--- Log opened Sun Aug 04 00:00:03 2013
--- Day changed Sun Aug 04 2013
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01:56 < poppingtonic> paperbot: http://link.aip.org/link/doi/10.1063/1.4754343
01:57 < paperbot> TooManyRedirects (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 236, in _build_response)
01:58 < poppingtonic> paperbot: http://proceedings.aip.org/resource/2/apcpcs/1480/1/135_1?isAuthorized=no
01:58 < paperbot> http://libgen.org/scimag/get.php?doi=doi%3A10.1063%2F1.4754343
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04:24 < anannie> hrm how about creating a stirling engine that purifies dirty water? Producing electricity at the same time. You could replace the inertia of the fly wheel with a motor like action by the dynamo... (when it's in that phase of the cycle)
04:32 < anannie> This is disappointing. Dean Kamen has already been here
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06:06 < anannie> Hrm the more I study this the more  I think that I can make the entire thing cheaper, better, and more efficient through a battery and some electronics.
06:07 <@kanzure> that's often the case
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06:20 < chris_99> i presume you need some fancy materials to filter viruses, as the cheapest filter i've seen is around £100 iirc
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07:04 <@kanzure> preparing for the cryptopocalypse http://www.slideshare.net/astamos/bh-slides
07:06 < panax> thats why we use ECC
07:08 < ParaSa1lin> i dont think anyone's built a stirling cycle engine that's actually useful
07:09 < ParaSa1lin> nobody's ever achieved the promised efficiencies
07:13 < anannie> ParaSa1lin: That's what makes it a very interesting challenge
07:14 < anannie> ParaSa1lin: Perhaps what's needed is the elimination of the mechanical components of the engine?
07:15 < anannie> ParaSa1lin: I'm serious, what if we changed the entire thing and replaced the piston with a magnet with a very high curie temp. and then wind a coil around the piston and basically capture energy and push it down as it goes up and down
07:18 < anannie> That said, I'm actively looking for a job - does anyone know how I can find an opportunity that'll be a fit?
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08:19 < ParaSa1lin> anannie, what is your immigration status
08:19 < anannie> ParaSa1lin: If I get the money, then I can make the immigration happen, but right now I'm working remotely with a UK based company
08:20 < ParaSa1lin> make the immigration, how so?
08:20 < ParaSa1lin> self-sponsor h1b through a shell
08:22 < anannie> Well I'm eligible for asylum due to a complex set of circumstances. I've been in touch with human rights lawyers and they think that I have a very strong case. I was planning on getting some money together and just working over here
08:23 < ParaSa1lin> im curious about those circumstances if its not too personal
08:23 < anannie> It is a bit personal and I prefer not to inject that negativity into things
08:25 < ParaSa1lin> you have a resume?
08:25 < anannie> should I pastebin it and PM it to you?
08:26 < ParaSa1lin> you can email to ropoctl@gmail.com
08:31 < anannie> ParaSa1lin: Sent.
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08:35 < ParaSa1lin> how much does asylum cost?
08:36 < anannie> ParaSa1lin: For me? It's the cost of the ticket to Vancouver / the US + the lawyer's expenses. So under $20k
08:36 < anannie> I was hoping to hit $30k and keep $10k for expenses such as my medication, food, and a place to stay
08:37 < ParaSa1lin> you know how to weld, braze etc?
08:38 < anannie> No, but I can learn. I've handled power tools a lot in my life, just never a welding torch.
08:39 < ParaSa1lin> i dont think thiel picks any females for that thing
08:39 <@kanzure> she's over 20 or w/e i think
08:40 < anannie> The fellowship?
08:40 < anannie> He has picked females in the past. Just not too many.
08:40 < anannie> kanzure: Yeah I'm over 20 now, but I was a dewy eyed 18 year old back then
08:40 <@kanzure> he doesn't pick anyone, the advisors do
08:41 <@kanzure> jojack happens to be one of those advisors
08:41 < anannie> kanzure: Yes
08:41 < anannie> to be clear he == Thiel Foundation in my sentence
08:41 <@kanzure> okay
08:42 < anannie> he represents it for people, so I just use Thiel instead of saying that it's a complex multi-stage process
08:42 < anannie> that six people had to say yes for me to get to the finalist round
08:44 < anannie> and then you had the mentor match event and so on... It was an exhausting process
08:44 <@kanzure> oh, i didn't know what you were talking about
08:44 <@kanzure> is this something i would understand if i was looking at your resume?
08:45 < anannie> kanzure: Hrm?
08:45 <@kanzure> why are we talking about thiel?
08:45 < ParaSa1lin> yes it is on her resume
08:45 <@kanzure> got it. makes more sense.
09:30 < fredox> nmz787: what sort of volumes of reactants were you planning on running for your synth design?
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09:31 < delinquentme> paperbot, http://www.nature.com/nchembio/journal/v9/n8/full/nchembio.1276.html
09:31 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnchembio.1276
09:31 < delinquentme> paperbot, http://www.sciencedirect.com/science/article/pii/S0142961212003237
09:31 < paperbot> http://libgen.org/scimag3/10.1016/j.biomaterials.2012.03.036.pdf
09:32 < delinquentme> kanzure, the elsevier link no worko
09:33 < delinquentme> libgen is ehh
09:33 < delinquentme> erm the nature...
10:08 <@kanzure> huh?
10:08 <@kanzure> fredox: don't ask him. he's going to say 1 micron cubed. but that's for microfluidics. i don't think microfluidics is a good v1.
10:09 < gradstudentbot> Why did I go to grad school?
10:14 <@kanzure> a microfluidic synthesizer is going to take a tremendous amount of debugging and time
10:14 <@kanzure> and i don't think working on things that are unlikely to work is a good use of resources
10:15 < chris_99> if the payoff is good enough though...
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10:27 <@kanzure> chris_99: theoretical payoffs wont make it happen faster
10:27 < chris_99> indeed
10:27 <@kanzure> and theoretical payoffs wont make it easier
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12:43 < chris_99> don't spose anyones got usenix video accesss
12:50 < Urchin[emacs]> like live feed?
12:51 < chris_99> yeah
12:51 < chris_99> i'm really curious about the car hacking talk
12:52 < Urchin[emacs]> no idea, sorry
12:53 < chris_99> not to worry, i'll wait until it gets leaked heh http://www.theguardian.com/technology/2013/jul/26/scientist-banned-revealing-codes-cars is what i mean
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13:06 <@kanzure> some 0day related to tor/freedom hosting http://pastebin.mozilla.org/2777139
13:07 <@kanzure> "This appears to be an exploit in the Firefox 17 JS runtime. The script does not attempt the exploit unless running on Firefox 17 on Windows."
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13:17 <@kanzure> http://wiki.echelon2.org/wiki/Endgame_Systems
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13:22 < rigel> fuck, so half of tor exit nodes are down now?
13:22 < rigel> what the shit
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13:37 < poppingtonic> paperbot: http://wwwlib.umi.com/dissertations/fullcit/3012272
13:38 < paperbot> TooManyRedirects (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 236, in _build_response)
13:38 < poppingtonic> hmmm...
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14:05  * brownies pokes gradstudentbot 
14:05 < gradstudentbot> I should take a break, my pipetting arm is killing me.
14:05  * brownies pokes gradstudentbot 
14:05 < gradstudentbot> I can't help it, I just like science so much.
14:05 < brownies> heh. that's a good one.
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14:16 <@kanzure> "This business with the FBI spraying JS hijacks around the web is more than a little troubling. Is this the first widely-publicized case of the feds indiscriminately deploying an exploit on this scale?"
14:16 <@kanzure> more about the js payload http://www.twitlonger.com/show/n_1rlo0uu
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14:27 < panax> kind of like this: https://www.youtube.com/watch?v=kLt_uqSCEUA
14:28 <@kanzure> .title
14:28 < yoleaux> DEFCON 20: Owning Bad Guys {And Mafia} With Javascript Botnets - YouTube
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14:55 < anannie> gradstudentbot: Why do you do what you do?
14:55 < gradstudentbot> I could never be a PI.
14:55 < anannie> That's awesome
14:59 < heath> kanzure: do you know how to write a multiline statement within the phantomjs repl?
14:59  * heath is trying to determine the best way to debug a phantomjs session
15:00 < heath> in the coffeescript repl, you have to press ctl-v
15:00 <@kanzure> don't use the repl
15:00 <@kanzure> it doesn't work
15:00 < heath> did you use the remote debugger?
15:00 <@kanzure> not yet. it probably doesn't work, just use weinre.
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15:01 <@kanzure> the remote debugger is more likely to work than the repl
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15:08 <@kanzure> https://blog.torproject.org/blog/hidden-services-current-events-and-freedom-hosting
15:08 <@kanzure> .title
15:08 < yoleaux> Hidden Services, Current Events, and Freedom Hosting | The Tor Blog
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15:57 <@kanzure> "I don't have any specific advice here, but I will say that I just built and sold a company that does precisely this - basically cloud instances of mitmproxy for inspection and rewriting traffic. So it's possible, and mitmproxy is well-suited to the task."
15:57 <@kanzure> i wonder what cortesi is up to
16:12 <@kanzure> i think that paper thomas landrain just posted is full of shit
16:12 <@kanzure> in his disclaimers he claims there is no conflict of interest
16:12 <@kanzure> but his name is plastered all over the paper
16:12 <@kanzure> what a fucking liar
16:13 <@kanzure> "oh yeah, by the way, i directly benefit from the point of view i present in this narrative"
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17:41 < nully> Maybe he feels that there is no conflict of intrest because he provided a disclaimer that usually is intended make a reader aware of a conflict (thus removing the conflict to some degree)... or... wait did i go full circle?
17:55 <@kanzure> writing "No conflict of interest" doesn't make it true, it's supposed to be a safe place to list conflicts
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18:04 <@kanzure> http://atlantisrky4es5q.onion/leaderboard
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19:14 <@kanzure> knivesMILLION: hi
19:14 <@kanzure> augur: where are you?
19:14 < knivesMILLION> oi
19:15 < knivesMILLION> im a regular on r/nootropics but it's dead and saw the link so i figured i'd say hey
19:15 < augur> kanzure: what hi hello
19:16 < knivesMILLION> so what's this room about, i'm still confused with the description
19:17 <@kanzure> we build things. then we kill redditors.
19:17 < knivesMILLION> i'min
19:17 < augur> noo dont kill redditors D:
19:17 < gradstudentbot> My parents keep asking when I'm going to finish.
19:18  * kanzure pokes gradstudentbot
19:18 < gradstudentbot> I am busy doing science, go away.
19:20 < Urchin[emacs]> science is never finished
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19:31 < fredox> not a lot of scrollback this morning
19:31 <@kanzure> don't expect me to do your work for you
19:31 <@kanzure> i was busy on https://github.com/kanzure/pokemon-reverse-engineering-tools/commits/master
19:31 <@kanzure> and https://github.com/kanzure/pokecrystal/commits/master
19:32 <@bkero> kanzure: https://bugzilla.mozilla.org/show_bug.cgi?id=901365
19:33 <@kanzure> nice, these guys are still running their service http://www.onlinedisassembler.com/odaweb/HeZjTV
19:33 <@kanzure> that's good
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19:36 < gradstudentbot> Who used the last of the growth medium?
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19:43 < fredox> kanzure: fyi i am looking at ~5nMol loading per well/column
19:44 <@kanzure> why?
19:44 <@kanzure> wells and columns are pretty different. what are you actually doing?
19:44 <@kanzure> also, not to link to reddit or anything, but this looks disgusting and evil http://www.reddit.com/r/AskAcademia
19:44 <@kanzure> (people tricking other people into going into academia)
19:45 <@kanzure> look at all this evil shit they put up with:
19:45 <@kanzure> http://www.reddit.com/r/AskAcademia/comments/yyrts/need_advice_on_how_to_proceed_with_a_terrible_lab/
19:45 <@kanzure> http://www.reddit.com/r/AskAcademia/comments/12alkf/being_screwed_by_a_professor/
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19:46 <@kanzure> http://www.reddit.com/r/AskAcademia/comments/11x352/giving_up_on_a_phd_after_12_years/
19:46 <@kanzure> man what a terrible work environment
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19:46 < fredox> why? practical constraints of accurate volume dispensing with relatively inexpensive parts
19:47 <@kanzure> what are you doing though? a pipettor on a moving arm?
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19:53 < fredox> nah reservoir pump
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19:59 <@kanzure> does anyone have a copy of "Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method"?
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20:02 <@kanzure> "Examples of methods disclosed to date are the photo-lithographic light-directed based synthesis [McGall, G. et al; J. Amer. Chem. Soc. 119; 5081-5090; 1997], the projector-based light-directed synthesis [PCT/EP99/06317], the fluidic synthesis with separation of reaction chambers, the indirect projector-based light-controlled synthesis using photo acids and suitable reaction chambers in a microfluidic reaction support, the electronically ...
20:02 <@kanzure> ... induced synthesis by means of spatially resolved deprotection at individual electrodes on the carrier and fluidic synthesis by means of spatially resolved deposition of the activated synthesis monomers.  The use of support-bound libraries is described for the synthesis of synthetic genes in PCT/EP00/01356. One disadvantage of this method is that the matrix of molecules is destroyed by the dissolving-out step. A second important point is ...
20:02 <@kanzure> ... the amount of synthetic DNA which can be prepared per reaction site in the support, i.e. per type of oligo. In addition, the small scale which is associated by definition with the synthesis makes it not easy to handle the dissolved-out oligonucleotides. One use of support-bound nucleic acids which are prepared in an array arrangement is indicated on the home page of Dr. J. Hoheisel's research group at the Deutsche Krebsforschungszentrum ...
20:02 <@kanzure> ... Heidelberg (DKFZ). One topic here is, for example, the use of nucleic acids as PCR primers. However, in this case too detachment of the molecules directly from the support is described. A use as template is not described. A further use of support-bound nucleic acids which are prepared in an array arrangement is described in Bulyk et al. [Bulyk, M. et al; Nat. Biotech. 17; 573-577; 1999]. In this application, microarrays are assembled by ...
20:02 <@kanzure> ... means of Affymetrix photolithographic light-directed synthesis in such a way that different 25-mers with free 5' ends are prepared on the solid phase. These are then filled in to give double strands by proximally binding primers. These double-strand arrays are then used to analyze binding events with DNA-binding proteins. In addition, enzymatic digestions with restriction enzymes are described for analytical purposes. A use of the ...
20:03 <@kanzure> ... generated copies after separation from the oligonucleotides serving as templates is not described. Nor is repeated or cyclic copying described. Since the synthetic method used is based on photolithography, it is moreover evident to the skilled worker that considerable effort, including the creation of appropriate masks, is necessary for a new array design and new nucleic acid sequences."
20:03 <@kanzure> i have no idea how this works http://www.patentstorm.us/applications/20070087349/description.html they seem to have an array of oligos but i don't see how it's selectable
20:04 <@kanzure> haha here's more evidence of all of the patent wars over dna synthesizers, this one is from 1985 concerning a "second generation" of dna synthesizers http://online.liebertpub.com/doi/abs/10.1089/blr.1985.4.219a
20:05 <@kanzure> paperbot: http://online.liebertpub.com/doi/pdfplus/10.1089/blr.1985.4.219
20:05 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/aacc7cccb6391222ad44a0211683f702.txt
20:05 <@kanzure> paperbot: http://online.liebertpub.com/doi/pdf/10.1089/blr.1985.4.219
20:05 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/de98b98ecf345e151708f5ff2acf665f.txt
20:05 <@kanzure> meh nevermind
20:06  * brownies pokes gradstudentbot 
20:06 < gradstudentbot> Why aren't you doing science right now?
20:06  * brownies pokes gradstudentbot 
20:06 < gradstudentbot> When did they learn how to do that?
20:06  * brownies pokes gradstudentbot 
20:06 < gradstudentbot> I'm busy sciencing as fast as I can.
20:08 <@kanzure> man, it's really hard to follow the history of all of the patent lawsuits
20:09 <@kanzure> http://www.the-scientist.com/?articles.view/articleNo/17260/title/Today-s-Peptide-Chemists-Face-A-Dizzying-Array-Of-Synthesizer-Choices/
20:10 <@kanzure> "The array of choices in peptide synthesizers is almost dizzying, especially when one considers that only about 1,000 automated synthesizers are currently installed and about 200 to 300 are sold each year, according to industry sources. Industry insiders report that today there are five major manufacturers of peptide synthesizers in terms of sales, with an aggregate of 10 individual units on the market and two more soon to be released. Each ...
20:10 <@kanzure> ... product is intended for a different type of user. They range in price from a low of about $20,000 for a unit that synthesizes three peptides simultaneously to as much as $250,000 for a machine capable of producing large amounts of single peptides for pharmaceutical use. Most of the midrange models go for between $65,000 and $85,000."
20:10 <@kanzure> what a terrible market
20:10 <@kanzure> "All of the automated synthesizers use the solid-phase synthesis method developed in the early 1960s by chemist Robert Bruce Merrifield, now an emeritus professor at Rockefeller University. Merrifield says he never got rich off of his invention. "When I developed the methodology, patents were very much discouraged," he recalls. He was, however, rewarded in another way. For his important contribution to peptide chemistry, he received the Nobel ...
20:10 <@kanzure> ... Prize in chemistry in 1984."
20:11 <@kanzure> "Another process-monitoring peptide synthesizer on the market is the Model 9050 from PerSeptive Biosystems. This system was originally developed by the Bedford, Mass.-based Biosearch subsidiary of Millipore Corp., which recently sold this division to PerSeptive. The 9050, running with a 486-based personal computer, will synthesize up to three peptides at once, with yields ranging from 0.05 millimole up to 5.0 millimoles. The system runs a bit ...
20:11 <@kanzure> ... like a liquid chromatograph. The solvents flow continuously through packed columns of solid-support resin, for what the manufacturer claims is enhanced reaction chemistry. The eluant from the column can then be monitored as it flows through a UV-absorbance detector. A dye is added to the solid support and released as the coupling reaction proceeds. When the UV-absorbance signal plateaus, the coupling is as complete as it is going to be at ...
20:11 <@kanzure> ... that stage. If the signal is not strong enough at this point, indicating that incomplete coupling took place, the reaction can be extended."
20:13 <@kanzure> "Meanwhile, Kelly Wasmund, director of peptide synthesis at Research Genetics Inc., a manufacturer of custom oligonucleotides and peptides based in Huntsville, Ala., is finding that the diversity of instruments has made his buying decision difficult. He will be buying an additional synthesizer to accompany the Advanced ChemTech system he bought a few years ago, when the company was the only game in town for multiple-peptide synthesizers."
20:13 <@kanzure> heath: this was in the 90s but it would be col if you go check if that guy is still there
20:13 <@kanzure> *cool
20:28 <@kanzure> "The ABI 3900, designed by Northwest Engineering, is a 48 column rotary design oligonucleotide synthesizer. "
20:28 <@kanzure> huh? applied biosystems didn't design the ABI 3900?
20:29 <@kanzure> " To meet that need, PE Biosystems has entered into a strategic licensing agreement with Northwest Engineering of Alameda, CA, to release the ABI 3900 High Throughput DNA Synthesizer. A compact, bench-top instrument, the 3900 system features parallel, unattended, 48-column synthesis and <5-minute cycle times/48 couplings. The instrument, which uses proprietary FastPhoramiditeâ chemistry and polystyrene supports, synthesizes primers, probes, ...
20:29 <@kanzure> ... and sequences >50-mers. A convenient PC controller allows automatic transfer of sequences, functions, and cycles to the 3900 synthesizer. Note:The 3900 High Throughput DNA Synthesizer will be on display at the upcoming TIDES 2000 conference, May 9-12, Las Vegas, NV."
20:30 <@kanzure> here's someone that worked on it: http://www.linkedin.com/pub/robert-tjan/16/267/4bb
20:32 <@kanzure> this one has good references: https://www.google.com/patents/US6932943
20:32 <@kanzure> like a "Multi-well rotary synthesizer" by "Northwest Engineering" https://www.google.com/patents/US6270730
20:35 <@kanzure> paperbot: http://online.liebertpub.com/doi/pdf/10.1089/dna.1984.3.401
20:35 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/5219a56a9bf86b0cb968ee9a1446fb3c.txt
20:35 <@kanzure> it's supposed to be "Construction and Evaluation of an Instrument for the Automated Synthesis of Oligodeoxyribonucleotides"
20:36 <@kanzure> "The details for constructing an easily used and maintained laboratory instrument capable of routine oligode-oxyribonucleotide synthesis are presented. The synthesizer consists of relatively inexpensive, commercially available components and is controlled by an Apple IIe computer. Since reagents are distributed from pressurized reservoirs through a liquid manifold by opening solenoid-activated valves, no pump is required. More than 600 ...
20:36 <@kanzure> ... oligomers containing up to 122 bases have been produced with a condensation cycle time of approximately 15 min with apparent coupling yields of 98.5%. A unique bidirectional flow reactor and controlled reagent distribution system provide for rapid mass transfer during solvent and reactant equilibrations and for long-term stability of reagent solutions. Aspects of the system should also find use in other solid-phase synthetic and ...
20:36 <@kanzure> ... analytical strategies."
20:59 <@kanzure> also updated https://github.com/kanzure/python-requestions because apparently it was uninstallable (oops)
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21:29 <@kanzure> oh he cared enough to submit a solution
21:29 <@kanzure> https://github.com/kanzure/python-requestions/pull/2
21:29 <@kanzure> but he was a little slow
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22:14 <@kanzure> hey does anyone feel like taking a stab at https://github.com/kanzure/python-requestions/issues/3 ?
22:14 <@kanzure> join #python-requests
22:14 <@kanzure> oops
22:14 <@kanzure> irc fail
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22:44 <@kanzure> nevermind i think i got it
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23:20 < anannie> I have a stupid question
23:20 < anannie> Why hasn't anyone invented a heart rate monitor that uses the EM field generated by the heart to figure out the pulse?
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23:24 <@kanzure> interference
23:25 < anannie> ah but we have algorithms for that
23:26 < anannie> entire realms of signal processing have been devoted to that
23:27 <@kanzure> aww crap i forgot to reply to the n55 person
23:27  * kanzure sleeps
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--- Log closed Mon Aug 05 00:00:46 2013