2012-09-06.log

--- Log opened Thu Sep 06 00:00:18 2012
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kanzurebrownies: what was wrong with knockout.js when you tried it?07:51
chris_99http://prometheusfusionperfection.com/07:53
archelshttp://filer.case.edu/dts8/thelastq.htm08:06
archelsoh man, very thought-provoking story, but what a shitty ending.08:06
archelsDid anyone ever make it through Tipler's book?08:17
archelsHave it on my shelf, never read it fully, not sure what to think of it.08:17
kanzureeat it08:27
chris_99i got molecular biology of the cell today :)08:31
chris_99apparently this works great for SMD work - http://www.argos.co.uk/static/Search/searchTerms/TOAST+OVEN.htm08:47
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archelsJesus fucking Christ, why would *anyone* use MatLab?09:41
archelsWhy am I using it, for that matter? :(09:41
Urchinit is a bit archaic09:42
Urchinlarge codebase though09:42
archelsYou would think the shitty performance, unresponsive GUI and shitty memory mangement might be offset by great debugging capabilities...09:42
archelsbut no.09:42
* archels would be doing this in Python if there wasn't so much existing code to port09:43
Urchinlike I said, large codebase09:44
UrchinI was never fond of python for some reason09:45
Urchinnot really sure why09:45
chris_99what do you use Urchin09:45
Urchinnot much lately09:45
UrchinI did most of my stuff in C09:46
Urchinsome Fortran 9009:46
archelsC is beyond any form of criticism09:46
Urchinlisp to set up emacs09:46
UrchinC is great if you know what you're doing09:47
chris_99C is pretty awesome09:47
kanzurearchels: what code is there to port?09:48
chris_99you could compile it to C archels and use that ;)09:49
archelskanzure, it's not worth doing it at this point in the project. I'll just have to live with these minor annoyances...09:50
kanzureyou could write a wrapper in python09:51
kanzureand it sends everything off to matlab09:51
kanzureand then it spits out the result to you09:51
archelsyes, I did that once, for something else09:51
archelsI guess it avoids the GUI... but it's a little silly.09:52
archelsDoesn't really solve anything.09:52
kanzurehttp://diyspartanbiotech.wordpress.com/2012/05/11/transforming-e-coli-with-pvib-plasmid/09:52
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kanzure"I believe a critical component of igem technology revolves around t-shirt design skills."10:45
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brownieskanzure: hmmmm10:58
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brownieskanzure: oh, right, knockout is the one with the data-bindings and the magic auto-updating10:59
brownieskanzure: yeah, it's just too damn magical10:59
browniesit sounds nice, but you basically end up jumping through all these hoops just so you don't have to call (e.g. like you would in backbone) myView.render()11:00
kanzureso it's the views that you hated?11:02
kanzurewas meteor the one with the weird event propagation?11:02
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browniesgiven that knockout is a view/template library, yes, that seems fair -_-11:07
browniesmeteor is the dumb one that tries to have even more magic by automatically writing changes to teh server11:08
kanzurebrownies: apparently hittail.com will write articles for you to match the keyboards you've found through them11:08
kanzurei think it's hilarious, but it makes sense because that's what you'd probably pay someone to do after you use them anyway..11:08
brownieskanzure: not unreasonable11:08
browniesyeah, exactly11:08
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kanzurenmz787: so i'm looking at benchling..11:28
kanzureits tagline is "GitHub of Biology" ... :/11:28
kanzurei doubt they even implement git11:29
kanzure"Scientists build with DNA, just like programmers do with code. Major biotech companies account for 2% of the US GDP. Despite this value, there is no version control in life science."11:29
kanzureoh wait they actually say version control. maybe they do really mean git.11:29
kanzurehrmm. https://benchling.com/beta/ "Annotations, BLAST, plasmid maps, primer design, and more without leaving your browser." ok this just sounds like connor's thing..11:31
kanzurei don't know how they expect to implement git in a browser. maybe they're using git.js?11:31
kanzureto be fair i'm probably the trifecta of their worst possible customer (someone who understands version control and plasmids and is critical of both)11:31
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nmz787lol11:35
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delinquentmeOh shart.12:09
delinquentmejmil, I just emailed one of your guys there at hive 7612:10
kanzurewhich one of hive76's guys is jmil's guy?12:10
delinquentmetell Chris Thompson i said " HOWDAR "12:10
jmildelinquentme: nice. what about?12:10
delinquentmesomeone there is building a lasersaur12:11
delinquentmeSo I had emailed about sourcing parts12:11
delinquentmebuy from OSH owners == support OSH12:11
chris_99how much does it cost to build one delinquentme12:18
delinquentmei dont remember the number12:19
chris_99http://labs.nortd.com/lasersaur/bom-zero-suppliers-eur12:30
chris_99http://labs.nortd.com/lasersaur/bom-zero-suppliers-usd12:30
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chris_99this stuff is interesting http://www.fibrephotonics.com/page/143/High-Power-Polycrystalline-Infrared-HP-PIR-.htm12:34
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nmz787hmm, that fiber is cool12:43
chris_99attach that to a RepRap and your CO2 laser, bish-bash-bosh ;)12:44
chris_99actually it'd be cheaper to buy a chinese laser cutter12:44
chris_99the laser they use in the BOM is v. expensive12:51
chris_99£100012:51
nmz787how many watts12:53
chris_99just 10012:54
chris_99i think you can get them on fleabay for £200 or so12:54
chris_99but they may not be the same quality i guess12:54
chris_99oh i stand corrected12:57
chris_99they're more like £50012:57
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kanzurekingjacob_: having some trouble? :P13:58
Mariu=]13:58
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chris_99nmz787, did you see that spectrino thing btw14:14
loansharkhurro14:15
chris_99hello14:15
loanshark:314:15
chris_99read any books recently loanshark?14:16
chris_99i just got the cell book :)14:16
loansharkchris_99: i have been incredibly busy at work so no14:17
loansharkmy Kindle does not read PDF's otherwise i would be reading text books, but alas i do not have 50-60 dollars to spend on a textbook in the amazon store.14:18
chris_99weird, thought the kindle supported pdfs14:18
loansharkcurrently reading a book on basic economics - have to decide what college courses I will take next semester14:18
loansharkchris_99: i have an older kindle14:19
chris_99ah darn14:19
Mariuget a Samsung Galaxy pad14:19
chris_99that's not eink though is it14:19
loansharkuhh14:20
loansharkO.o $51014:20
loansharkmy kindle is eink14:20
chris_99yeah that's why i like the idea of the kindle14:20
chris_99http://www.solidoodle.com/ seems pretty cool, not open source though afaik14:21
loanshark$99 is hard to beat xD who needs color when all you are reading is books?14:21
loansharkalthough colorful diagrams in textbooks are helpful14:21
chris_99yeah colour eink will be sweet14:22
loansharkchris_99: is that possible?14:22
chris_99yeah theres been prototypes14:23
loansharkhttp://www.eink.com/display_products_triton.html14:23
loansharkyou can buy the jet book, which has tritons imaging film - essentially color sink, but its $50014:25
chris_99sounds interesting14:27
loanshark10,000 page turns on a single charge14:28
loansharkXD14:28
loansharkits worth the money i guess, but i bet in a year or two it will be $10014:28
chris_99yeah14:29
strangewarpFirst day on a noopept/citicoline/alpha-GPC cocktail.14:32
strangewarpVery distinct improvement.14:32
loansharkstrangewarp: whats that?14:34
strangewarpnootropics, natch14:34
loansharkimproves… brain?14:35
loansharkxD14:35
strangewarpNoopept is an ultra-potent relative of piracetam; citicoline is another sort of nootropic that's new and patented; alpha-GPC is a form of choline that allows for more efficient absorption than choline citrate or CDP-choline.14:35
strangewarpIn general, nootropics improve mental abilities, and mood.14:35
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loansharkinteresting. what do you notice is different?14:36
HighSpeedso um14:38
HighSpeedguiz14:38
HighSpeedwe have a nootropic chat here on freenode14:38
HighSpeed#reddit-nootropics14:38
loansharkcool14:39
strangewarpmeh, reddit...14:40
HighSpeedwhy? its pretty good14:40
HighSpeedthe premier BLTC freenode chat14:40
strangewarploanshark: I'm feeling very calm and focused, and self-confident, which is very different from how I usually am14:42
strangewarpWe'll see how it affects my productivity..14:42
loansharkinteresting14:43
loansharkI am on anti-depressants… would this have adverse affects with nootropics?14:43
strangewarpMaybe. I am not a doctor14:43
loansharkok14:45
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sylph_makoHighSpeed, why is it named after reddit? It's not reddit. It's an IRC channel.15:16
sylph_makoIf you think the imported redditers will confer some special property, I think you'll be disappointed.15:17
archelsdrama?15:17
* archels runs15:17
Mariu=]15:18
* sylph_mako sprays anti-hysteria aerosol in archels' wake.15:19
HighSpeedsylph_mako: nah i dont even go on reddit lol15:20
HighSpeedjust happens to be a nootropics chat15:20
Urchinprobably started by redditers, so why not?15:21
Mokbortolan_1huh what?15:21
Mokbortolan_1yeah, I run that room15:21
sylph_makoso why the name.15:22
Urchinimminst's nootropics forums were good last time I've checked15:22
Mokbortolan_1it's officially associated with /r/nootropics15:22
Mokbortolan_1there's a link on the sidebar15:22
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kanzurei need a machine to be invented that punches programmers in the face every time they try to vaildate an email address with a regular expression18:19
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ThomasEgithe famous "punch people over tcp ip"?18:28
kanzureis that a feature? i haven't checked the standards.18:29
ParahSailin_im sure regex _could_ validate email addresses18:30
kanzureParahSailin_: there's this super-long regular expression that jrayhawk likes to link to that is supposed to be correct18:31
kanzurebut it's a few hundred kilobytes i think18:31
ParahSailin_yeah, there's a similar huge regex for html18:31
kanzuredon't do it18:31
kanzureor else i will tcpunch yuo18:31
ParahSailin_its pretty much write-only18:31
ParahSailin_http://tools.ietf.org/html/rfc2822#section-3.4.118:33
kanzureParahSailin_: what would make biologists hate computers less?18:34
ParahSailin_hard ai?18:34
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kanzurewell, it's odd because they certainly don't lack dedication or attention.. if they can spend hours reading a paper, they can spend a few minutes figuring out a website or something18:36
kanzurehm https://github.com/cathalgarvey/biohacking-protocols18:37
kanzure"cathalgarvey authored 10 hours ago"18:37
kanzure"Low-overhead, highly explicit protocols in Markdown format for Biohacking"18:37
jrayhawki think scientists are explorers and resent being constrained to a problemspace18:38
jrayhawkthey like finding new problemspaces18:38
kanzurestreety: you sound like the sort of person who would be able to tell me a reference to someone who has studied this18:39
jrayhawkthe web is made by a phycisist18:39
jrayhawkit shows18:39
jrayhawkphysicist18:39
kanzurejrayhawk: i want to include https://github.com/cathalgarvey/biohacking-protocols stuff in diyhpluswiki.git18:39
kanzurewill a submodule render with ikiwiki?18:40
streetyreference for what?18:40
kanzurestreety: someone who has studied the general hatred biologists harbor for computers18:40
jrayhawkno, no useful or interesting integration with submodules has been done18:41
streetylol, I'm not sure I've seen that phenomenon but then I've spent most of my time on the more chemical side of biology18:42
jrayhawkwe can do some hacks to make it work as a submodule, but it'd probably be easier to just have it as a separate repository18:42
kanzurejrayhawk: okay.18:44
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kanzureremote: skipping bad filename E.coli Transformation With PEG+MgSO4.md18:46
kanzurejrayhawk: doh.. spaces in filenames.18:46
kanzurehttp://diyhpl.us/cathal-biohacking-protocols/E.coli%20Transformation%20With%20PEG%20MgSO418:46
jrayhawkecho '$conf->{"wiki_file_chars"} = "-[:alnum:]+/.:_ "' > /etc/ikiwiki/piny/cathal-biohacking-protocols.setup.pl; rebuildrepo cathal-biohacking-protocols18:55
nmz787kanzure: is the share alike thing good?19:02
kanzureyes19:03
nmz787anyone use this http://windows.github.com/19:05
kanzureno.19:08
nmz787kanzure: wasn't asking /you/19:12
nmz787:P19:12
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nmz787this looks interesting http://www.horizonsnyc.org/site/speakers/21:31
kanzurekingjacob: hi21:32
nmz787i've actually thought that you should be able to RF tune a designer psychedelic-type molecule to feed video in and get neural output out21:32
nmz787eliminating through-skin ports21:32
nmz787since it seems psychedelics already hit the sensory and a/v parts of the brain21:33
kingjacobI could see building a RF activated psychedelic being possible21:39
kingjacobany ideas how you'd get more than a bit through?21:40
nmz787I've got a ton of PDFs on radio waves and their molecular action... but mostly it says molecules rotate and cause heating21:41
kanzurehow about a magneto-optical receptor switch thing21:41
nmz787I think kanzure would have some ideas about spatial resolution in bit banging gadgets that exist21:42
nmz787isn't there some way to use 2 beams?21:42
nmz787or maybe you'd need a mix of different molecules21:42
kanzurewell, you can use a phased array of multiple beams if you want the effect to be additive at some location21:42
nmz787each type representing a different freq channel21:43
* kanzure is bullshitting21:43
kanzurenmz787: you're familiar with anselm's work right?21:43
nmz787and each targeting a different visual neuron type21:43
nmz787no21:43
kanzurelike http://anselmlevskaya.com/publications/Nature%202009%20Levskaya.pdf21:43
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nmz787kanzure: but optical/freqs that high don't penetrate the body very well21:46
kanzurei think he had mice with physical glass windows in the skull21:46
nmz787other than the pit viper IR detectors, there isn't any receptor with lower freq sensitivity21:46
kanzure(because fuck skulls)21:46
nmz787heh21:47
nmz787yeah21:47
nmz787i can't do that to myself21:47
nmz787yeah I tried finding info on other freqs when I was all gung-ho about finding some proof of telelpathy type stuff21:49
nmz787but I really didn't find anything below light and heat IR21:50
nmz787ears don't count because its physical waves, not EM21:50
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kingjacobyou wouldn't need to do an implant21:50
kingjacobjust pair it with a system on the surface21:51
nmz787right21:51
nmz787but how to get spatial respones from the nerve bundle21:51
nmz787say we know the drug is there, around all the cells21:51
nmz787kanzure: wtf are phased arrays21:51
kanzure"We have determined that the best way to implement telepathy is to strap a 2.9 GeV particle accelerator to your head. Naturally, you can't ever move, but you do get electrons blasted into your brain which is pretty cool. Also deadly."21:52
kanzureoh i just meant for stimulation21:52
kanzurelike http://diyhpl.us/~bryan/papers2/neuro/ultrasound/500-element%20ultrasound%20phased%20array%20system%20for%20noninvasive%20focal%20surgery%20of%20the%20brain%20-%20A%20preliminary%20rabbit%20study%20with%20ex%20vivo%20human%20skulls.pdf21:52
kanzurephoto is on page 221:53
nsh-so21:53
nsh-at the risk of one or more of us sounding stupid21:54
nmz787I wish we lived in an era where people could still sell good cure-alls21:54
nmz787this seems appropriate http://www.springerlink.com/content/v2175688r1w4862x/fulltext.pdf21:54
nsh-isn't there already a pretty tried and tested method of getting data from optical wavelengths into the brain?21:54
nsh-with reasonably high bandwidth21:54
nsh-why do people think they're achiving something miraculous by bypassing sensory organs?21:54
nsh-that's pretty ridiculous way of going about augmentation21:54
nmz787well the eyes are for input, but you can't output21:55
nsh-sure you can21:55
nsh-have you ever looked someone in the eyes?21:55
nmz787sure21:55
nsh-the entire region around them acts as pretty good transmitter21:55
nmz787I21:55
nmz787I21:55
nmz787I'd rather have neural to electrical adapter21:56
nmz787or electronic21:56
nsh-that's because you think silicon is advanced technology21:57
nmz787well no, I just think faster than i can move my muscles21:57
nsh-prove it21:58
nmz787so my output is pretty limited21:58
nmz787not sure how to do that, since you can't hear my thoughts21:58
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kingjacobit took me less than a second to think up this sentence but almost 10 seconds to type it21:59
nsh-sure, there's a bottle neck21:59
nsh-but are you sure about the veracity of the timeline?21:59
nmz787what do you mean?22:00
nsh-you percieve the creation of the sentence as being instantaneous, almost22:00
nsh-but is that necessary an accurate reflection of internal process, or a presentation layer to consciousness?22:00
nsh-i don't doubt that we think quicker than we can talk/type22:00
nsh-but the thought evolves as we do so22:00
nmz787i've heard some people don't have an internal monologue22:00
nmz787but some do22:01
nmz787if that means anything22:01
* nsh- doesn't percieve a monologue22:01
nsh-i am only aware of words when working with them22:01
* Mokbortolan_1 takes a shot of jaegeracetam.22:01
nmz787sure it evolves as we do, but maybe if I had faster I/O I would learn to hold my tongue, so to speak, before outputting22:02
nmz787i often have music looping in my head22:02
nmz787it used to get quite annoying as a kid, i remember22:02
nmz787but not so much anymore22:02
strangewarpI've always had a pretty powerful internal monologue; when I was a child I had to work for a few years to suppress the urge to whisper it to myself. Nowadays it alternates between subvocalization and regular thoughts22:03
nmz787I have monologues about some things, but it isn't necessary for all actions22:05
nmz787like painting for instance, i wouldn't tell myself 'up, down, up, down'22:05
nmz787but for counting money, i would be like '20, 40, 60, 80, 100, and 50 cents', etc...22:05
strangewarpWell yeah, painting is the interaction of physical objects, so it would be a second-order command if you were saying the names of directions to yourself...22:06
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kanzurekingjacob: maybe it takes you too long to type things because you're slow?22:08
kanzurewww.seanwrona.com/typeracer/profile.php?username=kanzure22:08
kanzureerm.. i meant http://www.seanwrona.com/typeracer/profile.php?username=kanzure22:08
kingjacobkanzure: that's probably 10% of it22:09
nmz787kanzure: why waste the ATP on muscle contractions though?22:09
nmz787and then you get typers wrist or whatever that is22:09
kanzurenmz787: because i don't have anything else working22:10
nmz787but do you want better?22:10
kanzureof course22:10
nmz787actually i think the permittance changes with EM frequency22:13
nmz787if so, maybe you just need to adjust the frequency to get depth22:13
kingjacobdo yall remember the name of th paper where they got video out of the brain?22:14
kanzurekingjacob: http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20of%20natural%20scenes%20from%20ensemble%20responses%20in%20cat%20visual%20cortex%20-%20Stanley%20-%201999.pdf22:15
nmz787199922:19
nmz787I saw something recently22:19
browniesare you multilingual nmz787 ?22:19
nmz787a bit22:20
nmz787I picked up Thai pretty quickly, grammar was bashed horribly but I knew numbers and foods well, directions... and started picking up the symbols too22:20
nmz787my girlfriend speaks bengali and hindi and I've been hanging around indians for about 4 years22:21
kanzurei am also skilled in the binary language of moisture vaporators22:21
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nmz787kanzure: so how many electrodes in that paper?22:21
kanzurethey probably used a utah array of <100 electrodes22:22
nmz787looks like 722:22
nmz787Neighboring geniculate cells were recorded with a multielectrode array22:22
nmz787(Eckhorn and Thomas, 1993). The array allows seven fiber electrodes to22:22
nmz787be positioned independently with a vertical accuracy of 1 mm. We used a22:22
nmz787glass guide tube to restrict the lateral scattering of the electrodes in the22:22
nmz787array. The inner diameter at the tip of the guide tube was ,400 mm. All22:22
nmz787recordings were made in layer A or A1 of the LGN.22:22
nmz787Recorded signals were amplified, filtered, and passed to a personal22:22
nmz787computer (PC) running Datawave (Broomfield, CO) Discovery software.22:22
nmz787The system accepts inputs from up to eight single electrodes. Up to eight22:22
nmz787different waveforms can be discriminated on a single electrode, but two22:22
nmz787or three is a more realistic limit. The waveforms were saved on disk.22:22
nmz787Spike isolation was based on cluster analysis of waveforms, and the22:22
nmz787Neighboring geniculate cells were recorded with a multielectrode array (Eckhorn and Thomas, 1993). The array allows seven fiber electrodes to be positioned independently with a vertical accuracy of 1 mm. We used a glass guide tube to restrict the lateral scattering of the electrodes in the array. The inner diameter at the tip of the guide tube was ,400 mm. All recordings were made in layer A or A1 of the LGN. Recorded signals were amp22:23
nmz787fractory period, which is reflected in the shape of22:23
nmz787autocorrelations22:23
nmz787kanzure: do you understand the coding they talk about?22:24
nmz787or de-coding?22:24
kanzureuh, i've done some basic neural ensemble coding software stuff22:24
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kanzurethe visual system is pretty well understood at this point22:24
nmz787so it looks like they moved the fiber with the 7 channels around22:24
nmz787to sample abou 177 cells22:25
nmz787so I guess they sortof did a sweep22:25
kanzureyeah i guess they replayed the video multiple times22:25
kanzureand just sampled at different times22:25
nmz787so can you tell an idiot what the visual protocol is?22:25
kingjacobhere's the more recent one http://www.cell.com/current-biology/abstract/S0960-9822%2811%2900937-722:25
kanzureno there's lots of different encoding things going on22:26
kanzuretopographica is some open source software to simulate some of it22:26
nmz787here's a good review http://diyhpl.us/~nmz787/biological%20radio%20research/Quantitative%20Evaluations%20of%20Mechanisms%20of%20Radiofrequency%20Interactions%20With%20Biological%20Molecules%20and%20Processes.pdf22:28
nmz787on RF + biology22:28
nmz787I read somewhere that medium frequency EM is essentially quiet in the universe, so that's probably why we never developed sensors for it22:29
nmz787"22:31
nmz787Biochemical reaction yields can be changed by both static and RF magnetic fields that alter the number of spin-coupled radical pairs that recombine. Several distinct mechanisms exist to explain radical pair recombination effects that occur with static and RF magnetic fields over the range from millitesla to microtesla levels. Radical pair mechanisms depend on the magnetic properties of the nuclei comprising the spin-coupled radical pai22:31
nmz787"22:31
nmz787"The question arises as to whether absorption of multiple RF photons in the GHz range can excite low-lying absorption modes in biological molecules such as the mode at 184 GHz (6 cm^-1) calculated for myoglobin by Rai and colleagues (Rai et al. 2003) Prohofsky 2004). In principle, multiple photon processes could upshift incident energy to a region where resonant interactions are known to occur. In general, multiphoton absorption requir22:34
nmz787"22:34
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maraineindoes this imply magnetic fields (like MRI machines) can damage organisms?22:53
nmz787not really, unless it heats you up too much in some area22:58
nmz787or it hits some apoptosis RF receptor we don't know about22:58
nmz787http://www.foxnews.com/health/2012/09/05/colorado-girl-recovering-from-bubonic-plague/?utm_source=BNT+September+6%2C+2012&utm_campaign=BNT090612&utm_medium=email23:03
nmz787"Sierra Jane's life got the first inkling that she had bubonic plague. Dr. Jennifer Snow suspected the disease based on the girl's symptoms, a history of where she'd been, and an online journal's article on a teen with similar symptoms."23:03
nmz787hell yeah internets23:03
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skorketnmz787:  http://imgur.com/haQoe23:55
skorketnot there yet, but getting closer23:55
--- Log closed Fri Sep 07 00:00:19 2012

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