2008-12-21.log

--- Day changed Sun Dec 21 2008
kanzure_PeerInfinity: did you see my cosmeng post?02:18
geneyou there kanzure?02:34
kanzure_no02:35
geneoh ok02:43
kanzure_fenn: do you remember if you got a good lead on the xmms2 demo ogg?04:13
xp_prghi all :>04:23
willPow3rwhats happening xp_prg?04:42
xp_prgredoing my website in flash :>04:43
xp_prgwhat you doing?04:43
willPow3rgoing over some mit opencourseware04:45
willPow3rthe lag between semesters makes my brain go to mush04:45
willPow3rso i need to keep it active04:45
xp_prgwhat is your major?04:47
willPow3rneuroscience, but im really studying for neural engineering04:47
willPow3ru in school?04:47
xp_prgnope done, I work now04:49
willPow3rwhere do you work?04:49
xp_prga small web development company in the bay area of ca04:50
xp_prgdo you know synthetic biology well?04:50
kanzure_I think Gavin Fauss is William Abaris.04:52
willPow3rim not sure if i know either of those people04:55
willPow3rwhat04:55
willPow3rwhat's their significance?04:55
fenn"Ah, the smell of new pseudonym."04:57
kanzure_if only I magically knew everything about brlcad.05:07
xp_prgwhat is brlcad?05:12
kanzure_xp_prg: http://brlcad.org/05:18
kanzure_open source CAD app.05:18
kanzure_ideally I'd know how to draw various objects off the top of my head, but the help interface for the commands isn't intuitive to me [yet]05:18
kanzure_will be soon though. am wokring on that.05:18
genekanzure, I think we just need to make something in solidwerks or what not05:19
kanzure_what are you talking about05:19
kanzure_for om? that's retarded, solidworks is proprietary05:19
geneoh05:19
geneyou're doing om stuff05:20
geneok05:20
genehttp://www.hnsa.org/doc/op1140/index.htm05:20
kanzure_yes.05:20
kanzure_what's the link to?05:20
geneanalog computers anyone?05:20
kanzure_vacuum tubes?05:20
genethe basics of mechanical analog computing05:20
geneor a book on mechanical fire control mechanisms05:21
kanzure_there's a way to write a program to convert VLSI/Verilog into gears and other mechanical computing elements05:21
geneyeah and this is how05:21
kanzure_"a way to write a program"05:21
kanzure_this looks more like a book describing computing elements in mechanical forms05:21
kanzure_which is related, but not the same thing.05:21
genestep one make blue prints, step two give blueprints to machinist and have him compile the program05:22
geneI'm thinking of making a business card that is a computer05:23
kanzure_no, step one is write the program05:23
kanzure_this is the same idea as the programs that convert C/C++ into neurons05:23
kanzure_the p-machines thing man from the U.K. was a nice example way the hell back when05:23
genethey have things that do that?05:24
kanzure_programs being converted into specific networks of connected discrete components, in this case apparently [simulated neurons]05:24
geneoh05:24
kanzure_the schematics can be generated, is my point.05:24
genesimulated neurons05:24
kanzure_that's what EDA is, anyway05:24
kanzure_electronic design automation.05:24
genemy dad does that05:24
kanzure_except machinists don't read the schematics, since everything's too tiny to work with large bulky man hands05:24
genewell you have mechanical cicuitry05:25
genecan have mechanical circuitry05:25
kanzure_hahah. on a yahoo group about space-based solar power: "well given the obama administration, I highly doubt SSP will be a serious consideration. obama will probably try to use vegetable oil based propulsion"05:26
kanzure_so many things wrong with that statement.05:26
geneyeah they forgot the H2O2 oxidizer05:27
genehmmmm.... we should try making an algae-diesel rocket05:27
kanzure_yeah, John Carmack and friends were discussing that the other day on the arocket mailing list05:27
genereally?05:27
kanzure_apparently the California folks were getting their freezing temps, and some of them didn't know to keep their biodiesel warm05:27
geneoops05:28
kanzure_yeah, these are the XCOR/SpaceX/Armadillo Aerospace people05:28
geneah shoot 05:28
genedoes algae diesel have that problem?05:28
kanzure_you mean biodiesel?05:28
kanzure_they were talking about biodiesel in general. I'm pretty sure it wouldn't matter whether or not it came from algae.05:28
geneas in diesel made from algae05:28
kanzure_bkero: the blend proportions would be the only thing that matter here, right?05:29
genedang, the analog computing manual is a navy manual, which means it's written in idiot's guide style, it's nearly impossible to not learn05:29
kanzure_maybe if you try really hard you can pretend to not learn.05:30
bkero?05:31
kanzure_but yeah, the brlcad manual is written in that style too05:31
bkeroBlend with what?05:31
kanzure_I've read a lot of military documents in that style05:31
kanzure_bkero: in biodiesel. the 'bp' is blend, right?05:31
bkeroI'd assume05:31
bkeroI've just run straight oil extract05:31
bkeroSome folks mix it with kerosene05:31
kanzure_temperature sensitivity issues?05:31
bkeroTank warmers05:31
bkero:P05:31
bkeroThat's what all diesels do05:32
kanzure_ah.05:32
bkeroJust small resistor packs next to the tank05:32
genereally all diesels have tank warmers, even big trucks?05:33
bkeroSome people mix it with things to boost the octane levels05:33
bkeroYes05:33
genethat's a relief05:33
bkeroIt's completely simple05:34
bkeroGrow algae, extract oil with hexane bath, or heated press05:34
bkeroFill tank05:34
bkeroRun05:34
geneHAHAHAHAHAHA05:35
bkero?05:35
genewe don't use hexane baths05:35
bkeroWhy not?05:35
geneit's wasteful05:35
bkeroit's also efficient05:36
genedo you work with alga-diesel too bkero?05:36
bkeroHexane is ~98% efficient compared to a heated press, which at best is 70%.1.105:36
bkero(ignore the .1.1)05:37
bkeroI have05:37
-!- Irssi: #hplusroadmap: Total of 17 nicks [0 ops, 0 halfops, 0 voices, 17 normal]05:37
bkeroI'm trying to get kanzure_ to send me some oil-rich algae prints05:37
genethere are much better ways of doing things05:37
bkeroLike what?05:38
genea billion tiny knives05:39
bkeroSo cut and pressure05:40
bkerolol make an array of boxcutter blades05:40
geneexactly05:41
geneyou need really small boxcutter blades thought05:42
bkeroHas anybody tried that?05:42
genethat's the hard part05:42
bkeroHow efficient is it?05:42
geneuL/min05:42
kanzure_search for 'nanoknives' and berkeley.05:43
genelike I guess 100%05:43
bkeromicroliters per minute?05:43
kanzure_or 'bead mills'05:43
geneyup05:43
kanzure_bead mills do better than microliters per minute05:43
kanzure_nobody has done a bead mill of nanoknives05:43
genebad idea kanzure05:44
genevery bad idea05:44
genehow do you get the knives out?05:44
bkeroSounds complicated to set up05:44
kanzure_bkero: hah, as if buying hexane is cheap?05:44
bkeroWould that even be possible for me to build?05:44
geneever grown algae for biofuel bkero?05:44
bkeroAye05:44
geneis that a yes?05:45
bkeroYes05:45
genewhat species?05:45
bkeroNo idea.  Whatever was native to the pond near me :P05:45
bkeroWasn't very many lipids to extract05:45
geneoh ok, so you did this on a hobbyist scale?05:46
bkeroWhich is why I was pestering kanzure_ to see if I could get something with higher oil density.05:46
bkeroWhat would a hobbist scale be?05:46
genenot done with a company or research group or funded by a grant05:47
bkeroSo no external funding = hobbist scale?05:47
kanzure_but that tells you nothing about volume..05:47
bkeroYea.05:47
kanzure_wtfc05:47
genefishtank size bioreactors, ponds05:47
bkeroIf I did it with giant septic tanks and produced acres of algae05:47
bkeroWould that still be hobbist scale?05:47
geneno05:48
bkeroSo I wouldn't necessarily corrolate funding with scale05:48
genewe might be able to get you some high lipid content species05:48
genebut they aren't native05:48
genewhich is bad, very, very bad if they get into the environment05:49
bkeroWouldn't matter, I've got a pretty sterile environment for it to grow, so there shouldn't be any problem with heartier native species impacting it05:49
bkeroThere's no real bodies of water for them to grow near me.05:49
genethat doesn't matter05:49
bkeroBut yea, I understand the implications of disposal.05:49
geneit might escape by migratory birds or what not05:50
geneplus, I don't think we can give free samples05:50
bkeroHum05:51
genebut if you contact us in a couple of months we might have a super algae harvester to sell to you05:51
kanzure_what the fuck are you talking about05:51
kanzure_fuck this shit05:51
* kanzure_ pad locks his refridgerator with samples05:51
bkeroHehe05:51
genecool you took some samples kanzure?05:52
kanzure_uh, actually I don't remember05:52
kanzure_I might have. I should double check everything.05:52
bkeroI'm gonna have to set up another automated growing environment.  Dismantled it when I moved.05:52
bkeroCO2 tank and an air compressor with check valves and servo-controlled bleeder valves05:53
kanzure_blah, why don't we have servo-controlled valves yet, gene?05:53
kanzure_that would be a good reason to get an arduino, pic or some other board05:53
genecan you program arduino05:53
kanzure_uh yes?05:54
bkeroServo controlled valves are the only way to do it :)05:54
genebecause the people who lead the project are biologists05:54
* kanzure_ has done microcontroller programming :)05:54
bkeroPlus there's tons of open source microcontrollers out there05:54
bkeroArduino clones are $1705:54
kanzure_gene: maybe we could just ask sata to buy them05:54
geneheh05:54
kanzure_bkero: yeah yeah yeah, no need to preach to me :)05:54
bkeroServo's and circuits to control them are less than $1005:54
genedid you make it yourself bkero?05:54
kanzure_servo valves aren't anything special, are they?05:54
bkeroNothing special05:54
bkerogene: yea05:54
bkeroI used a BASIC Stamp for mine05:55
geneservo valves, why not go for solenoid valves?05:55
kanzure_I mean, the way the biologists assembled this setup was "ok, here's a bin of randomass valves"05:55
bkeroBut that was before Arduinos were popular05:55
kanzure_parallax?05:55
kanzure_:(05:55
bkerogene: solenoids are binary while servo controlled bleeders are adjustable05:55
genereally05:55
genenever heard of bleeder valves before05:56
bkeroI mean, I guess I could hook up a timer and have it open and close really fast, but that's not what solenoids were for05:56
bkeroBleeder valves are what you use on car brakes to bleed them05:56
bkeroIt's essentially a check valve05:56
geneI've made air cannons with solenoid valves so I have a fondness for them05:56
bkeroIt's basically so I can inject air/co2 and not worry about having them come in contact with the metal on the bottle/compressor05:57
bkeroA diode for fluids/gasses, if you will.05:57
genehuh?05:57
geneso it doesn't get corroded?05:58
bkeroYea05:58
genedue to carbonic acid formation05:58
kanzure_wait, I thought this was a basic concept05:58
kanzure_servo valves seem more intuitive to me05:58
kanzure_I'll be quiet. :p05:58
genewell if you can program it and make it safe kanzure05:58
bkeroThe order goes (co2 tank)->servo valve->check valve->algae05:58
kanzure_http://www.ntsb.gov/events/usair427/valve_2.jpg05:59
genethe grow chamber door is like air tight, a CO2 leak could be fatal05:59
kanzure_http://npgroup.pd.infn.it/euroball/autofill/flux_box.gif05:59
bkeroJust be sure your valve and servo motor have enough torque to combat the water pressure06:01
bkeroweight of the water, whatever06:01
geneare you putting water through it06:01
bkeroNo, but you potentially have tens of gallons on one end of it, and potentially 125psi of air on the other side06:02
gene125 psi isn't too bad06:02
bkeroJust depends on how much you awnt to keep in your compressor tank06:03
genealmost forgot, Kanzure, walmart sells GFP and RFP, just not in a very pure form06:03
genemight be useful for biohacking06:04
bkeroGFP/RFP?06:04
kanzure_hm06:04
kanzure_where's meredith?06:04
kanzure_she was working on some GFP+yeast stuff06:04
genegreen fluorescent protein and red fluorescent protein06:04
kanzure_glow in the dark yeast06:04
genewalmart sells glow in the dark fish06:04
kanzure_although she was working on just expressing the gene really06:04
kanzure_in the yeast for the yogurt06:05
kanzure_erm, bacteria06:05
geneHAHAHAHA06:05
kanzure_not yeast06:05
bkeroFor staining?06:05
geneacidophillus?06:05
kanzure_for glow in the dark yogurt06:05
genegood luck getting that past the FDA06:05
kanzure_don't know. she might be awake in #diybio06:05
kanzure_nope, nevermind06:05
bkeroHeh06:05
genewho is meredith?06:06
genebioartist or biohacker?06:06
kanzure_hacker06:06
geneok that tells me a lot06:06
kanzure_she's like me, except with time on her hands06:06
kanzure_and money06:06
kanzure_she posts occassionally to the diybio mailing list06:07
bkerokanzure_: That's impressive.  Marry her.06:07
kanzure_good friend of bram cohen..06:07
kanzure_she's married already to a friend of bram :)06:07
bkeroHeh06:07
genemoney really06:07
kanzure_not really06:07
kanzure_"Bram Cohen (born 1975) is an American computer programmer, best known as the author of the peer-to-peer (P2P) BitTorrent protocol, as well as the first file sharing program to use the protocol, also known as BitTorrent. He is also the co-founder of CodeCon, organizer of the San Francisco Bay Area P2P-hackers meeting, and the co-author of Codeville."06:08
geneyou mean she does that for a  company06:08
kanzure_no06:08
kanzure_she does it for the hell of it, 06:08
genedamn06:08
kanzure_but I mean that she at least has a little cash to go fetch a refridgerator or something06:08
geneor enzymes06:08
kanzure_'cept she can hardly get people to ship to her06:08
kanzure_so anyway.06:08
kanzure_the Vermont stuff might change some of that06:08
genehahahaha06:09
kanzure_re: virtual incorporation.06:09
geneof course06:09
kanzure_yeah..06:09
genewe can't ship to you, you might be a trrrist06:09
kanzure_trrist, is that a racial slur?06:09
kanzure_heh06:09
geneyeah, someone told me to do that06:09
geneon instructables06:10
genethey wanted to know if I was a biohacker06:10
bkerolol06:10
genethere was something highly suspicious about it...06:10
bkeroBiohackers are the new 'cool' thing.06:10
genenot everyone thinks biohackers are cool06:11
geneespecially not DHS06:11
bkeroYea06:11
bkeroWell, easy-to-startle republicans wouldn't, I'm sure.06:12
genebut we can't do biohackery without enzymes and knowledge06:12
bkeroand the religious zealots might take offense to mucking about with biology in general06:12
geneyeah I was about to say that06:12
bkeroBut hopefully nobody cares about them06:12
kanzure_"omg! biology! holy shit, don't anybody tell me about sex"06:12
bkeroReligion was a good explanation back in the dark ages, but now we have better methods.06:13
geneI'm thinking of posting some highly disruptive diy tech online that might freak those types out06:13
kanzure_gene: kinda like http://biohack.sf.net/ eh?06:13
kanzure_*cough* beat you to it *cough*06:13
genenot even close06:13
kanzure_ppft. what could be more disruptive?06:13
genemore likely to be considered unethical06:13
bkerogene: I'd recommend it06:13
bkeroThen again, I'm morally and ethically bankrupt.06:14
kanzure_you get no points if you don't specify what it is.06:14
genewell, first off it may not be possible to do cheaply06:14
bkeroThere aren't many things that you can'd do cheaply :P06:14
gene2 it involves chemicals that might be hard to obtain06:15
gene3 it would be gross to test06:15
geneit's not very transhumanist either06:16
bkeroI think you should do it, then do a complete writeup and publish :)06:16
bkeroOr post it online and get someone(or many people) to do it for you.06:17
geneheh I wonder who would actually be willing to test it06:18
bkeroI'd do it if I can get the correct supplies from chem stores and the lab surplus store here, and find it interesting enough :P06:19
bkero(and if I understand it) :P06:19
bkeroSometimes I can be a bit thick.06:19
geneI don't think you'd want to do it06:19
genebut another thing I have been thinking of doing is nuclear transfer cloning06:23
fennyo plebes, i'm thinking of posting some highly disruptive recipes online, that would totally freak the gourmet scene out. but I dont think you'd want to eat it, so I won't even tell you what it is06:36
geneso is it possible to fluorescent flow cytometry at home?06:36
fennof course06:36
fenn1) buy a flow cytometer06:36
fenn2) ???06:36
fenn3) Profit!06:36
geneie with a diy cytometer06:36
genefenn I have a reason for not telling what it is06:37
fennthey're just inkjet printers combined with a static electricity generator and some coils and fast light sensors06:37
fennpiece of cake right?06:37
geneyeah, I think you forgot the laser part and the dye part06:37
fennyeah whatever06:38
fennthey do it with diamonds all the time06:38
geneI need Hoechst 3334206:38
genethis requirement severly limits the disruptiveness06:39
geneand the laser06:39
genebut that might not be a problem06:39
fennsounds ... carcinogenic06:40
fennso, nuclear transfer, DIY flow cytometry, DNA stain... where's he going with this06:41
genenuclear transfer is unrelated06:42
genedamn you might be right about the inkjet cartridge fend06:43
genefenn, I don't think you'd have any use for it06:43
fennO RLY06:44
geneYA RLY06:45
fennw/e06:45
geneyou wouldn't even want to test it out06:46
genelet's end it right there06:46
geneit isn06:46
gene't even well thought out06:47
genein other words I don't have a recipe07:17
fennhmm this is interesting, especially since all you need is an accelerometer or other 2d-no-buttons interface08:36
fennhttp://wiki.openmoko.org/wiki/Qwo08:36
fennyou could write with your eye movement for example08:39
fennstuffed animal cad.. this seems quite useful for inflatable structures in general: http://www.den.rcast.u-tokyo.ac.jp/~yuki/plushie/index-e.html09:02
fennand brainwashing children of course.. muwahahahaha09:03
fennpepakura yadda yadda09:05
fenni should write a program to do quikwrite on an avr with a 9 button keypad (or a reverse biased LED array ooooo)09:12
bkerofenn: That looks insanely awkward09:21
fenntry the java demo09:23
fennhttp://mrl.nyu.edu/projects/quikwriting/Quikwrite2.html09:23
fennto type 'k' you "press" 5 1 3 509:23
fennit's a lot harder to explain than to learn09:24
fennthis seems to me, to be supremely useful in a wearable heads-up display09:26
fennespecially if there were a 'tab' key ;)09:26
fennspace twice could work09:27
fennhuh. this is pretty close to hexegrity: http://mrl.nyu.edu/~perlin/experiments/demos/Platform.html12:22
fennrawr why dont we have embedded python apps in browsers yet12:56
UtopiahGHMLPylons?12:57
fennthat12:58
fennis server side. i'm talking about client side, like "click the cow to win a prize" crap12:58
UtopiahGHMLyou can embed that in a webserver like XAMPP or lighter packages12:59
fennapparently grail.sf.net is a sort of java incomatibility layer12:59
fennUtopiahGHML you are off in left field13:00
UtopiahGHMLrunning a python app or running in the browser from a webserver, what else do you need?13:01
UtopiahGHMLthey are even some ways (experimental I guess) to run in a JVM AFAIK13:01
fenn<script language="Python"> or <applet13:02
fenncode = foo.py>13:02
fenni guess it would be .pyc to match the java .class format13:02
fennanyone here written or hacked on java applets?13:05
UtopiahGHMLJPython http://www.python.org/workshops/1997-10/proceedings/hugunin.html13:06
fennfennetic.net will be down for relocation16:56
-!- gene_ is now known as gene18:14
kanzure_http://mysite.verizon.net/wsbainbridge/system/software.htm oh god wtf is this bullshit18:22
kanzure_http://www.publico.es/184626/biohackers/reventar/reinventar/biologia/garajes  diybio hitting spain..18:27
genelike a hurricane?18:29
geneseems like they aren't very probiohacker18:30
geneLa biolog?a sint?tica ha hibridado con una media naranja, la inform?tica, para alumbrar uno de los fen?menos m?s curiosos e interesantes de los ?ltimos a?os: los biohackers , biotecn?logos con el sue?o prometeico de robar a la naturaleza el secreto de la vida ya los centros de investigaci?n el poder para manejarla, crear organismos hasta en un garaje y que todo ello sea abierto,...18:30
gene...compartido y...18:31
gene...p?blico; vida 2.0. Synthetic biology has hybridized with a better half, computers, to illuminate one of the most curious and interesting phenomena of recent years: the biohackers, biotechnologists with the Promethean dream of robbing the secret nature of life and centers investigative power to handle it, to create organisms in a garage and that this is open, shared and public life 2.0.18:31
genePlasmids and restriction enzymes are the basic toolkit from biotechnology, which allow, remove, change or save genes. Despu?s llegar?an las librer?as de genes y las m?quinas sintetizadoras de ADN, pero la bacteria intestinal Escherichia coli contin?a siendo el obrero biol?gico imprescindible. Then would come the libraries of genes and DNA synthesizer machines, but the intestinal bacterium...18:31
gene...Escherichia coli remains the worker biological imperative.18:31
generight they are18:31
generead the translated comments there are some useful tidbits like this: En uno de ellos, Whitesides y sus colaboradores detallaban c?mo construir una centr?fuga cl?nica a partir de una batidora de huevos de manivela. In one, Whitesides and his colleagues detailing how to build a centrifuge clinic from an egg beater crank. Pegando con cinta a una de las aspas un trozo de tubo de pl?stico y...18:33
gene...haciendo girar la batidora, se separan f?cilmente las c?lulas sangu?neas del plasma, lo que permite extraer muestras para anal?ticas. Sticking with tape to a blade of a piece of plastic tube and spinning the blender, easily split the blood cells from plasma, which can extract samples for analysis. 18:33
genenot the comments one of the articles18:34
geneso kanzure how can we make restriction enzymes?18:35
kanzure_gene: the same thing we do every night18:50
genehuh?18:50
genesleep is how you make restriction enzymes18:50
gene???18:51
geneactually purifying restriction enzymes is what we need to do 18:52
kanzure_right18:52
kanzure_antibody purification is the usual method18:52
kanzure_but maybe the filter will magically be the solution18:52
genemkae the bacteria make antibodies18:53
geneor attach the RE to a magnetosome18:55
genea small body that is magnetic18:55
genelook up magnetococcus18:55
geneit has an interesting method of finding down18:56
genemagnetococcus likes anoxic conditions, anoxic conditions are down, so it has a magnetosome in it so it lines up with the magnet flux and points down18:58
geneoh did you see this in OM http://www.westword.com/2008-12-18/news/hed-the-gundersons-get-us-ready-for-basil-the-robot-of-our-dreams/19:06
fennthat was the most boring robotics article i've ever read19:19
kanzure_yeah I didn't get through even a few paragraphs actually19:34
kanzure_it just sounded stupid19:34
kanzure_what is it actually about19:34
fennsome robot that sucks19:48
fennsupposedly it can use sonar to tell if something's a chair or a person19:49
fennbut it's batteries died halfway through the demo, so nobody knows for sure if it works19:49
fenninternet is killing my spelling19:49
* fenn sleepz19:50
geneoh shoot19:56
geneI just skimmed the thing19:58
genewell looks like thats useless19:58
geneoh yeah did you hear that ponoko will laser cut metal now?19:58
kanzure_gene, even growing antibodies requires purification itself too.20:57
kanzure_Hm, I wonder if we can make a packaging assistance tool22:13
kanzure_or modeling assistance tool.22:13
kanzure_I mean, the models are what are holding things back more than anything else22:13

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