2012-07-24.log

--- Log opened Tue Jul 24 00:00:17 2012
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Utopiahhttp://edge.org/conversation/biology-at-the-speed-of-light02:15
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strangewarpAha08:12
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strangewarpI wish PZ Myers were less confrontational, because he makes some decent points, but then all his fans get whipped up into a splendour of strawman-beating..08:15
strangewarpRegardless, have a thing: http://scienceblogs.com/pharyngula/2012/07/14/and-everyone-gets-a-robot-pony/08:15
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kanzurerafael: hi09:02
rafaelhi kanzure09:02
Vicarioushi09:13
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delinquentmeAnyone know offhand the RUBY string interpolation thats python-esque?  puts "ops %s %s" % ( busted[i-1], busted[i+1] )09:40
delinquentmesomething like that09:40
kanzurehttp://gen9bio.com/g-prize/09:45
kanzure"Gen9 has developed a unique technology to synthesize DNA constructs and has used it to build a novel fabrication capability for next-generation gene synthesis known as the BioFab® platform. The BioFab® platform has the capacity to generate tens of thousands of synthetic gene fragments per year in just a few square feet of laboratory space."09:45
kanzure"Today, Gen9 is manufacturing and shipping double-stranded GeneBits™ DNA constructs, or gene fragments, from 500 to 1,024 base pairs long."09:45
kanzure"If you also believe in the potential of synthetic biology, tell us how you want to revolutionize an industry through your research – you could win up to 500 synthetic DNA constructs (GeneBits™) to pursue your big idea."09:45
delinquentmeyar!09:48
delinquentmecool ish eh?09:48
delinquentmei mean its smart ish advertising-ish on their part09:48
kanzurenot cool at all09:49
kanzurejust something i saw.09:50
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delinquentmeyou dont like it?09:50
kanzurei am surprised they are calling it biofab09:50
kanzuresince endy just got done with biofab w/ juul09:50
delinquentmejuul is working w endy??09:51
delinquentmelucky ass dude.09:51
kanzurehas been for a long time09:51
delinquentmehes not here09:52
delinquentmei was gonna tell him that I hate him.09:52
kanzureyou hate him now?09:52
delinquentmekanzure, you want to start a GFP poison dart frog business w me?09:52
kanzureno09:53
delinquentmeno_me_gusta.gif09:53
delinquentmemodified puppys?09:53
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kanzureyo nmz78709:54
kanzurenmz787: http://gen9bio.com/g-prize/09:54
kanzuredelinquentme: linking does not imply endorsement09:54
delinquentmekanzure, i just like frogs09:55
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nmz787hmm09:56
nmz787"A panel of judges which includes, amongst others, David Baker, Sri Kosuri and Christopher Emig has been chosen by Gen9"09:57
nmz787kanzure: kosuri was mentioned on that phone interview with syngenomics09:57
nmz787he did some high-fidelity pooled oligo synthesis09:58
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nmz787this might be decent to have around http://twitter.com/SynBioNews/10:29
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nmz787hi azonenberg11:11
azonenberghi11:11
nmz787you were doing some kind of lithography, or am I wrong?11:11
nmz787was it with visible light?11:13
nmz787did you have a beam expander?11:13
nmz787ahh you're doing homecmos11:16
kanzurenmz787: hmm i got an email from him. Sriram Kosuri <sri.kosuri@wyss.harvard.edu>11:24
kanzureforwarded some things.11:28
delinquentmehttp://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/  << Stacey K pushed out her Open PCR11:29
kanzureugh instructables.com11:32
kanzurewell. at least she posted it. :(11:33
kanzurehttp://staceyk.org/pcr/pcrFinal.ino11:33
delinquentmeyou think thingverse woulda been better?11:37
nmz787kanzure: know anyone here http://www.beatrizdacosta.net/wetwarehackers_site/11:37
kanzuredelinquentme: i think software should be in software repositories11:39
kanzuredamn, stacey isn't giving me a name for this11:39
kanzurehow am i supposed to name the git repo11:39
kanzurenonsucky-openpcr.git?11:39
kanzurearduino-thermal-cycler.git is a bit generi11:39
kanzuregeneric11:39
delinquentmeOpenPCR_gen211:43
delinquentmeOpenPCR_build211:43
nmz787kanzure: there are seemingly a lot of cool diybio instructables... http://www.instructables.com/id/Paper-disk-DNA-preparation/  http://www.instructables.com/id/DIY-StirrerHot-Plate/11:44
kanzurehttps://github.com/kanzure/wiremound-pcr11:44
kanzurealso backed up here http://diyhpl.us/cgit/11:46
delinquentmenmz787, theres a fusion reactor on there :D11:46
nmz787kanzure: seems like time you started linkdumping on DIYbio again... lots of new folks there now that want info11:46
kanzurenmz787: or it's time people actually contribute to http://openwetware.org/wiki/DIYbio/FAQ11:47
kanzurea lot of content is missing11:47
kanzureand it should probably be moved off of openwetware, since nobody has an account there11:48
nmz787i was just signing up for the OWW mailing lists :P11:48
delinquentmemoved to where kanzure11:48
kanzurewtf11:48
nmz787i've had an account there ... was thinking it seems pretty stable11:48
kanzuredelinquentme: well, probably http://diyhpl.us/wiki11:48
nmz787and unhacked AFAIK11:48
kanzurenmz787: but people need to wait to get an account11:48
delinquentmeand what has jcline been up to?11:48
kanzureso, wtf, i'm looking at the "FAQ Revision History"11:48
kanzureand it says "1.0 - copied on 4/7/2009 from heybryan.org...DIYbio_FAQ"11:48
kanzurewut.11:48
nmz787lol11:48
nmz787daym11:49
nmz787i mean duh-yam11:49
kanzureone of the videos is dead on that page11:49
kanzurenobody has fixed that in a year11:49
nmz787kanzure: why did you call it wiremound?11:49
kanzurenmz787: that's what staceyk said the name was11:50
kanzurewhen i asked her.11:50
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kanzurenmz787: i definitely think a lot of this needs to be rewritten11:55
nmz787can we rip the instructable? did you ask her that?11:55
kanzuredidn't ask her, she claims that she is bbl-ing at the moment11:56
kanzurethough she still looks online11:57
nmz787bbl?11:58
nmz787oh11:58
kanzureyou know.. brb, bbl.11:58
nmz787yeah yeah11:58
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kanzure"My former coworker would use the mouse to copy and paste even 3-letter variable names rather than typing them in again. He'd also scroll his terminal window up and copy and paste old commands (again, all with the mouse) rather than using the up arrow, even after I told him about command line history and tab completion in case he didn't know,"12:43
kanzure"and would frequently mis-copy and miss the first letter off or have a stray $ at the front, causing him to start his mousing over from scratch rather than using the keyboard to correct it."12:43
* Urchin facepalms12:44
Urchinthough it does remind me of when I first started using Emacs12:44
nmz787i dont know emacs12:45
nmz787should I?12:46
UrchinI was doing something repetitive that could be done esily with the regular keyboard commands, and at one point half-way trough (after several minutes), I said "what am I doing?" and finished the job in couple of seconds12:46
Urchinthe admin that was watching me behind my back said he was asking the same question12:47
Urchinnmz787: it's a traditional unix text editor12:47
Urchinone of12:47
Urchinand one of the two that started religions12:47
Urchinthough that was just the effect of me being a complete beginner at it12:48
Urchinit takes a while to learn and master12:49
UrchinI still reach for the manual daily12:49
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kanzurenmz787: personally i use vim12:57
kanzureso if you choose emacs then i can't help you as much12:57
nmz787good enough13:00
nmz787ttyl13:00
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Urchingiven how much vim is bloated these days, it's mostly down to the question of interface and what you're used to13:06
kanzurewell clearly the correct solution is the emacs emulation of the vim emulation of emacs13:07
Urchinnah, doesn't work13:07
Urchinjust use whatever13:08
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obscuritehave you folks been talking about the stanford whole cell simulation at all?13:24
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obscurite(mycoplasm genitalia, simplest bacteria)13:24
archelsobscurite: will attempt to interest my labmates for it tomorrow.13:25
yashgarothneeds more quotation marks around simulation13:25
obscuritearchels: http://wholecell.stanford.edu/13:25
archelsI read it, thanks13:25
obscuriteyashgaroth: har har :P13:25
obscuritearchels: any thoughts?13:26
archelsobscurite: dunno, a tad underwhelming?13:26
obscuritearchels: really? seems to break new ground, even if they recycled the pathways13:26
archelsthe task of cobbling this together was obviously the size of a mammoth13:27
archelsbut what fundamental grounds is broken, really?13:27
obscuritearchels: i don't think anyone has made that complete a simulation before have they? it's mostly metabolism/translation but there are 26 other categories of submodel13:30
obscuritearchels: it seems more ambitious in that way and the visual instrumentation is really impressive13:30
obscuritebut i'm also fairly new to the field, so my comments in context13:30
obscuritetake*13:30
yashgarothit didn't surprise me to find that JCVI did it; very similar to their "synthetic bacterium" in that there's a massive effort to make something that's marginally useful, unless you count all the pop-sci speculation13:33
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archelsthis ^13:33
obscuriteyashgaroth: i belive it was only marginally related to JCVI13:33
obscuriteyashgaroth: mostly a stanford thing with Dr. Covert13:34
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obscuritethe paper barely even mentions JCVI13:34
obscuriteit's just a name people know so they latch on to it :)13:34
yashgarothI'm sure JCVI's contribution was just to say "put in a massive effort for this marginal project, it worked for us"13:35
obscuriteoy vey. cynical commentary always enlightens me13:35
yashgarothheh sorry I try not to be cynical but I'm very rarely successful13:35
obscuriteat least you're aware13:36
obscuriteit's like "hey, where's my flying car"13:36
obscuriteinstead of just enjoying how cool things are :)13:36
yashgarothman I am constantly enjoying how cool things are13:36
obscuritegood to know13:36
yashgarothin a few years a synthetic genome or a cell simulation will be useful, but doing it before then is just looking to spend money13:37
obscuritei have a feeling that public funding agencies disagree13:38
yashgarothalso fuck 'em for publishing in Cell, even if there isn't a more perfectly named journal for the article13:39
obscuritearchels: do you do compbio?13:40
obscuritebrb13:42
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archelsobscurite: I'm in computational neuroscience13:48
obscuritearchels: do you know of any attempts at whole neuron metabolic reconstruction?13:51
archelsmetabolic? no.13:51
obscuritearchels: just went to a presentation on this work: http://cnl.salk.edu/Research/Synapses/13:53
obscuriteold now13:54
archelsneat13:56
kanzureis jcvi's model open source?13:56
obscuritekanzure: yes, but it runs on matlab13:56
kanzureor is this more proprietary crap that i will never see unless i work for them and steal their code?13:56
archelsobscurite: If the Cell guys had built their model entirely in MCell, I would have been impressed. :)13:56
obscuriteand it's not jcvi13:56
kanzureobscurite: there's also things like channeldb for ion channel kinetics13:57
obscuritearchels: the process of creating physiologically accurate 3d models of those tiny bits was not easy from what i hear13:57
archelsobscurite: that's actually exactly what I am working on. :)13:58
obscuritearchels: do you still trace tiny silvers of tissue and stitch the splines all together?13:58
obscuritekanzure: ahh cool13:59
kanzurewell there's software for that13:59
obscuritekanzure: apparently these guys just finished making the software reasonably effecient13:59
obscuritekanzure: took several years of work13:59
obscuritei am guessing the advent of decent 3d printer slicing software that's open source might help new researchers14:01
archelsobscurite: yes, that's how neural reconstruction is done usually14:01
kanzuretodd/3scan has been using unpaid labor to write his image reconstruction software14:01
kanzure(or so i hear)14:01
obscuriteany decent open source software for slice reconstruction?14:02
kanzureoops s/labor/interns14:02
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kanzurei don't know any yet14:02
kanzurebut i think any that do exist should use something like http://github.com/kanzure/netmorph to test it with14:02
kanzuree.g. by knowing the network and cell structure ahead of time you can then test that your image analyzer doesn't suck hairy nuts14:04
obscuritekanzure: makes sense14:04
obscuritekanzure: high res 3d printed scaffolds should also be a good test14:04
kanzurejmil: what do you think?14:05
kanzurejmil: here's some sample data..14:06
kanzure(18 MB) http://diyhpl.us/~bryan/papers2/neuro/nematodeuploadproject/PAG722L.png14:06
kanzurejmil: does your printer have this sort of resolution?14:06
kanzurei think the scale is 1 nm/pixel14:06
yashgarothhahaha14:06
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kanzurejrayhawk: well my bandwidth just died, oops14:08
kanzuremaybe i should put that on gigapan14:11
kanzureor what's a non-awful site like gigapan?14:11
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obscuritethat better be one high res image14:11
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yashgarothhow close of a reproduction of that are you guys hoping to print?14:11
delinquentmeOK theres lots of talking going on here14:12
delinquentmewhat are you guys doing14:13
kanzuredelinquentme: writing some flask/sqlalchemy crap14:13
delinquentmefor image recognition?14:13
kanzureno14:13
kanzureit's a project to mathematically model rate limits on remote servers14:13
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delinquentmeyou guys heard about Theils newest investment right?14:27
kanzurehi jonnyATroot14:29
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jonnyATroothi14:31
kanzurejonnyATroot: what brings you here?14:31
jonnyATrootbiohacking14:31
kanzureneat.14:33
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jmilkanzure: we could print at that nematode resolution if we got a big enough grant :-D14:48
kanzurei mean for individually placing neurons14:49
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eudoxiawhat is the local opinion on the Open Source Ecology movement?14:56
eudoxiaany thoughts on how it may influence transhumanism?14:57
kanzurewell, fenn used to follow them more closely14:57
kanzurei met marcin a few times14:57
kanzurei really wish their plans and designs were better organized on the interwebs14:58
kanzuresomeone from their clan posted to diybio a few months ago asking for some volunteers.. about something?14:59
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kanzureBennyLava: hi.15:00
kanzurearchels: did you by any chance meetup with yashgaroth when he was over a few weeks ago?15:01
BennyLavahi15:01
yashgarothnope15:01
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yashgarothhe's in eindhoven? or something15:05
kanzureever since i published my email address in a paper i have bee getting these weird spam emails about molecular biology products15:16
kanzurethis latest spam is from genetex15:16
kanzure*been getting15:16
kanzure"Dear Colleague, Through your publications, we have noted that our Rad54 antibody [C3], C-term may be useful to your current work. Rad54 is a dsDNA-dependent ATPase belonging to the Snf2/Swi2 family of SF2 helicases. It appears to have multiple roles in recombinational DNA repair. This Rad54 antibody has been validated in one western blot."15:17
kanzure"We are offering our Rad54 antibody [C3], C-term to select researchers at a discounted price of $1,999 USD per 100ug vial (regularly $2,890 USD)."15:17
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kanzurei wonder if this spam works for them15:18
yashgarothI often wonder, how can all these antibody production companies stay in business? and then I remember, it's because they charge $20,000/mg15:18
kanzureand patents15:18
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kanzurei wonder if anyone sells fake antibodies and gets away with it15:21
yashgarothplenty of people sell really crappy antibodies and get away with it, but there's not quiiite enough slop in biotech for an entire vial not to work15:23
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fennheh wiremound-pcr15:47
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AdrianGkanzure: do you ever get depressed15:57
kanzureno15:58
kanzurei mean, no i don't get clinically depressed15:58
kanzurecan someone look over my python/flask-sqlalchemy comments here?15:59
kanzurehttps://github.com/mitsuhiko/flask-sqlalchemy/issues/6015:59
kanzurei think i might have some inaccuracies that i'd like to edit15:59
delinquentmeAdrianG, depression is a focus thing methinks16:00
AdrianGdelinquentme: overfocusing?16:00
AdrianGor underfocusing?16:00
delinquentmeno lack of focus16:00
delinquentmeyeah!16:00
AdrianGuh huh16:00
AdrianGvery novel theory16:01
AdrianGhow do I proceed16:01
delinquentmereally?!16:01
kanzureAdrianG: hah don't feed the troll16:01
delinquentmeI thought that was the whole idea?16:01
delinquentme*MEAN FACE*16:01
AdrianG:E16:01
kanzurewait, no, AdrianG is the troll in this scenario16:01
kanzureermm16:01
kanzureAdrianG: stop instigating him?16:01
AdrianGwait wat16:01
AdrianGi just got banned from reddit-depression16:02
AdrianGso now i have no ouetlet16:02
kanzureAdrianG: you know very well that delinquentme is incapable of reading meaning and sarcasm out of your sentences (like "very novel theory")16:02
delinquentmeAdrianG, reddit is dumb sometimes16:02
delinquentmehahah16:02
kanzureso, i think the right word is instigating16:02
delinquentmeAdrianG, if you're trolling me I've got coding to do16:02
delinquentmebut if you're being serious ill totes halp16:02
AdrianGok halp16:03
AdrianGi needs all halp i can has16:03
AdrianGpm16:03
delinquentmesure sure16:03
AdrianGim srs16:03
AdrianGim on the bipolar swing right now :O16:03
delinquentmesure talk to me homeslice!16:03
delinquentmepm16:03
kanzurewtf.16:03
delinquentme?16:04
fennAdrianG: http://george-eby-research.com/html/depression-anxiety.html and http://krispin.com/ are advice worth trying16:12
fennat the very least get yourself a little bottle of magnesium citrate16:12
AdrianGi have it right in front of me16:12
AdrianGa whole pile, take it erryday16:12
fennhuh16:12
AdrianGfenn: amphetamines are failing to keep it at bay16:12
AdrianGi dont think mag citrate will save me16:12
AdrianGor protein basics16:13
yashgaroththis sounds like a job for lsd16:13
fenni'm sorry, since when was a nutrient the same as a drug?16:13
kanzureso, i assumed you were banned from reddit because you were trolling depressed peeps16:13
delinquentmeyashgaroth, lol16:13
delinquentmeyashgaroth, well hang out sometime16:14
yashgarothalso since when are amphetamines used for depression16:14
* kanzure does some quick mental math16:15
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fenni disagree with eby's views on homeopathy and glutamate, but it doesn't detract from his message too much16:22
delinquentmehio fenn16:22
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delinquentmeanyone offhand know of a house hold substance I can feed algae with?16:24
delinquentmeYES yashgaroth i want to grow algae16:24
delinquentmeMy inner flower child is blooming16:24
yashgarothdo you have lights in your house?16:25
yashgarothI have no idea if they fix their own nitrogen, but light+fertilizer is probably fine oh and salt water16:25
delinquentmeyeah fertilizer is what was reccommended but I dont have any laying around?16:28
delinquentmeand really just like that mulch stuff?16:28
delinquentmeOOO wait I do have a compost pile...16:28
delinquentmelol god16:28
* delinquentme has said too much16:28
delinquentmebrothers / sisters preez no judge me.16:28
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kanzureyashgaroth: usually you want to cycle carbon dioxide through the tanks if you want to optimize their growth logs16:30
yashgarothoh well if you're gonna be fancy about it16:30
kanzuremiracle growth works pretty well especially with that nitrogen conte--16:30
kanzureyes why would you want to be fancy :(16:30
yashgarothdamn straight, but yeah just don't go and buy a 50-lb bag of ammonium nitrate and you'll be fine16:31
kanzuretell them it's for "rocket experiments"16:32
kanzurealso be muslim when doing that16:32
delinquentmelolol16:32
delinquentmekanzure, so when im logging in via a form16:32
delinquentmeI need to store cookie information on whatever program I'm using to automate the login with?16:33
kanzureyes16:33
delinquentmeis this a form of mutual authentication?16:33
kanzureno16:33
kanzurei highly recommend http://python-requests.org/ btw16:33
delinquentmeSo whatever is in the cookie is the chrome profiler needs to be written into a mechanize cookie?16:34
kanzurewell yes, but why not just write code to do the login and save the cookie too?16:35
kanzurethe cookie will expire on the remote server eventually16:35
kanzureso it's better to just add the login step to the scraper16:36
delinquentmeyeahh I've got the login step16:37
delinquentmeits just that after submission Im getting no feedback that the request was sucessful16:37
kanzureit might be a redirect16:37
delinquentme( i've verified the form fields as filled and correct )16:37
kanzurevia the Location header16:37
delinquentmeyeah but mechanize usually handles those16:38
delinquentmei can check redirects in chrome right16:38
delinquentmeahh ok im geting a 30216:38
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delinquentmeOOGA-WOOGA-BOOGA17:34
delinquentme=p17:34
BennyLavamy loony bun is fine17:34
delinquentme^^17:36
kanzuredelinquentme: btw you should also consider pyphantomjs http://github.com/kanzure/pyphantomjs17:39
kanzureespecially since it's.. python.17:39
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kanzureneat, the fbi paid me today18:43
yashgarothman that undercover work is gonna get you killed one day18:44
kanzurenah this was just their meal coverage18:45
yashgarothoh, right18:45
kanzure$316.50 i think is just the minimum they were paying out18:45
kanzurei'm sure nmz787 asked for >$500 with all that gas money..18:45
kanzurediesel money, i mean.18:45
yashgarothhas he converted it to biodiesel yet?18:46
kanzurenmz787: ping?18:46
yashgarothI suppose it's only recommended if he does move to the best coast, it'd probably solidify in the frozen northlands of NY18:47
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kanzureall this coursera/udacity/courseware stuff is nice in theory but in practice there's only ever "intro to x" videos, which don't really teach you anything20:30
kanzurewhere's my "5th year phenomenenology" videos20:31
kanzure*phenomenonology20:31
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kanzurehmm so mac uses reddit, how disappointing20:39
kanzurehttp://www.reddit.com/r/hwstartups/comments/x3xjc/whitebox_blog_another_open_pcr_project_16_wells/20:39
klafka_i  thought reddit was banned here kanzure20:44
klafka_:P20:44
yashgarothto be fair he's not posting atheist rage comics or anything20:45
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kanzureklafka_: i think tastefully making fun of friends for using reddit is totally ok20:46
klafka_:P20:46
klafka_JK20:46
kanzurebut, you're right20:46
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kanzurei guess i should get delinquentme and _sol_ to meetup sometme21:02
delinquentmeHMMm he /she is not in le channal?21:02
kanzurewell, maybe you're the same person.21:03
kanzurebut i sort of doubt you have two residential ip addresses by the same provider21:03
klafka_lol21:03
delinquentmeO_o;;;21:06
delinquentmei KNEW that TSA scan was a little too personal!21:07
delinquentme... if that wasn't funny to anyone, I'm sorry you missed out bc it was hilarious in my head.21:07
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kanzuredaeken's been in the news for his onity hack: http://www.bbc.co.uk/news/technology-1896822522:37
kanzurehttp://demoseen.com/bhtalk2.pdf22:39
kanzurehttp://demoseen.com/bhpaper.html22:39
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