--- Log opened Thu Feb 23 00:00:14 2012
--- Day changed Thu Feb 23 2012
00:00 < rdb> *yawn* morning
00:00 < Mokbortolan_1> morning
00:01 < Mokbortolan_1> rdb: check this out: http://www.senseg.com
00:01 < rdb> looks interesting
00:02 < rdb> of course, patented :-/
00:02 < Mokbortolan_1> now this: http://vision.wicab.com/technology/
00:02 < Mokbortolan_1> and once you're done with that, read this abstract: http://www.ncbi.nlm.nih.gov/pubmed/8606771
00:04 < rdb> electrode array, huh? is that how the senseg works, too?
00:04 < Mokbortolan_1> nope
00:04 < Mokbortolan_1> similar in the sense that it's a grid, I suppose
00:05 < rdb> so why are you showing me these links?
00:05 < Mokbortolan_1> don't they fit together like puzzle pieces in your head?
00:06 < rdb> remember that I just woke up
00:06 < Mokbortolan_1> oh
00:06 < Mokbortolan_1> basically it's a brain input
00:07 < Mokbortolan_1> over which you can carry visual data, among other types
00:07 < Mokbortolan_1> through any skin densely populated with touch receptors
00:09 < Mokbortolan_1> of course, an internal implant would be better in the long term, but this is something that is approachable by the average person and achievable within a relatively short time frame, seeing as how the major components of the technology have already been created
00:09 < rdb> but the data would be experienced as tactile sensations, right, not as visual perception?
00:09 < Mokbortolan_1> did you read the third link?
00:09 < Mokbortolan_1> and the second
00:09 < Mokbortolan_1> the brain doesn't care where the data comes through
00:10 < Mokbortolan_1> the brainport was used successfully to replace the vestibular sense of a woman who lost hers due to gentamycin treatment
00:10 < Mokbortolan_1> as well as the visual sense of a blind man
00:10 < Mokbortolan_1> and a reporter wearing a blindfold
00:10 < rdb> so how is the data 'targeted'? is it just a matter of right frequency etc?
00:10 < Mokbortolan_1> in the case of the first example, it was basically a level
00:11 < Mokbortolan_1> the brainport is a square grid of electrodes
00:11 < Mokbortolan_1> a group of X electrodes were used to represent the bubble of the electronic level strapped to this lady's head
00:11 < Mokbortolan_1> when the level was centered, the group was in the center of the tongue
00:12 < Mokbortolan_1> when she shifted, the group shifted its position on the grid
00:12 < Mokbortolan_1> the brain just said, "Hey! balance data! gimme!"
00:12 < Mokbortolan_1> and she could walk upright for the first time in years
00:12 < Mokbortolan_1> they projected a pixellated camera view onto it, brain says, "Visual data! yeah!"
00:12 < rdb> that's very interesting
00:13 < Mokbortolan_1> I'm sure you could do the same with auditory
00:13 < Mokbortolan_1> ....somehow.... :)
00:13 < Mokbortolan_1> so I was thinking of putting an electrostatic display version of that on the fingertips
00:14 < Mokbortolan_1> or entire hand
00:14 < Mokbortolan_1> the fingertips would be the foveas, the rest would be peripheral
00:14 < Mokbortolan_1> could do multiple foveas for the three primary colors
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00:15 < Mokbortolan_1> switch to IR, UV, long-wave IR
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00:16 < Mokbortolan_1> a friend of mine is going blind
00:16 < Mokbortolan_1> and I'd like to have some eyes ready for him when it happens
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00:18 < Mokbortolan_1> I've been bugging them about a dev kit for a while
00:18 < foucist> Mokbortolan_1: you know about that from 'the brain that changes' ?
00:19 < Mokbortolan_1> about which?
00:19 < Mokbortolan_1> I read a lot of stuff
00:19 < foucist> the brain port/balance
00:19 < foucist> read that book too
00:19 < Mokbortolan_1> I think I read about first in an article
00:19 < Mokbortolan_1> of a magazine
00:19 < foucist> ah
00:19 < Mokbortolan_1> then I read a few more magazine articles as I researched it more
00:19 < Mokbortolan_1> this was a few years back
00:19 < Mokbortolan_1> I'll check out that book though
00:19 < Mokbortolan_1> that sounds relevant :)
00:19 < rdb> it all sounds very interesting, and I definitely want to look deeper into it
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00:20 < Mokbortolan_1> my goal is to get some VC up to pursue input technologies
00:20 < Mokbortolan_1> maybe kickstarter
00:20 < Mokbortolan_1> and sell 1" squares of the stuff
00:20 < foucist> Mokbortolan_1: i read the book before/after basic surgery to stick a brain port in my ear! a la, cochlear implant :P
00:20 < Mokbortolan_1> flexible
00:21 < Mokbortolan_1> you have a cochlear implant?
00:21 < Mokbortolan_1> cyborg!
00:21 < foucist> word
00:21 < Mokbortolan_1> the brain is in-credible
00:21 < rdb> ^^;
00:22 < Mokbortolan_1> how long did it take you to adjust to the implant?
00:22 < rdb> now to find a paper that doesn't cost me $32 to download
00:22 < foucist> Mokbortolan_1: about 3 weeks
00:22 < Mokbortolan_1> was it static at first?
00:23 < Mokbortolan_1> or, I should ask, what was it like at first? :p
00:23 < foucist> no, mickey mouse voices @ first
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00:23 < Mokbortolan_1> rdb: I'm sure someone can dig it up if you really wanna read it
00:23 < foucist> they start it off slow, low volume/low electricity input and ramped it up over time..  but the input was more or less recognizable as 'sound'
00:23 < foucist> took about 3 weeks for it to sounds normal
00:24 < Mokbortolan_1> how long ago was this? what hearing range do you have now?
00:24 < rdb> Mokbortolan_1, read it? I wanna make it
00:24 < Mokbortolan_1> I'm curious to see if there have been any advances in terms of the hearing range of the devices
00:24 < foucist> surgery oct 6 2008, turned it on relatively late dec 1 or so (so about 5-6 weeks of healing)
00:24 < Mokbortolan_1> make the input thing I'm talking about?
00:25 < rdb> I'm interested in brain-computer interfaces both ways
00:25 < foucist> Mokbortolan_1: i definitely get more hearing range/input now
00:25 < Steel2> I missed this discussion
00:25 < Mokbortolan_1> the one I linked to was just an fMRI of a blind guy when a doc poked his braille-finger
00:25 < Steel2> foucist, what did you have done?
00:25 < foucist> but there's some significant bandwidth limitations w/ the current level of cochlear tech
00:25 < Mokbortolan_1> Steel2: he got turned into a 'borg
00:25 < Steel2> what particular way? :P
00:26 < foucist> i went with american company advanced bionics, 16 electrodes instead of the 22 electrodes that the Cochlear brand has..  however, AB has a much higher stimulation (capable of something like 7200HZ or something, i forget the #) and it's actually able to do current steering
00:26 < foucist> and basically fake 121 electrodes as a result
00:26 < foucist> so 121 virtual electrodes
00:26 < foucist> from the 16 + current steering
00:27 < Steel2> foucist, what did you have implanted?
00:27 < Mokbortolan_1> wow
00:27 < rdb> Steel2, cochlear implant
00:27 < foucist> Steel2: wire into the ear :P
00:27 < Steel2> were you deaf before, or was this a mod?
00:27 < Mokbortolan_1> expensive mod :p
00:28 < foucist> Steel2: basically been hard of hearing since 2 years old, but i decided i wanted better hearing so i got this at age of 27
00:28 < foucist> Mokbortolan_1: canadian healthcare..  free :P
00:28 < Mokbortolan_1> augh
00:28 < rdb> and given the audio quality of those things it's probably not something you'd want if your hearing was fine
00:28  * Mokbortolan_1 moves to canadia.
00:28  * rdb stays away from canadia.
00:29 < foucist> actually i would've gotten it a lot sooner but i made assumptions about the risk level/surgery
00:29 < Mokbortolan_1> rdb: do you have any formal degrees in neurobiology?
00:29 < Mokbortolan_1> I need a neurobiologist with a strong interest in vision
00:29 < rdb> no, I don't
00:29 < Mokbortolan_1> I'm putting together a team
00:29 < rdb> are you an electrical engineer?
00:29 < foucist> read a blog about someone's experiences w/ getting a cochlear implant when i was 26 and got the ball rolling
00:29 < foucist> anyways, i think the tech is awesome .. computer/brain stuff is amazing
00:29 < Mokbortolan_1> no, I'm the wacky visionary that will get pushed out of the picture once real money starts to roll in
00:29 < foucist> i want to hack on my implant :P
00:30 < Steel2> I'm hopefully the money that does the pushing
00:30 < Steel2> but probably not, that'll be thiel or something :V
00:30 < Mokbortolan_1> hahaha
00:30 < rdb> I'm an engineer and I'm interested in developing the technology
00:30 < Mokbortolan_1> though, if it helps my friend see, that's what's important
00:31 < foucist> there's a paper out there where some phd scientists tested interactive evolutionary computation to improve a guy's experience with his older tech Cochlear (brand) implant.. they got pretty good results with it
00:31 < Mokbortolan_1> sweet, what kind of engineering?
00:31 < rdb> electrical :3
00:31 < Mokbortolan_1> I've got a mechanical engineer and an embedded systems programmer
00:31 < rdb> I've got a lot on my plate though so I can't guarantee that I'll always have time
00:31 < foucist> i thought that the AB technology had even more potential for getting great results out using something like IEC
00:31 < Mokbortolan_1> awesome, though it's a bit early to start a mailing list
00:32 < Mokbortolan_1> rdb: once I get everything together we can work out the contract details
00:33 < Mokbortolan_1> which may never happen
00:33 < Mokbortolan_1> but, I'm going to try
00:33 < Mokbortolan_1> my poor friend, first he shattered his femur, now he's going blind
00:33 < Mokbortolan_1> he has terrible luck
00:34 < Mokbortolan_1> the least I can do is make him some new eyes
00:34 < rdb> ouch :-(
00:34 < foucist> ftp://ftp.cs.bham.ac.uk/pub/authors/W.B.Langdon/biblio/gecco2005wks/papers/0133.pdf
00:34 < Mokbortolan_1> oooh
00:34 < Mokbortolan_1> that's a good oe
00:35 < Mokbortolan_1> +n
00:35 < Mokbortolan_1> I figure if I keep my goals lofty I might get some traction
00:35 < Mokbortolan_1> nothing kills an idea quicker than trying to suck money out of it
00:36 < Mokbortolan_1> or a sudden heroid habit
00:36 < Mokbortolan_1> heroin
00:36 < foucist> actually http://www.genetic-programming.org/hc2007/01-Collett/Collett-Paper.pdf is where i first saw it from the human competitive EC awards
00:37 < Mokbortolan_1> time for bed, nn
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00:38 < rdb> night
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00:43 < Steel2> mok: I can make you a subforum
00:43 < Steel2> oh, he left
00:43 < Steel2> no need for mailing list, just use my site, I'll keep it private >_>
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05:24 < kanzure> "Henry wants €1 billion to model the entire human brain" http://www.nature.com/news/computer-modelling-brain-in-a-box-1.10066
05:24 < kanzure> and he should get it.
05:25 < rkos> i dont know, some of the other fet flagship competitors seem pretty interesting too
05:25 < rkos> http://cordis.europa.eu/fp7/ict/programme/fet/flagship/6pilots_en.html
05:27 < kanzure> ah this is new for me: http://channelpedia.net/
05:32 < kanzure> rkos: have you ever watched henry's 2006 talk? http://video.google.com/videoplay?docid=-2874207418572601262
05:32 < rkos> i remember seeing some talk of his but im not sure if it was that
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05:44 < kanzure> mm cake ftp://ftp.w3.org/pub/old/
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06:37 < delinquentme> packaging up code https://github.com/delinquentme/jython_oscar
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08:40 < kanzure> haha someone has installed a botnet on hplusmagazine.com
08:40 < kanzure> just got an email from an undernet sysadmin..
08:49 < jrayhawk> oh yeah, if you install wordpress or drupal on that vserver i gave you, you might end up with a forcibly detached robot arm in your bed
08:49 < jrayhawk> (because i don't really have a good analogue for a horse, here)
08:51 < kanzure> i have no idea what you just said
08:52 < jrayhawk> okay well you should feel ominously threatened
08:52 < kanzure> i feel ominously threatened
08:52 < jrayhawk> keep up the good work
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09:10 < kanzure> quartzy has received $1.2 mil in funding
09:10 < kanzure> http://blogs.wsj.com/venturecapital/2012/02/23/quartzy-scores-1-2m-to-help-life-scientists-stay-organized/
09:10 < kanzure> 'life sciences angel network' hrmmm
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09:16 < kanzure> i wonder when backyard brais is going to raise some cash
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09:27 < delinquentme> OMG
09:27 < delinquentme> HI
09:27 < delinquentme> <3
09:27 < delinquentme> LOVE YOU GUYS
09:27  * Mokstar_AFK gives delinquentme a cookie.
09:27 -!- Mokstar_AFK is now known as Mokstar
09:27  * delinquentme hugs Mokstar 
09:28 < delinquentme> kanzure, they've got a 3rd (?) product out now right?
09:28 < Mokstar> looks like SOMEONE's been in the entactogen cabinet again.
09:28 < delinquentme> haha
09:29 < delinquentme> http://www.globalpost.com/dispatch/news/regions/middle-east/120222/nadarkhani-sentenced-death-converting-christianity  << im reading this
09:29 < delinquentme> and it just makes me so fucking sad
09:29 < delinquentme> as I said on FB .. religion however you want
09:29 < Mokstar> yep, people killing each other again
09:29 < Mokstar> it feels so much more tragic when it's drawn out
09:29 < kanzure> you know about bill clinton's rescue mission to north korea?
09:29 < Mokstar> rather than simply a syrian shell landing on a civilian house and killing all inside
09:30 < kanzure> you should grow some balls and go do that next time
09:30 < Mokstar> no, is that a current thing?
09:30 < kanzure> nope it was a while back
09:30 < kanzure> but basically he hopped on a plane to go save a journalist in north korea
09:30 < delinquentme> but again I guess we're killing over oil they're killing over religion
09:30 < delinquentme> kanzure, what happened w that?
09:31 < jrayhawk> North Korea likes gamesmanship; Iran does not.
09:31 < delinquentme> gamesmanship?
09:32 < jrayhawk> North Korea is only stable because of diplomatic concessions it pulls from China and the U.S.
09:33 < kanzure> i like how their surprise birthday party was misinterpreted as an assassination
09:33 < kanzure> i wish my birthday parties were that cool
09:36 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/enzyme_classifications.yaml
09:37 < kanzure> ennnzymmmess
09:38 < uniqanomaly> delinquentme: screw the retarded memes like religion
09:39 < uniqanomaly> from one pov its somewhat funny how they slow down evolution of some
09:39 < delinquentme> uniqanomaly, <3
09:40 < kanzure> oh wow, according to nate, the EC classification/hierarchy is manually currated
09:40 < kanzure> not an automatic database
09:40 < uniqanomaly> delinquentme: it keeps their progress in line
09:40 < uniqanomaly> ^^
09:41 < delinquentme> uniqanomaly, im shaking my head
09:41 < delinquentme> so true man
09:42 < kanzure> http://pfam.sanger.ac.uk/family/browse
09:42 < delinquentme> But I mean.. When I fuck up .. its just not my fault! Utterly out of my control! Just makes life SOO MUCH EASIER   << previous FB status
09:42 < kanzure> hmm maybe this is a better way
09:53 < Stee|> NSF site visit on wednesday for a new bionano constellation
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10:43 < Stee|> how goes, roksprok
10:43 < roksprok> a bit slow
10:44 < Stee|> take speed
10:44 < roksprok> apparently there is no insect breeder that keeps a steady stock
10:44 < roksprok> i thought i'd be able to go online and just buy moths or something
10:44 < roksprok> but its all 'set up a monthly order of at least 100 units'
10:44 < roksprok> or 'we ship these in march every year'
10:45 < Stee|> what are you hoping to do?
10:45 < roksprok> i'd like to reproduce some of the remote control insect stuff
10:45 < roksprok> because from the papers i've read its all really rudimentary stuff
10:45 < roksprok> like, 3 electrodes
10:45 < Stee|> Hmm
10:46 < Stee|> don't certain animals eat insects?
10:46 < roksprok> yea, but to hold all the stuff you need pretty large ones anyway
10:46 < Stee|> hrm
10:47 < roksprok> and i live in ohio so other than cockroaches relatively large insects are not exactly common
10:47 < roksprok> pet stores stock scorpions and some spiders but they may be a bit too difficult
10:48 < roksprok> and i'd like to start with something that's been done a lot so i can troubleshoot the circuit
10:49 < roksprok> and know that i'm not just putting the electrode in the wrong place
10:50 < roksprok> so, hopefully i'll catch a few roaches tonight
10:51 < roksprok> anyway, anything up with you?
10:51 < roksprok> do you graduate this june?
10:51 < Stee|> hopefully sooner
10:51 < Stee|> I have a 'lot' (relative to previously) of money waiting as soon as I finish
10:52 < roksprok> a job lined up?
10:53 < Stee|> yeah
10:53 < roksprok> nice
10:53 < roksprok> what area of the country?
10:56 < Stee|> DC
11:06 < ThomasEgi> roksprok, so you are aiming for more electrodes? got an array?
11:09 < roksprok> ThomasEgi: i don't really have much of anything yet, but yea the end goal is to have an array
11:09 < roksprok> though a 3 dimensional one
11:09 < roksprok> as opposed to something like the utah array
11:09 < roksprok> though the progression will be more like 2 electrodes, 3, 4, 8, and so on
11:10 < roksprok> rather than going straight from 2 to a 16 or 64 electrode array
11:10 < roksprok> if you have any links on making arrays, i'd appreciate them though
11:11 < roksprok> i've found mouthbrain and hexatrode
11:11 < roksprok> although hexatrode is just input
11:11 < roksprok> http://hackteria.org/?p=480 and http://www.zachhoeken.com/mouthbrain
11:12 < roksprok> first one is the hexatrode and second is mouthbrain
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11:13 < roksprok> from what i can tell, most of the current research is in 'stimulate an antenna or optic nerve and promote an instinctive turn'
11:14 < roksprok> rather than, 'activate part of the CNS that drives the [start turning] commands'
11:16 < ThomasEgi> well , you have 2 choices. either rely on the reflexes of the insect.
11:16 < ThomasEgi> or you controll each of the nerves yourself.
11:17 < ThomasEgi> the later option requires a lot more work and is harder to do
11:17 < ThomasEgi> 3d electrodes are very difficult to manufacture
11:19 < ThomasEgi> a high-resolution 2d array is already very dififcult for diy folks. altho it can be done
11:20 < roksprok> would it be impractical to attempt to 'trim' a utah array or something similar?
11:21 < ThomasEgi> in order to trim something you need to have it in first place
11:21 < ThomasEgi> i would have no clue how to get my hands on one, and i'd love to.
11:22 < Stee|> if I have 80 grand spare laying around I can build an electrohydrodynamic inkjet setup and print some out for you :P
11:22 < ThomasEgi> you can print structures as small as electrode arrays? including wiring them up?
11:23 < kanzure> $80k sounds too much for that setup
11:23 < kanzure> is that just your fee or what
11:24 < ThomasEgi> my best bet was to bundle a bunch of very fine insulated wires. glue them together to a a rigid bundle.
11:24 < ThomasEgi> then cut it at an angle.
11:24 < ThomasEgi> and try to etch out a few micrometers of the glue
11:25 < ThomasEgi> guess most wires are ways to flexible for that.
11:25 < ThomasEgi> at leat if you want to penetrate anything. but might make a cheap diy-surface array
11:30 < ThomasEgi> wire diameters ranging from 25μm (38 with teflon coating) and bigger are available
11:30 < ThomasEgi> http://www.science-products.com/Products/CatalogG/Wires/wires.html
11:30 < ThomasEgi> price is dirt cheap compared to an 80k upfront investment
11:38 < roksprok> ooo that is a lot better than what i was looking at
11:38 < ThomasEgi> that company is only a few km off a road i travel bout every 2 month
11:39 < ThomasEgi> they sell a lot of lab and medical-grade stuff.
11:39 < roksprok> its nice that they sell in relatively low quantities too
11:39 < kanzure> kinda unfortunate, utah arrays are pretty cool :)
11:39 < ThomasEgi> cool yeah. but, what good are they if you dont have access to them?
11:40 < kanzure> access? i thought that cyberutahthing sold them
11:40 < roksprok> are they good about selling to non-academics?
11:40 < kanzure> cyberkinetics in utah
11:40 < ThomasEgi> they sell array????
11:40 < ThomasEgi> link, addres, phone.. and what price?
11:40 < kanzure> well i remember like $80/pop
11:41 < ThomasEgi> 80 or 80k ?
11:41 < kanzure> $80.00
11:41 < ThomasEgi> per "pin" ?
11:41 < kanzure> and that's a fucking american decimal point, not a european decimal point
11:42 < kanzure> i'm searching for the link
11:42 < kanzure> http:/tdt.com/ is another supplier
11:42 < kanzure> http://alascience.com/
11:42 < kanzure> contact: Andrew Lee <andy3328@yahoo.com> (works at ala)
11:43 < kanzure> oh hell.
11:44 < kanzure> http://www.qwane.com/products.html
11:44 < kanzure> yeah sorry. i'm reading through some emails and it looks like someone was complaining abuot a $75,000 system
11:44 < kanzure> but really i recall this el-cheapo source for microelectrode arrays...
11:45 < kanzure> ok how do i become these guys: http://autom8.com/
11:45 < kanzure> price list (no MEAs) http://www.autom8.com/shop/allprods.php
11:46 < Stee|> kanz, you want to start a firm like that?
11:46 < kanzure> yeah if i can get sales
11:46 < kanzure> why not
11:46 < kanzure> a single project is enough to cover the costs of design/development/production of customized equipment
11:46 < kanzure> and that equipment might as well be open hardware
11:47 < kanzure> it'd be pretty easy to get total market share pretty fast
11:47 < kanzure> if you had sales.
11:47 < Stee|> basically, the way those firms usually start is they know someone at a given lab and make something for them
11:47 < Stee|> or they come up with a new piece of equipment
11:47 < Stee|> or they just have contacts who will need equipment shortly
11:47 < kanzure> yes i know
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11:48 < kanzure> i happen to not know many people willing to pay $50k for things that cost $500
11:50 < ThomasEgi> hm..those microwire seems to be pretty close to what i had in mind as diy thing
11:52 < roksprok> except everything is probably proprietary with connectors that only work on their equipment
11:52 < roksprok> protected by patents so you can't just sell a drop in replacement
11:53 < ThomasEgi> those connectors look pretty industry-standard
11:53 < ThomasEgi> same stuff they use in mobile phones and crap
11:54 < roksprok> which site are you looking at?
11:54 < ThomasEgi> http://tdt.com/products/MW16.htm#OMN1010
11:55 < roksprok> ah cool looks a lot more reasonable
11:56 < roksprok> i wonder what the prices are like on this stuff
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11:59 < roksprok> ThomasEgi: have you done diy electrode recording/stimulation before?
12:00 < roksprok> or know of a ircchannel/forum/group with people who have?
12:00 < ThomasEgi> other than poking needles into my arm and connecting it to my signal generator. not yet
12:00 < kanzure> roksprok: diybio and backyardbrains
12:00 < roksprok> kanzure: thanks
12:00 < ThomasEgi> rdb and me ordered a bunch of ADS119x chips from TI, i plan to use them to record muscle-activity, and on long term.directly wiring them up to neurons
12:00 < ThomasEgi> given i can find an array for it
12:01 < ThomasEgi> the breakout pcb;s for the chips should ship within march
12:01 < rdb> hopefully
12:02 < rdb> if those children in those factories in china work hard enough
12:02  * rdb is joking.
12:07 < ThomasEgi> https://bugs.php.net/bug.php?id=61095 i wont let php touch my nervous system now :D
12:07 < kanzure> why would you even..
12:07 < kanzure> fathom.. of such a possibility
12:13 < uniqanomaly> heresy
12:15 < ThomasEgi> kanzure, never had any intention :D
12:16 < ThomasEgi> if anything, then c
12:22 < ThomasEgi> hm. but then. i'd be extremly interested in that diy-wire-electrode idea. especially as it would keep an implantable device rather small.
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12:33 < ThomasEgi> roksprok, have you given moth a thought?
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13:52 < delinquentme> im cross spamming sooo many channels
13:53 < kanzure> http://www.labguru.com lab management stuff
13:55 < delinquentme> kanzure, I should be able to deploy any database to any application on heroku right?
13:56 < kanzure> no i think it's just what they have installed iirc
13:56 < kanzure> unless you can install it with a gem
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14:28 < kanzure> http://biospot10.blogspot.com/2012/02/biosafety-part-i-biosafety-biohackers.html
14:31 < kanzure> http://www.biobuilder.org/ wtf..
14:31 < kanzure> so they're doing 3d animations about synthetic biology
14:32 < kanzure> http://www.biobuilder.org/request-reagents/
14:33 < kanzure> "but what happens if there's a G and T, and the in between A is missed?"
14:33 < kanzure> "Dude, you're smart, but so are the chemists. On to the next part.."
14:33 < kanzure> um... this isn't science
14:36 < kanzure> "If this other tech really works and can do perfect DNA reading, including knowing which genes are expressed, then Halcyon will shift its focus to writing genes."
14:36 < kanzure> http://pandodaily.com/2012/02/22/new-competitive-threat-forces-halcyon-molecular-to-accelerate-its-game-plan/
14:36 < kanzure> what.. since when is halcyon going to do synthesis?
14:37 < Juul> it's a synberc thing huh
14:38 < kanzure> i like how they just lied to me about their long-term plans
14:38 < kanzure> wait, no i don't
14:39 < roksprok> ThomasEgi: yeah that's actually what i'm leaning towards
14:39 < roksprok> kanzure: i wouldn't trust anything from pandodaily
14:39 < roksprok> thiel probably wanted to reassure investors
14:40 < kanzure> why would he reassure them with dna synthesis
14:40 < kanzure> surely he knows halcyon's plans better than this
14:41 < roksprok> because they are similar?  its not like founder's fund investors are biologists
14:41 < roksprok> most are probably used to consumer web tech, where pivots are super easy
14:42 < kanzure> ehh you don't give >$10mil to someone without knowing what they are doing
14:42 < kanzure> pete might not be a biologist but he's not stupid
14:42 < kanzure> oh also the quote was from elon musk
14:43 < kanzure> who is also not stupid heh
14:43 < roksprok> well he didn't exactly know that nanopore would work out
14:43 < kanzure> actually it's more likely that they were too late to the party
14:43 < kanzure> oxnano has been around for >5 years right?
14:44 < kanzure> in later stages of fundraising you usually dump in more cash
14:44 < roksprok> yeah, but isn't the sequencing industry full of companies giving predictions of cost-per-genome and how long it will take them to get there?
14:44 < kanzure> founder's fund doesn't seem to do late-stage stuff, but i'm not sure
14:44 < kanzure> sure.. they invested in halcyon because of other 'big vision' handwaving stuff
14:45 < kanzure> oh weird. oxnano is only from 2005
14:45 < roksprok> what's halcyon's 'big vision'?
14:45 < kanzure> longevity research
14:46 < kanzure> i was interviewing with them for a position and i found their plans behind their big vision to be lacking
14:46 < roksprok> that's a pretty big vision
14:46 < kanzure> i think it would be great if they had a good plan
14:46 < kanzure> but their plan is "do dna sequencing; sequence everything"
14:46 < kanzure> "if someone beats us to market, then we sell electron microscopes"
14:47 < roksprok> like, design their own electron microscopes?
14:47 < roksprok> or just be a reseller?
14:47 < kanzure> not sure, i asked that question though
14:48 < kanzure> i think it's great that they've hired a lot of interesting people, but i'm not convinced of their plan
14:48 < kanzure> and they didn't mention dna synthesis at all to me
14:49 < roksprok> well it's not unusual for a company to give a different story to employees/partners/potential hires, and investors/the public
14:50 < kanzure> sure
14:50 < roksprok> my main point is that i wouldn't be surprised if their 'dna synthesis' plans were thought up a few days ago
14:50 < kanzure> "what if we're late" was always a real possibility that they should have accounted for
14:55 < roksprok> maybe they hope that if they have enough interesting people someone'll come up with something?
14:55 < roksprok> do you remember about how many employees they have?
14:56 < kanzure> 50ish
14:56 < kanzure> there are many interesting and relevant transhumanist projects to work on
14:57 < kanzure> and it's really curious if none of them are oriented well.. i mean sorta hard to believe..
14:57 < uniqanomaly> acquire all the competition, they could come up with that
14:58 < roksprok> that costs a lot though
14:59 < kanzure> money is the main thing they have going :/
14:59 < roksprok> 50ish employees is enough that they could have a few side-projects going on
15:00 < roksprok> like koene's molecular ticker tape
15:00 < roksprok> and once they are certain they're beat maybe they'll just pivot to something like that
15:01 < roksprok> or they could have had a few people working on synthesis just for kicks
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16:22 < kanzure> hi tibtab
16:22 < tibtab> hi, did you see the video on #biohack?
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16:23 < kanzure> no
16:23 < kanzure> are you asking about genomecompiler.com
16:23 < tibtab> y
16:23 < kanzure> i think they are just some software outfit
16:23 < kanzure> honestly i feel better with directly manipulating genomes through ncbi's interfaces
16:23 < kanzure> and my own software.
16:35 < tibtab> sry, for stalking you, but you went to a waldorf school too? :)
16:38 < kanzure> yes
16:41 < tibtab> so what do you think about it retrospectively
16:42 < kanzure> well i think i know the spirit of a boulder quite well now
16:44 < tibtab> ;)
16:51 < kanzure> tibtab: i was out of control and kicked out
16:52 < kanzure> around the third/fourth grade
16:53 < tibtab> oh I was close to that too at one point :d
16:55 < kanzure> are you worth stalking
16:56 < tibtab> nah, probably not
16:58 < Mokstar> I love this stuff:  http://www.scarf360.com/files/SCARF-NeuroleadershipArticle.pdf
16:58 < foucist> WHAT
16:58 < foucist> i went to waldorf school too
16:58 < foucist> grade 1-3
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16:59 < Mokstar> it's about the relationship between environmental survival and social interaction
16:59 < Mokstar> in terms of the brain's circuitry
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17:00 < kanzure> can anyone get me a reasonable OCW lecture on rational protein design
17:00 < kanzure> and not one of the phony lectures where they just talk about the concept of protein design
17:00 < kanzure> i mean one that actually knows CHRMM or something
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17:00 < kanzure> foucist: ah then you too have been indoctrinated! cool
17:01 < tibtab> :D
17:08 < foucist> word
17:09 < foucist> did you guys do the daily calisthenics thing, going around in a big circle ?
17:09 < kanzure> of course..
17:10 < tibtab> sure
17:10 < foucist> heh
17:10 < kanzure> i also drew beautiful pastel gnomes
17:10 < tibtab> and with wax crayons
17:12 < foucist> big crayons ftw
17:13 < foucist> and knitting and recorders
17:13 < tibtab> and felting bags for the recorders, yey :D
17:13 < foucist> knitted a kleenex dispenser for mom & a holder for the recorder
17:14 < foucist> yeah
17:14 < kanzure> oh yeah? well i knitted a level 17 orc
17:14 < kanzure> or something
17:14 < kanzure> probably a gnome too :/
17:17 < foucist> a lot of moms there seemed to be earth mother types..  or rural or farmer types
17:17 < foucist> even tho the school was in the middle of the city
17:18 < kanzure> mine was mostly upper middle class people with lots of money
17:18 < tibtab> mine both, i would say
17:18 < foucist> i mean the people were pretty liberal/environment friendly/eco conservative etc
17:19 < foucist> they recycled
17:19 < foucist> and composted
17:19 < kanzure> they recycled??
17:19 < kanzure> oh man that's terrible
17:19 < kanzure> ?
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17:28 < foucist> kanzure: so your people didn't recycle? :P
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17:41 < kanzure> foucist: sure they did.
17:41 < kanzure> hi HEx1 are you tom
17:42 < HEx1> hi kanzure. I am. I also have an email reply for you that will be on its way very shortly :)
17:45 < kanzure> HEx1: regarding purposeful-indexes.. http://diyhpl.us/~bryan/papers2/
17:46 < HEx1> wow, that's quite an eclectic document collection there :)
17:48 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/ is regarding our immediate interest
17:50 < HEx1> sweet!
17:57 < kanzure> HEx1: do you work in some lab?
18:01 < HEx1> not exactly. I was going to be doing some lab work as part of my Masters attempting to replicate http://sphere.chronosempire.org.uk/~HEx/seelig3.pdf but that fell through before it got started (largely my own fault)
18:01 < kanzure> there's a few grad students in here
18:01 < kanzure> but more do-it-yourself biohackers
18:02 < kanzure> non-institutionalized stuff
18:02 < HEx1> (mRNA display looks one of the more interesting DE techniques, but probably beyond my level of competence to actually carry out)
18:02 < HEx1> I might've got myself involved in some CHARMM hacking over the next few months though. after that, who knows?
18:02 < kanzure> hmm i haven't seen mRNA display yet, sounds useful
18:02 < kanzure> i guess it makes sense- DNA display/aptamers, why not mRNA..
18:03 < kanzure> HEx1: my actual project at the moment is the development and production of a microfluidic DNA synthesizer
18:03 < kanzure> the enzymatic synthesis thing is more of a long-term goal a lot of people share
18:03 < HEx1> apparently library size is everything when it comes to DE, and mRNA display gets you perhaps 10^12 individual tagged proteins to screen
18:04 < kanzure> *or not so long-term ;)
18:04 < HEx1> kanzure: what, oligo synthesis?
18:04 < kanzure> yes but also an oligo library method
18:04 < kanzure> 6mers
18:04 < kanzure> target cost is <$5k-ish
18:05 < HEx1> you have a library of the 4096 possible 6-mers that you can then stitch together?
18:05 < kanzure> that's the plan
18:05 < HEx1> nice idea
18:06 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/
18:06 < HEx1> (more documents? my bedtime reading is *so* taken care of for the next several years :)
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18:14 < kanzure> hi yashgaroth
18:14 < yashgaroth> hoi
18:14 < kanzure> yashgaroth: mRNA display http://sphere.chronosempire.org.uk/~HEx/seelig3.pdf
18:15 < yashgaroth> yeah, there's dna display too
18:15 < kanzure> well yeah, but everyone knows about DNA display
18:15 < kanzure> i think.
18:15 < yashgaroth> how about mammalian cell display? aww yeah
18:16 < HEx1> there's also seelig1.pdf and seelig2.pdf for more description and less lists of reagents
18:24 < yashgaroth> I might try presenting that to my company, they do have such trouble with phage display :/
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18:39 < yashgaroth> well, turns out they tried it already, but still cool
18:39 < kanzure> aww
18:39 < yashgaroth> as well as cis display apparently
18:40 < kanzure> yashgaroth: HEx1 wrote up a draft proposal for RNA polymerase hacking http://sphere.chronosempire.org.uk/~HEx/tmp/prop.pdf
18:40 < kanzure> so that's why i dragged him in here.
18:44 < yashgaroth> hex1: there is a lot of work into getting transmembrane proteins, like photoreceptors, into soluble nanodiscs, rather than trying to solubilize them sans membrane
18:44 < yashgaroth> little discs of phospholipids wrapped in a protein to keep them intact
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19:35 < yashgaroth> it would also be good to know enough python to stop fumbling around in pymol all the time
19:36 < kanzure> well, complain loudly and the pythonistas in here can help
19:39 < yashgaroth> let me get the basics in first, I don't wanna be all 'how do I do pointers' every 5 minutes
19:39 < kanzure> http://try-python.appspot.com/
19:39 < kanzure> ^for prosperity's sake
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19:47 < foucist> s/prosperity/posterity
19:47 < kanzure> bah
19:48 < foucist> :P
19:48 < Juul> prosterity
19:49 < foucist> i googled 'posterity' and it didn't correct me
19:49 < foucist> pos·ter·i·ty/päˈsteritē/
19:49 < foucist> Noun:	
19:49 < foucist> All future generations.
19:49 < yashgaroth> hey, python programmers make money too right? that counts as prosperity
19:49 < foucist> :)
19:49 < foucist> they do! they make $100/hr! right?
19:49 < yashgaroth> totally, rails is for suckers
19:49 < kanzure> a bit more than that...
19:50 < kanzure> rails programmers do even more
19:50 < foucist> top ones do $150/hr on avg
19:50 < foucist> but most rails coders only get about $75/hr
19:50 < foucist> $50-75
19:51 < kanzure> i must be a top one
19:51 < kanzure> hooray
19:51 < foucist> you must be
19:51 < foucist> how about js coders
19:51 < foucist> ios coders
19:51 < kanzure> objective c monkeys are paid $120-$175/hr
19:51 < kanzure> javascript people vary since it goes from php coder quality to really really good coder
19:52 < kanzure> and nothing in between.
19:52 < foucist> yeah
19:53 < foucist> kanzure: lets make an agreement.. you outsource your $150/hr work to me for $100/hr (you make $50/hr profit).  i turn around and outsource it to someone willing to do it for $50/hr
19:54 < foucist> it will work!
19:54 < kanzure> unfortunately the lead time sucks
19:54 < kanzure> basically it will be 3am some morning when i say "GO GO GO"
19:54 < kanzure> and it will take you 2 weeks to find someone
19:54 < Juul> kanzure, you know of anyone who needs really good javascript programming?
19:54 < yashgaroth> fuck man, even directors in biotech barely make $120/hour...you guys make me sad
19:54 < kanzure> Juul: yes
19:54 < foucist> kanzure: :P
19:55 < Juul> doot doot. i wish i had a more general work U.S. permit
19:55 < Juul> U.S. work permit
19:56 < yashgaroth> you on an H1B visa, juul?
19:57 < Juul> yashgaroth, J-1 visiting scholar
19:57 < Juul> mega-restricted
19:57 < foucist> man, i'm a rails coder, probably have 2-3 years of experience under my belt, but a bit rusty and haven't built my skills that consistently (i.e. lacking js & bdd experience)..  i wouldn't feel good charging more than $30-40/hr but i'd be uncomfortable working less than $30/hr as a contractor.. )
19:57 < Juul> i would have to transition to H1B
19:58 < Juul> foucist, i was interviewing rails coders in Copenhagen last year (yeah ok Copenhagen) and most of them wouldn't even show up for an interview if it was less than $135 an hour
19:58 < kanzure> nice
19:58 < Juul> and the ones that did, turned out to suck
19:58 < Juul> with the exception of one polish student
19:58 < Juul> who didn't know what he was worth
19:58 < Juul> (we paid him more than he asked for)
19:59 < foucist> Juul: contract job or salaried?
20:00 < Juul> foucist, contract, but the difference isn't as great in socialist Denmark since the state provides lots and lots of benefits
20:00 < Juul> biggest difference is lack of paid vacation and no need for x-month notice upon termination
20:03 < Juul> damn, caffeine is crazy when you only have it on rare occasions
20:04 < Juul> i feel like a dense ball of focus and mental energy
20:05 < kanzure> Juul: do some writing on the enzymaticsynthesis doc? :D
20:05 < kanzure> http://github.com/kanzure/ezymaticsynthesis
20:05 < kanzure> erm
20:05 < Juul> kanzure, :)
20:05 < kanzure> http://github.com/kanzure/enzymaticsynthesis
20:05 < Juul> i have to finish a web app prototype for tomorrow, but if i have extra time after that and before i sleep, then i will
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20:06 < Juul> my friends back in denmark started a danish EFF-type organization
20:06 < Juul> BitBureauet
20:06 < Juul> it's super effective!
20:07 < kanzure> wait.. did you see my pokemon red disassembly
20:07 < Juul> ...nooo?
20:07 < Juul> was it... effective?
20:07 < kanzure> Juul: http://news.ycombinator.com/item?id=3473111
20:07 < kanzure> or maybe you're just quoting super effective for other reasons
20:08 < Juul> i'm just being a meme-monkey
20:08 < kanzure> aww. oh well.
20:09 < kanzure> well anyway. working source code to pokemon red by yours truly.
20:09 < Juul> you're iimarckus?
20:09 < kanzure> no i'm the other committer
20:09 < kanzure> http://bitbucket.org/kanzure/pokered/changesets
20:10 < Juul> interesting. do you have a writeup on how you did it?
20:10 < kanzure> nope
20:10 < kanzure> basically there's a makefile and some asm
20:10 < kanzure> the asm is compiled and then compared against the original rom
20:10 < Juul> the assembly was difficult because it was highly compressed using unknown methods?
20:10 < kanzure> the makefile passes only if the new rom is exactly the same as the original rom
20:11 < kanzure> oh that thing from the HN comments? some of the graphics have weird compression
20:11 < Juul> s/assembly/disassembly/
20:11 < kanzure> not all of the graphics are done yet; some are just 2 bits per pixel
20:11 < kanzure> others are RLE-compressed
20:11 < Juul> ok, i don't know much about gameboy disassembly, what is the challenging aspect?
20:12 < kanzure> it's not that challenging it's just asm coding
20:12 < kanzure> i wrote this disassembler that converts bytecode back into text
20:12 < Juul> ooooh
20:12 < kanzure> and then i annotate this
20:12 < Juul> you wrote the disassembler
20:12 < kanzure> and use variables and references
20:12 < Juul> ok. got it.
20:12 < kanzure> well sort of- the disassembler came *second* ;)
20:12 < kanzure> (and there's other disassemblers that exist, but i don't like them)
20:12 < Juul> ok
20:12 < Juul> so you manually disassembled it
20:13 < Juul> and then wrote a disassembler
20:13 < kanzure> https://bitbucket.org/kanzure/pokered/raw/e66818b266cf/main.asm
20:13 < kanzure> a disassembly dump is almost always unreadable junk
20:13 < Juul> i seee
20:13 < kanzure> so instead, you can imagine writing source code that compiles into the same thing
20:13 < kanzure> using disassemblers to help you investigate portions of the original code
20:14 < Juul> highly commented
20:14 < Juul> impressive
20:14 < kanzure> right :3
20:14 < Juul> and nintendo hasn't come after you
20:15 < kanzure> no
20:15 < Juul> like the big monolith of happy fun corporate evil that they are
20:15 < kanzure> and the fbi hasn't come after me for other things either
20:15 < Juul> hehe
20:15 < Juul> ok
20:15 < Juul> good good
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20:31 < kanzure> tonight feels like a manga night :\
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20:51 < kanzure> lego hadron collider http://i.imgur.com/kJkMw.jpg
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20:51 < ybit> 09:33 < kanzure> i wish my birthday parties were that cool
20:52 < ybit> if people didn't think your bday occurred everyday, they might be that cool
20:55 < kanzure> hey nobody seemed to notice the first ten times
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23:41 < foucist> kanzure: why would they think that
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--- Log closed Fri Feb 24 00:00:23 2012