw http://fabien.benetou.fr/ReadingNotes/Protocells08:40
Utopiahinterview for Science he made yesterday http://www.youtube.com/watch?v=47rUrlzdK3k08:46
* kanzure wonders if there's a machine shop in the middle of nyc08:55
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thesnarkhaha Utopiah I so agree with you about Wolfram, he's so full of himself :)09:22
Utopiahhis last blog post about 1 year W|A made me think about that09:23
thesnarkkanzure I think you can probably count on it09:23
thesnarkhttp://www.nature.com/news/2010/100520/full/news.2010.253.html09:24
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thesnarkoops09:24
thesnarksry09:24
thesnarkhttp://gizmodo.com/5543774/immaculate-creation-birth-of-the-first-synthetic-cell I think this is a good summary for the general public09:29
thesnarkok I'm done09:29
* Utopiah still can't believe that in 2010 scientific related article have religion connoted term in their title, seriously what the fuck.09:31
thesnarkjohn q public is still relatively...what's the word09:32
thesnarkstupid is too harsh09:32
thesnarkUtopiah we just have to work with things as they are I suppose09:33
UtopiahIll let the Church of the Flying Spaghetti Monster decide that.09:34
thesnark:)09:38
kanzurehttp://diybio.labitat.dk/index.php/Project_suggestions09:40
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kanzurehttp://justrade.co.uk/?tag=join-the-diybio "Dale has a piece for his O'Reilly Radar column on what he's dubbed "make-offs," low-budget knock-offs of scientific and industrial technology, ..."09:43
kanzurehttp://blog.makezine.com/archive/2010/05/make-offs_diy_indie_innovations.html09:44
kanzureoh please. pearl biotech. :/09:45
kanzure"It is a version of what China has been doing to America, benefiting from the R&D that goes into refining the specifications, developing prototypes and building a finished product.09:45
kanzureOnly now, with new digital fabrication techniques and open source hardware and software, individuals and small companies are in a position to compete globally with a distinctly DIY approach to innovation.09:45
kanzureIt's a new independent source of creative work, similar to what indie films are to Hollywood films developed in-house. It's open, collaborative and done on the cheap."09:45
kanzure"Tito Jankowski is one of the organizers of the DIYbio community" whaaat09:46
kanzurehttp://www.biocurious.org/index.php?title=Founding_Members09:47
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kanzurehttp://groups.google.com/group/biocurious09:48
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thesnarkkanzure great, they equate DIYbio with indie films11:08
thesnarknot sure if that's a flattering comparison11:08
neobiiargh going to miss maker faire this year11:57
neobiiwasn't that cool last year though11:57
neobiilots of kids and craft people11:58
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neobii_ls12:01
neobii_win 112:01
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neobiithere we go12:05
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Utopiahhttp://www.cyberpunkreview.com/news-as-cyberpunk/one-mans-quest-to-outfit-diabetics-with-robotic-pancreases/13:28
kanzurethat easily sounds like a slasher13:29
kanzurediabetics, you better watch out or the next thing you know your pancreas will be laying beside you on a surgery table13:30
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jrayhawkUtopiah: Re: synthetic cell: it's one small step for the field of science, but it's monumental in the field of philosophy. The journalist emphasized the more significant element.14:23
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UtopiahI think Venter likes to define tippings points before philosophers and journalists do so in order to leverage more press coverage. Once again "synthetic biology" is not really new and they are not the only team working on it; cf link posted earlier.14:26
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jrayhawkTrue dat.14:27
jrayhawkHe had remarkable discipline and competence in that antagonistic interview posted earlier. He clearly knows what he's doing in the PR department.14:31
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QuantumGhe's doing cool science and funding it with buzz..  I don't know whether that's a good or a bad thing :)17:08
QuantumG"We're not playing." - Craig Venter on accusations that he's playing God.17:22
jrayhawkNICE17:24
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QuantumGOMG, google homepage graphic ftw17:25
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kanzurewhat do you do when someone reveals to you that they sold their family-owned company for 9 digits?19:52
kanzurelike, what do you say19:58
fenngrumble mumble.. lost my laptop charger at google20:18
QuantumGkanzure: "nice exit strategy" I guess20:20
kanzureso i'm making a startup about excitement20:20
kanzureit's a pyramid scheme of excitement20:20
kanzurewhere i get ten people excited, who must pass on this pitch20:20
kanzurewe have no exit strategy yet20:20
fennshould i try to hack together a charger and possibly blow up my laptop?20:20
kanzurebut i'm really exicted20:20
kanzure*excited20:20
kanzuredamn it.20:20
kanzurefenn: probably not, no20:20
kanzure(10:22:46 PM) Spicko Vina: Have you ever read Transmetropolitan?20:21
kanzurebut about any of you guys20:21
kanzure*what20:21
fennno20:21
QuantumG:)20:21
kanzure(10:29:34 PM) Spicko Vina: are you familiar with another comic from ellis, doktor sleeples?20:27
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kanzurehi wilywonka :)20:40
kanzurelawl @ diybio troll:20:40
kanzure20:49 < noob_> Is there a gene you can put in a bacteria to make it produce  gold or some other precious metal?20:40
wilywonkahave you guys seen http://www.edge.org/3rd_culture/church_venter09/church_venter09_index.html20:40
* kanzure likes edge.org a lot20:41
wilywonkatakes quite awhile to watch but very good20:41
kanzurei usually just read the articles instead of watching20:41
wilywonkai ffmpeg'd it and watched it streamed to my xbox360 20:41
kristianpaulkanzure: how was the smart grid meeting?20:47
kanzurethe guy got into a car accident today and couldn't make it to the meeting21:29
JayDuggerGood evening, everyone.21:30
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kanzurehello Tuna 22:01
JayDuggerFenn: No. Buy a charger.22:13
JayDuggerKanzure: Yes, I like Ellis, but his endings all stink. Supergod's quite good. Planetary remains his best work to date. Doktor Sleepless, less so.22:14
JayDuggerOf H+ interest, his comics Orbiter, Supergod, Global Frequency, Mek, and Iron Man: Extremis all rank high.22:16
JayDugger(I'm forgetting one, at least, but--oh right. Your neighbor's blog reminds me: Ministry of Space.)22:16
JayDuggerhttp://strategicphilosophy.blogspot.com/2009/05/comics-of-transhumanist-interest.html22:17
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JayDuggerSigh. Scared away by off-topic talk, I suppose.22:17
JayDuggerI toss a quarter in the off-topic jar as penalty.22:18
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