2013-04-06.log

--- Log opened Sat Apr 06 00:00:49 2013
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AshleyWaffleHi00:14
AshleyWafflenight, I'll be on tomorrow00:14
kanzurehttp://www.neocomputer.org/projects/et "Fixing E.T. The Extra-Terrestrial for the Atari 2600"00:28
JayDuggerSeriously? "why do people hate E.T.?"00:32
JayDuggerAnswer: "It was completely non-violent. You can't hurt the bad-guys, and they can't hurt you. There isn't even any competition!"00:32
JayDuggerI remember playing that game as a child. Boring.00:32
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chidokanzure: he's part of my lab :)00:46
kanzureexcellent00:46
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kanzureredsocks really eats up cpu if you let it run forever01:03
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kanzure$35/hour for... well it doens't [A[A[A[A01:24
kanzureirssi error. bleh.01:24
nmz787http://en.wikipedia.org/wiki/List_of_animals_by_number_of_neurons02:11
nmz787we're billionaires!02:13
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paskyhttp://www.newscientist.com/article/mg21829114.700-hacked-medical-scanner-becomes-a-nuclear-forge.html - seems like the mainstream media notion of "hacking" is shifting in the good direction :)04:37
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kanzurepaperbot: http://www.plosone.org/article/info:doi/10.1371/journal.pone.006041009:12
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Non-Invasive%20Brain-to-Brain%20Interface%20%28BBI%29%3A%20Establishing%20Functional%20Links%20between%20Two%20Brains.pdf09:12
kanzure"Non-Invasive Brain-to-Brain Interface (BBI): Establishing Functional Links between Two Brains"09:12
kanzure"Transcranial focused ultrasound (FUS) is capable of modulating the neural activity of specific brain regions, with a potential role as a non-invasive computer-to-brain interface (CBI). In conjunction with the use of brain-to-computer interface (BCI) techniques that translate brain function to generate computer commands, we investigated the feasibility of using the FUS-based CBI to non-invasively establish a functional link between the brains ...09:12
kanzure... of different species (i.e. human and Sprague-Dawley rat), thus creating a brain-to-brain interface (BBI). The implementation was aimed to non-invasively translate the human volunteer’s intention to stimulate a rat’s brain motor area that is responsible for the tail movement. The volunteer initiated the intention by looking at a strobe light flicker on a computer display, and the degree of synchronization in the electroencephalographic ...09:12
kanzure... steady-state-visual-evoked-potentials (SSVEP) with respect to the strobe frequency was analyzed using a computer. Increased signal amplitude in the SSVEP, indicating the volunteer’s intention, triggered the delivery of a burst-mode FUS (350 kHz ultrasound frequency, tone burst duration of 0.5 ms, pulse repetition frequency of 1 kHz, given for 300 msec duration) to excite the motor area of an anesthetized rat transcranially. The ...09:13
kanzure... successful excitation subsequently elicited the tail movement, which was detected by a motion sensor. The interface was achieved at 94.0±3.0% accuracy, with a time delay of 1.59±1.07 sec from the thought-initiation to the creation of the tail movement. Our results demonstrate the feasibility of a computer-mediated BBI that links central neural functions between two biological entities, which may confer unexplored opportunities in the ...09:13
kanzure... study of neuroscience with potential implications for therapeutic applications."09:13
kanzure1.59 seconds, geeze.09:14
FooQuuxmanBeen waiting for non-invasive Mind-Machine interfaces for a while09:23
FooQuuxmangood to know they are starting to show up09:23
kanzureit said nothing about minds, what the fuck dude09:25
* kanzure finds lunch09:26
FooQuuxmansorry, wtf?09:26
kanzureread it again. it says nothing about minds.09:26
FooQuuxmanBrain, Mind, whats the difference?09:26
kanzuretremendous.09:26
FooQuuxmanor better way to put it: what is the difference as far as pluging in goes?09:28
kanzurestudying one of them will lead to actionable results09:29
kanzurethe other will not09:29
abetuskone is the organ, the other is what the organ does09:29
kanzurenot really09:29
abetuskunless you're a dualist09:30
FooQuuxmanoh I see, that makes more sense09:30
kanzurei am not a dualist, i just believe philosophers tend to suck09:30
FooQuuxman*tend* to?09:30
kanzureand that philosophy is no replacement for actually poking at the brain09:30
abetuskyou'll get no argument from me09:30
kanzurealso the other part of your comment that i found objectionable was the part about waiting09:32
kanzureperfect storm of terrible things09:33
AshleyWafflekanzure: I agree about the waiting thing. But it's pretty clear he meant brain09:53
AshleyWaffleI don't think you'll find any religious nuts here09:53
AshleyWaffleSo don't pretend that's the case09:53
AshleyWafflealthough... isn't FooQuuxman catholic or something?09:53
FooQuuxmancatholic, no09:54
AshleyWaffleAre you religious?09:54
FooQuuxmanyes09:54
FooQuuxmanI would be considered a dualist, but the 'line' between mind and brain is currently too blury to be useful09:55
FooQuuxmanI could even be convinced that the mind is just software09:55
AshleyWaffleFooQuuxman: Well, in a sense that's true I guess. A brain could just as easily be a random and meaningless neural network that does nothing. The configuration of neurons does matter a lot and I guess could be considered "software"09:57
AshleyWaffleBut I think we're all focused on the configuration aspect - computers can already do small neural network simulations09:57
ParahSail1nghoooooooooooossts09:57
FooQuuxmanwoooooooooooo09:58
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kanzuresee! i spotted the dualist from just a single comment.10:22
FooQuuxmanwoot! how many internets is that worth?10:22
kanzureone. why are you here?10:23
FooQuuxmanbecause people on #mises kept saying that if someone wanted ideas for projects to come here10:24
FooQuuxmanI was here to look around and figure out the channel10:25
kanzurewhat is #mises?10:25
FooQuuxmanas in ludwig von mises10:25
kanzurei'm not seing the connection.. why would they tell you to come here?10:30
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FooQuuxmannah, they weren't telling me, it was someone else10:31
FooQuuxmanKelvin maybe?10:31
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kanzurewhat sort of projects?10:39
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kanzurepaperbot: http://www.nature.com/ng/journal/v45/n4/full/ng.2528.html11:40
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Identification%20of%20seven%20loci%20affecting%20mean%20telomere%20length%20and%20their%20association%20with%20disease.pdf11:40
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kanzure"Also, at the cheapest how much would a PCR reaction be (with and without polymerase)? Any thoughts?"16:22
kanzurei think that goes away if you exercise more16:22
kanzureoops16:22
kanzurewhy would it be PCR if you have no polymerase16:22
browniesjust a regular ol' chain reaction16:23
ParahSail1nmaybe he means cost including and not including enzyme?16:24
ParahSail1nyou should ban mega from diybio mailing list16:28
kanzurei am not a moderator16:28
kanzurein fact i'm pretty sure they've considered banning me often16:28
ParahSail1noh is cathal moderator?16:28
kanzureno16:28
kanzureonly mac cowell and jason bobe16:29
yashgarothman I would ban so many people from the mailing list if I could16:30
kanzurekickbans for everyone!16:31
ParahSail1nwhat did you do to piss them off kanzure16:31
kanzurei have always been opposed to their ideas for making top-down policy decisions and shit16:32
ParahSail1ni didnt know they had any policy decisions16:33
kanzurebecause i kept yelling at them :P16:33
kanzurethings like, demanding that everyone signs on to a code of ethics16:34
ParahSail1nwhat were they trying to police16:34
ParahSail1nah geez16:34
browniesa code of ethics? for a mailing list?16:34
kanzureor pretending to represent all of the interests of everyone on the mailing list16:34
kanzureyes16:34
kanzurethey also wanted a moratorium on biohacking projects at one point16:34
ParahSail1nfucking busybodies should just get busy16:34
ParahSail1ndiybio:biohacking::siai:ai?16:35
kanzurejason gets grants from woodrow wilson foundation to "study" diybio16:35
brownies"Thou shalt not suffer a thread to be off-topic"16:35
kanzurebrownies: nah, more specific biohacking ethics things16:35
kanzurei think it is very misleading to claim to government bodies that everyone agrees to some code of ethics16:35
kanzurefor individual institutions/companies like biocurious and genspace, i think a code of ethics is a grand plan that works out pretty well.16:36
kanzureof course, that's not diybio.16:36
kanzureor, rather, it might be diybio but it's certainly not going to accurately represent the motivations of independent individuals working on their own biology projects16:37
kanzurelike cathal.16:37
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abetuskum, so what is the cheapest you can source reagents for a PCR experiment?17:53
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ParahSail1nassuming you can produce your own pol, dntps are the limiting reagent17:56
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kanzureParahSail1n: i don't think anyone in diybio has produced their own polymerase yet18:25
ParahSail1nhow that seems pretty incompetent-- i mean, i haven't either, but i haven't been in a wetlab for a while18:26
abetuskI thought there was a guy selling taq out of his garage...?18:26
kanzurewho was selling taq?18:26
abetuskMaybe I just have a faulty memory18:27
yashgarothwasn't avery doing something with opentaq18:27
abetuskI thought you linked to it at one point, though I would probably have saved that link and I can't find it...18:27
kanzureopentaq was what john schloendorn was selling on openbiotech.com18:28
kanzurei don't know if john was making his taq himself or not18:28
ParahSail1ncathal seems to be someone who does stuff, but he seems scared of patents18:28
kanzurejohn sells a taq expression vector i think18:28
ParahSail1nis it broken in some way?18:29
kanzureno i think avery claims he got it to work at least once18:29
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kanzurei still think a lot of his claims are unsubstantiated18:32
kanzure"Ultimately, we anticipate no less than an industry-wide collapse of biological reagent pricing as a direct result of our open source policies. "18:32
kanzureon http://www.openbiotech.com/Default.asp18:32
kanzure"Open MasterMix is an optimized convenient premixed formulation of Taq polymerase and dNTPs in a buffer solution at 5x concentration for simple dilution when primers and template are added."18:34
kanzurewell i guess he is selling taq.18:34
kanzuredamn he is also selling a 293 strain?18:35
kanzurei need to get in on this shit18:35
yashgarothand yet somehow not one e.coli strain18:36
abetuskpOpenTaq, that's pretty awesome18:37
ParahSail1ni can give you 293 cells18:39
ParahSail1nwow 100 is not a bad price18:40
yashgarothcan you give me some dh5a's?18:40
ParahSail1nyashgaroth, i can do you one better18:41
yashgarothwhat, competent ones?18:42
ParahSail1nget free samples http://lucigen.com/store/E.-cloni-10G-and-10GF-Chemically-Competent-Cells/18:42
yashgarothwell they're not relA1- but I can live with that for $free18:43
ParahSail1nrecA?18:43
yashgarothnah, relA is the relaxed response to amino acid starvation where they still produce plasmid18:44
ParahSail1noh18:44
ParahSail1nare 5alphas relA1-?18:45
yashgarothyeah, but honestly it's not a huge problem unless you're just doing overnight cultures, which I hope not to18:46
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yashgarothnow to just make up an 'institution' for the request form18:47
kanzureyou can say you're with blackhatbio.com if you want18:48
ParahSail1nput random words together18:48
yashgarothI don't think the local diybio lab is active enough to ship there, but I really doubt lucigen accepts residential addresses18:49
ParahSail1nthe employee reading the order form is not going to make more or less money depending on whether he vets all the institutions they send samples to18:49
yashgarothuniversity of the house I live in18:50
yashgarothoh god "E. cloni®"18:51
kanzurei thought it was a typo in the url18:51
ParahSail1nyashgaroth, hey, the shit works18:51
kanzure/store/E.-cloni-10G18:51
ParahSail1ncompetent as hell18:51
yashgarothI wonder how well they store at -2018:52
yashgarothand by -20 I mean whatever my kitchen freezer puts out18:52
ParahSail1noh yeah dont squander them like that18:52
ParahSail1nunless you just need a subcloning grade strain for making plasmid18:53
ParahSail1nyou can do pretty much anything to get e coli to make colonies on a plate18:53
yashgarothwell if I had the plasmid ready I could just do the transfection upon receipt, but fuck re-competentizing cells18:54
ParahSail1nso you could definitely store them as plate streaks or whatever18:54
yashgaroththe local lab's -80 should be working aaaany year now18:54
ParahSail1nyou can pretty much grow up a batch of cells and pellet them down and mix dna and youll get colonies18:55
ParahSail1ncompetency is for getting cloning to work18:55
yashgarothcan you just send me an agar stab of them? assuming that you recommend them from personal experience18:56
yashgarothI would be super appreciative18:56
ParahSail1ni dont have access to a lab anymore18:57
ParahSail1nthey'll give you a sample18:58
yashgarothhow long have they been giving samples out for? if it's an ongoing thing I may wait til I have a more legit address18:59
ParahSail1nthey've "always" given out samples19:00
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* brownies pokes kanzure 19:35
brownieshow many bookmarks do you have?19:35
browniesdoes Chrome slow down after some threshold # of bookmarks?19:35
kanzurei can't bookmark anymore because chrome crashes19:36
browniesi... see.19:36
brownieshow many bookmarks did that involve?19:36
browniesorder of magnitude19:37
kanzurenot many. i have a primary bookmark collection of about 57,000ish. the one in chrome is <5000.19:37
browniesyeah i have approximately the same amount in Chrome and it just... gave up on favicons19:37
browniesthat's a recent development, but i find it odd.19:37
kanzurei've been meaning to send a bug report to chrome upstream but since i don't have debug symbols i stopped caring.19:38
kanzurei get a segmentation fault when i add a new bookmark19:38
brownieskanzure: where the hell do you keep 57K bookmarks?19:38
kanzureelaborate file system19:38
browniesah, i can still bookmark. i just get major lag when i try to do so. or if i accidentally mouse over the bookmarks menu in the navbar.19:38
kanzureoriginally my collection began in firefox, then i moved to opera which seemed more able to handle larger numbers of bookmarks. then i switched to this weird flatfile system thing that i'm not 100% happy with yet.19:39
kanzurei think way back when my collection in firefox was using its dumb html bookmarking format before it got sqlite bookmarks :(19:39
ParahSail1ni hear firefox isnt terrible memory leaker anymore?19:40
kanzurefirefox has been making improvements in a lot of memory leaking areas but as far as i can tell it still can't handle >400 tabs well.19:41
ParahSail1nkinda reluctant to try it and see19:41
ParahSail1nheh 400 tabs19:41
kanzurei suspect that part of the problem was that firefox was always only 32 bit builds?19:41
kanzurei think there might be a 64 bit nightly build19:42
brownieseh, firefox's memory-leakage cured me of my desire to run >100 tabs. now i routinely stay under 50.19:43
browniesso in a sense... it was self-correcting.19:43
kanzurei want a better bookmarking solution19:50
kanzureall the online tagging things don't really handle more than a handful of bookmarks well19:50
kanzure"pfft only power users will have tens of thousands of bookmarks, and that will be just one guy"19:50
kanzurewell guess what that's me :(19:50
browniespinboard has been working fine for me19:51
browniesi have well over 10K bookmarks19:51
kanzurehm i admit i didn't try dumping everything into pinboard.in19:52
browniesit's well worth the $10 or whatever he charges19:53
kanzurei wanted to try historio.us at one point but it looked like it would break after two or three bookmarks19:55
browniesi liked the idea of historious, mostly because i had the exact same idea myself19:57
browniesbut by that time i had already paid for pinboard, and then the pinboard guy rolled out his archiving feature, so that was that.19:57
kanzurethug life.19:58
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ParahSail1npaperbot: http://www.jstor.org/stable/4156016020:10
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/f6398794044dc24e9a357ea9f9611625.txt20:10
rigelhttp://shop.lenovo.com/seind/SE/en/learn/products/laptops/thinkpad/thinkpad-edge/s430/index.html20:52
rigelso where the hell do i get this laptop in the US20:52
kanzurekeyboard sucks20:56
kanzurehttp://www.lenovo.com/shop/WW/products/splitter/notebooks/ThinkPad/Edge/gallery/ThinkPad-Edge-S430-Laptop-PC-Close-up-Keyboard-View-5L-940x475.jpg20:56
kanzurei recently picked up a thinkpad w52020:58
kanzurewhich has the non-sucky keyboard and 2x RAM capacity of the S43020:58
rigelthunderbolt20:59
rigelthats the only reason to get this laptop20:59
kanzureah.20:59
rigelbecause 1394 is apparently dead on laptops20:59
rigeland why the hell hasnt someone come up with a device/driver combo that can use a gigE port, like EVERY GODDAMN MODERN LAPTOP HAS NOW, as though it were e.g. 139421:00
rigeli mean sure you'd need to have some software to handle it somehow, but that should totally be possible21:01
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nmz787ethernet has a fair amount of overhead21:08
nmz787it's made to be able to pass through swithces and routers21:08
nmz787so it's not as cheap as peripheral protocols can use21:09
nmz787usb3 is pretty fast though21:09
nmz787i don't like that USB can fit into ethernet ports actually21:09
nmz787on my laptop, on the base station the ethernet is next to the power jack, and the power plug can fit into the ethernet port too21:10
nmz787so that's pretty anoyying21:10
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kanzureeleitl: alonzo is actually muted in here for those very reasons.21:33
ParahSail1n?21:35
kanzureParahSail1n: alonzotg believes that we are all conspiring to secretly upload him without his knowledge21:35
kanzureParahSail1n: and eugen has been debunking alonzotg's claims for years now21:36
ParahSail1nhow do you debunk such a claim21:36
kanzurewell, in particular, i was referring to eugen's recent emails21:37
ParahSail1nah21:37
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kanzurealso jrayhawk spent some time trying to debug him, i dunno if those logs are public21:41
ParahSail1nby upload you mean upload his brain to a computer?21:43
kanzureyes.21:43
kanzurethis thread- http://lists.extropy.org/pipermail/extropy-chat/2013-April/076485.html21:44
kanzuremore obvious from http://lists.extropy.org/pipermail/extropy-chat/2013-April/thread.html21:44
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ParahSail1nand why do you guys take that theory seriously enough to expend energy responding in any way?21:45
kanzureentertainment21:45
ParahSail1nthe mentally ill are always a good source of it21:45
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* strophariad glances topicward22:12
strophariadfor nootropics, consider hericium erinaceus22:12
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nmz787paperbot: http://scitation.aip.org.proxy.lib.pdx.edu/getpdf/servlet/GetPDFServlet?filetype=pdf&id=AJPIAS000078000007000671000001&idtype=cvips&doi=10.1119/1.3427413&prog=normal22:17
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/c162878fe64919687fc5b56b7b3553e4.pdf22:17
nmz787paperbot: are you getting old and/or tired? you seem a bit slow today22:17
yashgaroth.botstim22:18
nmz787or did it have to fail a ton of if statements?22:18
brownies.botsnack22:23
yoleaux:D22:23
kanzureit has to fetch the target url twice22:45
kanzureonce with zotero translation-server22:46
kanzureand then again with the python fallbacks22:46
kanzuremy guess is that when zotero translation-server tried to pull up scitation.aip.org.proxy.lib.pdx.edu it was hit with a series of redirects because most ezproxy instances are configured to let internal ip addresses through via http redirect22:46
kanzureand then it downloaded the pdf to zotero translation-server, which doesn't know how to handle raw pdf (it only returns metadata to paperbot)22:47
nmz787paperbot: http://www.opticsinfobase.org/ol/abstract.cfm?uri=ol-24-10-67022:50
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/5c1d93f8a531d09f81923f84a7abdc56.txt22:50
kanzureif you ever want to see something wacky..22:55
kanzurepaperbot: http://httpbin.org/get22:55
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/fcd8bef2d335baa2c57599bacdaf2c49.txt22:55
kanzurethere used to be this service similar to httpbin that would show you multiple incoming requests to a target url22:55
brownieshuh. that is wacky.22:55
kanzurethere's actually two outgoing requests to httpbin.org/get but obviously only one is going to be showed there22:56
kanzurethis could be eliminated with a simple caching server if i was not lazy22:56
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nmz787paperbot: http://link.springer.com/article/10.1007%2Fs00542-006-0367-923:03
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/A%20new%20DNA%20chip%20detection%20mechanism%20using%20optical%20pick-up%20actuators.pdf23:03
nmz787paperbot: http://pubs.rsc.org/en/content/articlelanding/2011/lc/c0lc00577k23:05
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Optical%20tweezers%20directed%20one-bead%20one-sequence%20synthesis%20of%20oligonucleotides.pdf23:05
kanzureanders will be speaking in stockholm tomorrow (monday) on whole brain emulation http://agenda.albanova.se/conferenceDisplay.py?confId=390423:19
kanzurearchels: i think you're close? maybe?23:19
archelstoo bad, I'm only going next weekend23:30
kanzureemail him and ask him to delay23:31
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--- Log closed Sun Apr 07 00:00:50 2013

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