| --- Log opened Thu Apr 12 00:00:32 2012 | ||
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| jrayhawk | http://chriskresser.com/rhr-chronic-stress-cortisol-resistance-and-modern-disease goddamn this is an interesting podcast | 00:54 |
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| delinquentme | cant slep | 02:02 |
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| delinquentme | kanzure, http://www.ingentaconnect.com/content/title?j_type=online&j_startat=Aa&j_endat=Af&j_pagesize=200&j_page=1 | 02:20 |
| delinquentme | who are these guys | 02:20 |
| delinquentme | im sorry wtf http://www.ingentaconnect.com/content/wb/bk17540/2009 ? | 02:41 |
| delinquentme | 1 MILLION queries http://www.youtube.com/watch?v=2Z4m4lnjxkY | 03:11 |
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| skorket | hey guys, I'm not sure if you'll know anything about this, but some guys around where I live want to make a hackerspace and I was curious about intellectual property issues. Do you know of any resources or hackerspaces where intellectual property is explicitely dealt with? | 05:07 |
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| Utopiah | skorket: there is #hackerspace AFAIR | 05:17 |
| Utopiah | (if there is nothing in the hackerspace wiki) | 05:17 |
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| skorket | Utopiah, yeah, I'm there asking, just carpeting all the relevant channels I can think of | 05:18 |
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| diginet | HEAD ON APPLY DIRECTLY TO THE FORE HEAD | 05:54 |
| delinquentme | ^^^^^^^^^^^^^^ | 05:58 |
| delinquentme | digi | 06:01 |
| delinquentme | diginet, do you know ruby? | 06:02 |
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| phryk | skorket: Intellectual property issues? You mean if you're going to be sued if you take a name like "Dr. Marios Lair" or something? | 06:39 |
| skorket | phryk, no, more along the lines of, if person X creates a product Y using hackerspace resources, person X gets to keep copyright | 06:44 |
| phryk | If unsure you should be able to define that in the spaces rules (if you are going to be an official organization) | 06:46 |
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| kanzure | skorket: usually copyright is not the thing that people are worried about when creating things at hackerspaces.. | 07:44 |
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| kanzure | hi charlieschwabach | 07:45 |
| charlieschwabach | hey | 07:45 |
| charlieschwabach | you ready for venter? | 07:46 |
| charlieschwabach | institute scientist who's name i cant remember and who inserted a synthesized yeast genome into a bacteria | 07:47 |
| charlieschwabach | :) | 07:47 |
| charlieschwabach | haha | 07:47 |
| Utopiah | Craig | 07:47 |
| kanzure | charlieschwabach: almost | 07:49 |
| charlieschwabach | kanzure: awesome, good luck today | 07:50 |
| kanzure | thanks | 07:50 |
| charlieschwabach | utopiah: meant Dan Gibson - http://en.wikipedia.org/wiki/Gibson_assembly | 07:51 |
| charlieschwabach | utopiah: who i guess works @ the craig venter institute | 07:51 |
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| Utopiah | my bad, wasnt sure how to interprete the sentence | 07:52 |
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| charlieschwabach | utopiah: haha yeah i worded that really weirdly | 07:54 |
| kanzure | from now on, all messages to ##hplusroadmap must be in Reverse Polish Notation | 07:58 |
| kanzure | haha | 07:58 |
| Coornail | lawl | 07:59 |
| charlieschwabach | kanzure: writing lisp this morning? | 08:01 |
| kanzure | writing code without breakfast | 08:01 |
| kanzure | a dangerous practice | 08:01 |
| Mariu | =p | 08:01 |
| charlieschwabach | haha | 08:02 |
| Mariu | http://mariakonovalenko.wordpress.com/2012/01/10/transhumanist-media-content/#comment-1099 | 08:02 |
| * delinquentme sleeps | 08:03 | |
| Mariu | lol | 08:04 |
| kanzure | charlieschwabach: gotta get started with the day on the good side of the bed.. http://www.youtube.com/watch?v=YwnM3eMh3Q8#t=1910 | 08:04 |
| charlieschwabach | kanzure: nice | 08:07 |
| charlieschwabach | typical morning before breakfast ;) | 08:07 |
| charlieschwabach | mariu: i think people work on transhumanism w/o calling that | 08:13 |
| charlieschwabach | cancer / anti viral research is very mainstream | 08:14 |
| charlieschwabach | and we definitely need that for radical life extension | 08:14 |
| kanzure | regarding cancer.. http://pinkarmy.org/ but andrew hasn't done any work on this in forever | 08:14 |
| charlieschwabach | kenzure: cool | 08:16 |
| charlieschwabach | yeah, i think we need to just sequence everyone's cancer and make all of the data available | 08:16 |
| charlieschwabach | along w/ their treatment / outcome | 08:16 |
| Mariu | got it, Charlie | 08:16 |
| charlieschwabach | mariu: not that i wouldn't love to see a life extension themed movie :) | 08:17 |
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| kanzure | http://diyhpl.us/~bryan/irc/aubrey.jpg | 08:17 |
| charlieschwabach | awesome | 08:18 |
| charlieschwabach | so if you make an laser to cut microfluidics chips | 08:18 |
| charlieschwabach | how hard is it to make a cheap sequencer? | 08:18 |
| kanzure | a cheap sequencer is at least 1 order of magitude easier than dna synthesis | 08:18 |
| kanzure | *magnitude | 08:19 |
| charlieschwabach | do you think you can beat illumina? | 08:19 |
| kanzure | a *competitive* sequencer.. not quite | 08:19 |
| charlieschwabach | ahh, cool.. yeah it is already cheap | 08:20 |
| kanzure | there's 30+ next-generation sequencing companies all with >$5M in funding | 08:20 |
| Mariu | Charlie, watch Curiosity with Adam Savage | 08:20 |
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| Mariu | the episode title is 'Can I live forever ?' | 08:21 |
| Mariu | nice, kanzure | 08:21 |
| kanzure | Mariu: i don't recommend television for learning about longevity research | 08:21 |
| Mariu | the picture of Aubrey | 08:21 |
| kanzure | that just sounds like a bad idea | 08:21 |
| Mariu | what does ? | 08:21 |
| kanzure | start reading instead: http://diyhpl.us/~bryan/papers2/longevity/ | 08:22 |
| Mariu | ah, yeah | 08:22 |
| kanzure | learning about longevity from TV | 08:22 |
| Mariu | gotcha | 08:22 |
| charlieschwabach | kanzure: discussing his blog post about promoting transhumanism.. so cool for discovery channel viewers to watch that over 'ancient aliens' / whatver | 08:24 |
| charlieschwabach | also nice directory, bookmarking that for later | 08:24 |
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| kanzure | hrmm http://blog.makezine.com/2012/04/12/open-source-hardware-association-announced/ | 08:53 |
| kanzure | http://www.oshwa.org/ | 08:53 |
| kanzure | "Here are your board members so far: Danese Cooper, Alicia Gibb, Catarina Mota, Windell Oskay, Nathan Seidle, Wendy Selzer." | 08:53 |
| kanzure | who elected those nuts? | 08:53 |
| kanzure | well at least there's windell | 08:54 |
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| kanzure | hi lichen | 08:59 |
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| _F7_ | whoo, new client | 09:35 |
| kanzure | hi _F7_ | 09:39 |
| kanzure | has anyone here used sqlmap before? | 09:39 |
| _F7_ | Not I. | 09:39 |
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| _F7_ | just reading the logs. | 09:50 |
| _F7_ | I'll be touch-and-go as I'm at work | 09:50 |
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| kanzure | why is dna most often portrayed vertically instead of horizontally? | 10:31 |
| kanzure | if you google image search for "dna" you get lots of vertical images | 10:31 |
| Mokbortolan_ | because it's described as a staircase or ladder | 10:42 |
| Mokbortolan_ | probably | 10:42 |
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| charlieschwabach | looks better that way bcs of aspect ratio of book/magazine pages too | 10:56 |
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| _F7_ | kanzure, did diginet ever dropbox you his arachnofiber papers? | 11:24 |
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| kanzure | _F7_: no | 11:32 |
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| kanzure | hah interesting.. their new 'open hardware association' was rejected by NY "for being too promotional". go figure. | 12:08 |
| kanzure | "As a 501c3 we won't be allowed to fund OSHW projects though." whaat?? | 12:09 |
| juul | weird | 12:09 |
| Mariu | whatever is a threat to them, gets rejected | 12:11 |
| kanzure | there are already 501c3s for open source hardware | 12:12 |
| kanzure | they were rejected because they are too spammy. which is my opinion of them. | 12:12 |
| kanzure | juul: see pm | 12:12 |
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| kanzure | yashgaroth: ok might not be needing you for today's call | 12:29 |
| yashgaroth | awww | 12:29 |
| kanzure | well | 12:29 |
| yashgaroth | I'll keep an eye on the channel just in case | 12:29 |
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| kanzure | i'm getting over a wicked headache right now heh | 12:29 |
| nmz787 | kanzure: uh oh! | 12:30 |
| kanzure | nmz787: nah i'll be fine | 12:30 |
| nmz787 | kanzure: simon msged again, this time including his 'friend' the shrinky dink lady | 12:30 |
| kanzure | gah we definitely don't want shrinky dinks | 12:30 |
| nmz787 | nope | 12:30 |
| nmz787 | she hasnt' replied | 12:30 |
| kanzure | is simon trying to throw us off? :P | 12:30 |
| nmz787 | i guess this is the engineering you get for free | 12:31 |
| nmz787 | or at least the free stuff from people who aren't excited to help, or who aren't good friends | 12:31 |
| kanzure | i thought we knew simon pretty well :( | 12:31 |
| nmz787 | i only internet know him | 12:32 |
| kanzure | me too | 12:32 |
| kanzure | but technically, i mostly internet know you | 12:32 |
| nmz787 | so for my human bio 3 lab course I'm teaching.... i had the students draw what we've been doing in class... for a agrade | 12:32 |
| nmz787 | since they're mostly art students | 12:32 |
| kanzure | what did they draw? | 12:32 |
| nmz787 | medical illustration, biomed photo | 12:33 |
| nmz787 | hah | 12:33 |
| nmz787 | bacteria being streaked on a plate | 12:33 |
| kanzure | anything good? | 12:33 |
| nmz787 | yeah a few | 12:33 |
| nmz787 | now i know who to email when i need illustrations done | 12:33 |
| nmz787 | :D | 12:33 |
| nmz787 | 'for extra credit. draw this dna synthesizer' | 12:34 |
| kanzure | pfft | 12:34 |
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| diginet | so I think with duckweed, I might just be able to get the density I need | 13:00 |
| diginet | hooray | 13:00 |
| _F7_ | cool | 13:00 |
| diginet | the problem is, it requires the use of a custom vector, which means expensive gene synthesis | 13:01 |
| diginet | (to target the chloroplast | 13:01 |
| _F7_ | Diginet, how goes compiling all of your arachnofiber papers onto dropbox for kanzure? | 13:01 |
| diginet | ) | 13:01 |
| diginet | _F7_ I keep coming across more stuff! my bandwidth drops off during the day, so I have to do it at night | 13:01 |
| _F7_ | ah | 13:02 |
| diginet | I think I could reasonably produce maybe 1kg of silk in a week using a not too unreasonable amount of land | 13:03 |
| diginet | (i.e. some spare area in my back yard I can put planters in) | 13:03 |
| _F7_ | You know, between your arachnofiber synthesis research and the 'urban armor' phryk is working on you have part of the opening chapter of snowcrash. | 13:03 |
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| diginet | haha | 13:03 |
| diginet | I would use it for something far less interesting | 13:03 |
| diginet | (well, to other anyhow) | 13:04 |
| _F7_ | His uniform is black as activated charcoal, filtering the very light out of the air. A bullet will bounce off its arachnofiber weave like a wren hitting a patio door, an excess of perspiration wafts through it like a napalmed forest. Where his body has bony extremities, the suit has sintered armorgel; feels like gritty jello, protects like a stack of telephone books. | 13:04 |
| kanzure | does anyone remember when tudor boloni was pitching us the explosive styrofoam armor cocoon? | 13:05 |
| diginet | I've not gotten through all of Snow Crash, the whole "Sumerian is the assembly language of the brain" thing kind of turned me off | 13:05 |
| diginet | Sumerian, except for freaks like me, is much less interesting than that | 13:06 |
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| yashgaroth | well you should finish it cuz snow crash is awesome | 13:06 |
| _F7_ | It's a story element. I liked all of the weird Enki stories. | 13:06 |
| phryk | _F7_: I'm not yet really working on it :P | 13:06 |
| _F7_ | what are you working on? | 13:07 |
| phryk | currently? not much… | 13:07 |
| phryk | only started project i have laying around is a little fun thing I call the 'penis proxy' :P | 13:07 |
| phryk | little perl script for fucking around with post data, not even working yet :P | 13:07 |
| _F7_ | I went to a party like that | 13:07 |
| _F7_ | oh | 13:07 |
| diginet | yashgaroth, _F7_ oh I know, I shouldn't get hung up on it, I just am of the mindset that history and linguistics are are interesting enough by themselves without the pseudoscientific technobabble | 13:08 |
| phryk | it's just going to be a little proxy server substituting words in post data with 'penis' mostly because I was stoned and thought that would be a good idea :P | 13:08 |
| _F7_ | hahahahaha | 13:08 |
| _F7_ | have you looked at mallory? | 13:08 |
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| _F7_ | Transparent TCP and UDP proxy | 13:09 |
| _F7_ | You can intercept and do fun fun fun | 13:09 |
| phryk | nope, i looked at privoxy, squid and some other proxies and none were really able to do what I wanted or had no doc on it. | 13:09 |
| phryk | The proxy needs to understand http :P | 13:10 |
| kanzure | phryk: jrayhawk has been working on a proxy that turns everything into TimeCube sites | 13:10 |
| diginet | phyrk, I implemented something similar with firefox, except for audiophile forums. I have a list of meaningless words they use like "air" and what have you, and substitute them with things more indactive like, instead of "all in all it has more air" "all in all it has more /needless expenditure of money/" | 13:10 |
| phryk | then a guy from the local hackerspace pointed me to a little proxy he wrote with HTTP::Daemon | 13:10 |
| phryk | diginet: Heh, but I need this to be an own service. My plan is setting up another AP on my freebsd box with only port 80 open and that tunneled through the proxy | 13:11 |
| phryk | so someone comes by the house, thinks "hey, free wifi!" logs on to facebook wanting to post something like "Haha, idiots can't secure their wifi!" and ends up posting "Penis penis penis penis lol!" | 13:12 |
| phryk | I know a real attribution to the cause of bettering humanity. :P | 13:12 |
| kanzure | isn't facebook behind ssl? | 13:13 |
| Mokbortolan_ | my sister got onto an unsecured wifi of one of her neighbors, found their wireless printer, and printed out instructions on how to secure their model of wireless router :p | 13:13 |
| kanzure | well i guess you can capture the ssl certs | 13:13 |
| phryk | kanzure: you can access it over port 80 as well. last time i checked that even was the default behaviour | 13:13 |
| _F7_ | Mallory is good at that stuff | 13:13 |
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| _F7_ | It's like wireshark+tampering | 13:13 |
| phryk | and when port 443 doesn't work, they ought to try it without ssl… | 13:14 |
| diginet | phryk, OOH I did something like that | 13:14 |
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| diginet | except I caught my neighbours using my wifi, so I played a little game, first I put ads (with help of ddwrt), then I caused the page to be flipped, then I put a customer support line if they were having "issues" (which was my google voice number) and basically told them to get their own internet | 13:15 |
| diginet | good times | 13:15 |
| phryk | heh | 13:15 |
| phryk | ddwrt is an open router firmware based on openwrt, right? | 13:16 |
| Mokbortolan_ | right | 13:16 |
| phryk | I knew something! \o/ | 13:16 |
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| kanzure | davidad guest lecturing in marvin minsky's class http://www.youtube.com/watch?v=xW77lANeJas | 13:36 |
| kanzure | hrmm | 13:37 |
| kanzure | ""Currently, the IRS has elected to take all recent applications for tax exempt status whose mission is to deliver open source technology for public benefit into a special review cycle. "" | 13:37 |
| _F7_ | Where are you reading that? | 13:39 |
| _F7_ | I need to go over whatever it is and make sure TX/RX doesn't get screwed with. | 13:40 |
| kanzure | http://www.trustthevote.org/contribute/irs-status | 13:40 |
| _F7_ | okay I'm in the clear | 13:41 |
| _F7_ | thx | 13:41 |
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| _F7_ | hello superkuh | 14:00 |
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| superkuh | Hello. | 14:01 |
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| kanzure | fenn: hi | 14:10 |
| kanzure | yashgaroth: will you be alright? | 14:11 |
| yashgaroth | with what | 14:11 |
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| kanzure | yashgaroth: not being on the call | 14:12 |
| yashgaroth | I'll live | 14:12 |
| kanzure | ok i just don't want to clutter it | 14:12 |
| yashgaroth | it's cool, I'll be here if y'all need anything | 14:13 |
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| kanzure | deep-fried-art: yo | 14:23 |
| kanzure | long time no see? | 14:24 |
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| dbolser | hello | 14:29 |
| kanzure | dbolser: hi! | 14:29 |
| kanzure | dr. bang? | 14:30 |
| kanzure | yashgaroth: dan has some info about tdt i think | 14:31 |
| kanzure | that you can possibly harvest | 14:31 |
| yashgaroth | TDT? | 14:31 |
| dbolser | I met Dr Bang in korea talking about engineering a new codon in bacteria | 14:31 |
| dbolser | tdt? | 14:31 |
| yashgaroth | the recombination polymerase? | 14:32 |
| kanzure | oops, one of the deoxy terminalases | 14:32 |
| kanzure | i think i meant terminal ligase | 14:32 |
| dbolser | I may have mis-remembered | 14:32 |
| dbolser | lets see ... where is teh 'enzymatic synthasis' group? google does a good job of hiding groups | 14:32 |
| kanzure | http://groups.google.com/group/enzymaticsynthesis | 14:33 |
| dbolser | ty | 14:33 |
| kanzure | _F7_: http://mach30.org/about/public-records/tax-exempt-status-documentation-and-process/ | 14:33 |
| kanzure | from a friendlie org | 14:34 |
| dbolser | Terminal DNA transferase # my mistake | 14:34 |
| nmz787 | dbolser: interesting | 14:34 |
| dbolser | TDT :-D | 14:34 |
| deep-fried-art | hey kanzure | 14:34 |
| dbolser | https://groups.google.com/d/topic/enzymaticsynthesis/0QXaktOWpU0/discussion | 14:35 |
| nmz787 | dbolser: did he elaborate at all how he might go about using TDT | 14:35 |
| dbolser | no, not specifically, but one could imagine a promiscous enzyme and dNTP cycles | 14:36 |
| dbolser | or ddNTP to 'terminate' then wash, cycle, etc. | 14:36 |
| kanzure | i think juul's strategy was interesting | 14:36 |
| kanzure | using nucleotide-binding enzymes that switch on/off similar to tRNA connectors | 14:36 |
| dbolser | anyone doing anything useful with nano-fluidics? | 14:40 |
| dbolser | I'm just wondering how many dNTPs you could put in a micro-bubble | 14:41 |
| dbolser | is it impossible to imagine using florescence to sort micro bubbles containing single dNTPs? | 14:42 |
| yashgaroth | as in single molecules or single types of bases? | 14:43 |
| dbolser | you could then sort the stream of bubbles into any given order and just drop them into a reaction chamber one by one... but I gues you need space for the DNA to grow, which means kinetics would suck | 14:43 |
| dbolser | yashgaroth: single molecules | 14:43 |
| dbolser | bubbles can flow at massive rates and flow sorting can be done in specific ways to very high accuracy | 14:44 |
| dbolser | I've seen a specific example of pairing bubbles from two different sources | 14:44 |
| dbolser | with 1000's of bubbles paired per second. | 14:44 |
| yashgaroth | you'd still need a 99+% guarantee of exactly one molecule per bubble | 14:44 |
| dbolser | of course, it's a different matter to sort 4 sources into an abitrary, pre-defined order, but it could work | 14:45 |
| dbolser | yashgaroth: I've changed my mind on that, I've just come up with a killer solution .... perhaps | 14:45 |
| yashgaroth | oh? | 14:45 |
| dbolser | you have 4 terminator ddNTP sources and one 'de-protection' source which needs to be chemical rather than enzymatic (for convenience) | 14:46 |
| dbolser | you have your growing DNA with a promiscous, template free pol, or TDT in a fixed volumn reaction chamber | 14:47 |
| dbolser | then you flow ddNTP, deprotect, ddNTP, deprotect, ddNTP, deprotect microfluidic bubbles at very high rates into teh chamber | 14:47 |
| dbolser | let me find the paper... | 14:48 |
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| yashgaroth | if you can find a chemical deprotection method that won't destroy the pol...though I suppose you could just add pol at every step | 14:48 |
| dbolser | true, but sticking enzymes in bubbles is challenging (it's totally doable though) | 14:49 |
| dbolser | http://www.bioc.cam.ac.uk/uto/hollfelder.html The lab I saw talk | 14:49 |
| yashgaroth | it's also starting to sound a lot like traditional phosphoramidite synthesis, except with a pol instead of a chemical condensation | 14:50 |
| dbolser | not familiar | 14:51 |
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| dbolser | can't find the paper right off... | 14:52 |
| dbolser | basically they designed a microfluidic gate that let them pair bubbles (emulsions) from two differnet sources with very high fidelity | 14:52 |
| dbolser | I wan't to find it to look up the flow rate, which IIRC was phenominal | 14:53 |
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| dbolser | bah, anyway, you also need some way to control the order of ddNTP bubbles | 14:56 |
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| dbolser | found it with google image search: | 15:04 |
| dbolser | http://web.media.mit.edu/~manup/research/bubble-logic/images/sync-motion-6.jpg | 15:04 |
| dbolser | that design synchronizes the two bubbles comming off on the right. you then send one round a little longer, and merge the flows to get perfect sorting of bubbles into a b a b a b | 15:05 |
| dbolser | http://web.media.mit.edu/~manup/research/bubble-logic/ | 15:06 |
| dbolser | Passive microfluidic bubble synchronizer | 15:06 |
| dbolser | still no info on rates | 15:07 |
| yashgaroth | it's not impossible to imagine syncing four types, or even five with the deprotectant | 15:07 |
| dbolser | right, but we need to precisely control the order of the four | 15:07 |
| dbolser | operating at a | 15:09 |
| dbolser | constant flow rate of Qw=0.5 µl/sec | 15:09 |
| dbolser | ?? I want bubbles per sec, to get a rough feel for how fast the reaction could proceed | 15:10 |
| yashgaroth | that's a rather high flow rate, half a microliter is huge | 15:10 |
| dbolser | obviously computer controling and error checking the flow would slow it down | 15:10 |
| dbolser | the value I have in my head is millions of bubbles per second, but I can't belive that's true | 15:10 |
| dbolser | http://www.stanford.edu/~manup/Manu_Prakash__Lab_website/Publications_files/MicroTAS-07-synchronization.pdf | 15:11 |
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| dbolser | although I feel like a this is just dumb speculation, I don't imagine that the technical challenge of electronically sorting 4 microbubble sources into a given order is very high | 15:14 |
| yashgaroth | indeed | 15:15 |
| dbolser | you then synchonize that source with your deprotectant, and wash the whole stream into some kind of reaction chamber | 15:15 |
| dbolser | that's tricky to design | 15:15 |
| dbolser | you want kinetics such that each wash is 99.999999% likely to add a given terminal dNTP (to synthesize up to a few kb) | 15:16 |
| dbolser | (with high accuracy) | 15:17 |
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| dbolser | so the contents of each new bubble should wash out the other.... or you could have wash bubbles.... dntp, wash, deprotect, wash, dntp, wash, etc. | 15:18 |
| yashgaroth | so you will need to mix pol in with the dNTPs | 15:18 |
| dbolser | ok, perhaps the design of the reaction vessle is secondary, it all comes down to computer cotrolled streams of arbitrary sources of bubbles | 15:18 |
| dbolser | unless you have the pol fixed, holding onto the growingdna | 15:18 |
| dbolser | growing dna | 15:19 |
| yashgaroth | mmmm with those kinds of flow rates you'll keep knocking it off, at least at some level | 15:19 |
| dbolser | it's much easier and cheper to just have chemical washes I think... (I'm not an expert in bio-microfluidics) | 15:19 |
| dbolser | yeah, I hadn't thought about that | 15:19 |
| dbolser | ensymes tend to stick to the bubble surface in emulsion | 15:20 |
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| dbolser | I'm not even sure of the mechanics of streaming all these bubbles into a 'reaction chamber'.... like where does the lipid go? | 15:20 |
| dbolser | anyway, I figure the idea has legs ;-) | 15:21 |
| yashgaroth | wait what lipids | 15:21 |
| dbolser | to make the bubbles, you emulsify your aquious solution of chemicals with a lipid IIRC | 15:21 |
| dbolser | or perhaps a zwiterion | 15:21 |
| dbolser | they are little aquious chambers in an oil emulsion | 15:22 |
| yashgaroth | ah right | 15:22 |
| dbolser | the chemical nature of the oil determines the surface properties, and needs to be taylored to the enzyme you want in the bubble | 15:22 |
| dbolser | because protins are quite oily, it can be a pain to get them 'in' the solution within the bubble | 15:23 |
| yashgaroth | proteins are typically amphipathic | 15:23 |
| yashgaroth | unless they're small enough to be totally hydrophilic | 15:23 |
| dbolser | but it all comes down to chemical engineering at the end of the day. Design the mixture right, and you can get what you need | 15:24 |
| dbolser | yup | 15:24 |
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| dbolser | I guess we need an expert to look at costs of various strategies... I've no lab experience, so I don't know the cost of enzymes :( | 15:24 |
| yashgaroth | if you're only using nanograms of enzyme at a time, their cost is negligible | 15:25 |
| dbolser | I figure an expert in the field would say, nice idea, but how are you going to make it work... | 15:26 |
| dbolser | perhaps... but you buy pure enzyme that works, not just by the gram ;) | 15:27 |
| dbolser | well... I have to find a file to send to some people... oh joy | 15:27 |
| * dbolser goes off to find a file... sigh | 15:27 | |
| dbolser | http://www.youtube.com/watch?v=S1fEHLarRZk | 15:30 |
| dbolser | 4,000 frames /s ... | 15:31 |
| dbolser | OK, I figure we have eough to go build a prototype ;-d | 15:32 |
| dbolser | :-D | 15:32 |
| dbolser | http://www.youtube.com/watch?v=AENnU0vdjPo | 15:35 |
| kanzure | ok i am back | 15:39 |
| dbolser | summary? | 15:40 |
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| kanzure | dbolser: you can make bubbles without lipids | 15:44 |
| kanzure | dbolser: devastation. i don't want to talk about it. | 15:44 |
| dbolser | oh | 15:45 |
| kanzure | see im | 15:45 |
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| kanzure | lichen: are you around? | 17:03 |
| kanzure | dbolser: beads are stored in drops | 17:17 |
| dbolser | yup | 17:17 |
| dbolser | where do 6mers come from (sorry) | 17:18 |
| kanzure | one sec. phone call >_< | 17:19 |
| dbolser | np | 17:19 |
| dbolser | actually I have to sleep now... | 17:20 |
| dbolser | night all | 17:20 |
| kanzure | it's first in first out storage of drops on the chip | 17:22 |
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| roksprok_ | hi all | 17:43 |
| kanzure | hi roksprok_ | 17:44 |
| roksprok_ | hope the call/pitch went/goes well | 17:44 |
| roksprok_ | i bet everyones been saying that to you guys today though | 17:45 |
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| roksprok_ | in other news i think lesswrong has officially become a cult | 17:45 |
| kanzure | roksprok_: i'm conflicted; could've been better, could've been worse | 17:45 |
| kanzure | roksprok_: it's been a cult ever since singularitarianism | 17:46 |
| roksprok_ | i applied for their 'rationality minicamp' and half the questions were 'would you start a lesswrong meetup in your home town?' | 17:46 |
| kanzure | oh their "SUPERPOWERS" camp? ugh | 17:46 |
| roksprok_ | and 'frequentists suck!' | 17:47 |
| kanzure | wait... dont you have to pay for the camp? | 17:47 |
| kanzure | why would you pay for that | 17:47 |
| roksprok_ | i would not pay...i more did it as a practice interview | 17:48 |
| kanzure | send me $12,000 and i'll put you through super transhumanism bootcamp | 17:48 |
| kanzure | ##hplusroadmap style bootcamp | 17:48 |
| * kanzure will bbl | 17:49 | |
| roksprok_ | i think that would actually take off...if i had 12000 dollars i would do it | 17:49 |
| kanzure | it would be Hacker School + Singularity University + some new things | 17:50 |
| kanzure | https://www.hackerschool.com/ | 17:50 |
| kanzure | http://devbootcamp.com/ | 17:50 |
| kanzure | then some molecular biology training | 17:51 |
| roksprok_ | could you contract with some h-plus oriented companies to make it free? i think practical training in high-tech stuff is the future of education | 17:52 |
| roksprok_ | also you would be able to get people to work on all the projects you want to see done | 17:52 |
| roksprok_ | i think its codeacademy or something where they get money by getting you hired at the end of your session | 17:53 |
| kanzure | that's also what those two links do | 17:53 |
| kanzure | recruiting fees. | 17:53 |
| roksprok_ | i wonder if there would be demand for something like that from biotech companies | 17:54 |
| roksprok_ | or if they have enough qualified post-phd people | 17:54 |
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| kanzure | roksprok_: there's a tremendous amount of available, cheap phd labor | 18:10 |
| kanzure | and cheap post-grad labor | 18:10 |
| roksprok_ | i figued...one reason i am not getting a phd | 18:11 |
| roksprok_ | it seems to be either you get lucky and get training in a good niche or you're an expensive lab tech | 18:11 |
| roksprok_ | and to be honest i doubt i would make it all the way from phd to post doc to assistant prof to tenure | 18:12 |
| kanzure | or you start a company | 18:13 |
| roksprok_ | well i am hoping that i can just start a company once i become a bit more capable | 18:13 |
| roksprok_ | without going through the long process | 18:13 |
| kanzure | how goes the protocol scraper? | 18:14 |
| roksprok_ | decently....it goes a bit slow because often i have to take a few hours to get up to speed on some new thing | 18:15 |
| kanzure | you should bug me when that happens :) | 18:15 |
| kanzure | i would be very happy to explain things | 18:15 |
| kanzure | and/or give you misinformation because i'm cruel | 18:15 |
| roksprok_ | i think there is enough misinformation on the internet....you would be wasting your cruelness | 18:16 |
| kanzure | aw. | 18:16 |
| roksprok_ | bioengineer a race plague or something | 18:17 |
| roksprok_ | give the fbi agents something to do | 18:17 |
| roksprok_ | :-P | 18:17 |
| kanzure | *shrug* they are busy organizing the next diybio/fbi conference | 18:22 |
| nmz787 | kanzure: i emailed mac a few days ago, havent heard anything back | 18:31 |
| nmz787 | kanzure: asked what was up, why the sites were down | 18:32 |
| kanzure | o.o | 18:32 |
| kanzure | awkward | 18:32 |
| kanzure | you should just call him | 18:32 |
| kanzure | 231-313-9062 or 775-553-5005 | 18:33 |
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| kanzure | delinquentme: ping? | 18:38 |
| Mariu | [04:39] [kanzure PING reply]: 1sec | 18:39 |
| Mariu | kanzure, do you play EvE - Online ? | 18:40 |
| kanzure | nope | 18:42 |
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| yashgaroth | oh that stuff about autoimmune induction was from biohack, I shoulda figured | 18:49 |
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| nmz787 | pretty good video of simple microfluidic production for cell culture | 18:58 |
| nmz787 | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586867/ | 18:58 |
| kanzure | "Shrinky-Dink Hanging Drops: A Simple Way to Form and Culture Embryoid Bodies" | 18:59 |
| kanzure | this? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586867/bin/jove-13-692.mov | 18:59 |
| kanzure | wtf why are they manually counting anything | 19:00 |
| roksprok_ | i tried shrinky dinks and they came out 'wrinkley' for lack of a better word...like they had unevenly shrunk. obviously i wasn't using as sophsticated a setup as them but i doubt it would be suitable for your micron-scale stuff | 19:02 |
| nmz787 | nah def not thinking for us | 19:02 |
| roksprok_ | i figured...but just in case | 19:03 |
| kanzure | roksprok_: when did you try it out? | 19:03 |
| roksprok_ | for that nematode maze thing | 19:03 |
| roksprok_ | i basically just made channels .5 mm by 50mm...so it was an entirely different scale than you're working with | 19:04 |
| roksprok_ | i ended up failing at keeping my nematodes apart/getting an accurate count and they died before i started class at a place with a microscope | 19:04 |
| kanzure | a common problem | 19:05 |
| roksprok_ | it was still fun though...so not all was wasted | 19:07 |
| roksprok_ | is davidad still planning on doing a nematode upload? | 19:08 |
| roksprok_ | his papers seem to be more computer science | 19:08 |
| kanzure | uhh let me ask | 19:09 |
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| kanzure | he might swing by the channel in a few minutes | 19:10 |
| roksprok_ | cool! | 19:10 |
| kanzure | also did you see the video from earlier today? | 19:10 |
| kanzure | dis one http://www.youtube.com/watch?v=xW77lANeJas | 19:11 |
| roksprok_ | yes...i am going to watch it on the bus tomorrow | 19:11 |
| roksprok_ | thank you | 19:11 |
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| kanzure | roksprok_: there you go sir | 19:12 |
| nmz787 | who is the prof and the speaker? | 19:12 |
| kanzure | nmz787: prof is marvin fucking minsky | 19:12 |
| kanzure | speaker is davidad | 19:12 |
| roksprok_ | sweet... | 19:12 |
| davidad | Hi. | 19:12 |
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| davidad | Actually, Marvin's middle name is Lee. | 19:12 |
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| kanzure | ah i wasn't aware | 19:13 |
| roksprok_ | hi davidad...are you still planning to do the c elegans 'upload' | 19:13 |
| davidad | Yes. | 19:13 |
| davidad | I'm a first-year Ph.D. student in a field I had absolutely no background in before arriving | 19:13 |
| davidad | so I've been full-time taking classes and learning basic lab techniques | 19:14 |
| roksprok_ | awesome....is it connected with your reconfigurable logic automata work? or are they pretty separated | 19:14 |
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| davidad | They're pretty separated. | 19:14 |
| davidad | You have to go to a fairly high level of abstraction to see any connection | 19:14 |
| davidad | which is that I'm generally interested in how to organize computations | 19:14 |
| davidad | RALA is one way to organize computations, which turns out to be not actually very good... | 19:14 |
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| nmz787 | davidad: what were you in before phd? | 19:14 |
| davidad | so I decided to change gears and see how Nature does it. | 19:15 |
| roksprok_ | ok that is good...honestly most of the math is over my head....was woried i was missing something | 19:15 |
| kanzure | ah you're doing wetlab training now? | 19:15 |
| davidad | Yep...did my first PCR and gel last week | 19:15 |
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| kanzure | hah. well. you'll probably do it 10,000 more times | 19:15 |
| davidad | Indeed | 19:15 |
| juul | hehe | 19:15 |
| juul | I did my first hela cell transformation yesterday | 19:16 |
| davidad | nice! | 19:16 |
| nmz787 | juul you still in emeryville? | 19:16 |
| davidad | nmz787: my background is in programming language theory, software engineering, computer architecture, AI | 19:16 |
| juul | nmz787, no, Stanford now. Only three days a week though. | 19:16 |
| nmz787 | davidad: cool | 19:17 |
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| kanzure | charlieschwabach: davidad is the one who wrote parts of kokompe | 19:18 |
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| kanzure | roksprok_: and why not mention your nematode troubles | 19:19 |
| juul | nmz787, where are you? | 19:19 |
| roksprok_ | davidad have you done neural recordings from nematodes yet? | 19:20 |
| nmz787 | juul: still in rochester, upstate NY | 19:20 |
| juul | ok | 19:21 |
| davidad | roksprok_: I'm afraid not. I've done some imaging with unc-119::GFP but I have yet to make D95N or GCaMP3 constructs. | 19:21 |
| davidad | My new PI suggests starting with ChR2 stimulation - much more reliable than readout - and see what can be learned from closed-loop behavioral perturbation | 19:22 |
| roksprok_ | ooo that is even better...does that mean you're leaning towards flourescent imaging rather than using contact electrodes? | 19:23 |
| davidad | Most certainly. | 19:23 |
| davidad | Although I haven't completely ruled out contact electrodes -- | 19:23 |
| davidad | Ed Boyden has a new patch-clamping robot which may make the protocol attainable for mere mortals | 19:23 |
| davidad | but despite his enthusiasm, it won't make getting through the cuticle any easier | 19:24 |
| kanzure | neat. iirc henry markram's group just does it manually with an xbox controller to guide the patch clamping | 19:24 |
| roksprok_ | http://www.princeton.edu/neuroscience/collaborative-research-in/AbstractsPDF/Franzesi.pdf | 19:24 |
| roksprok_ | Automated whole-cell patch clamp electrophysiology of neurons in vivo | 19:24 |
| davidad | That's the one | 19:25 |
| roksprok_ | cool thanks | 19:25 |
| davidad | But I'm in love with optics. Anything I can do optically, I will. | 19:26 |
| kanzure | haha. you wouldn't happen to know someone who could help me with the optics for a submicron laser cutter, would you.. | 19:26 |
| davidad | submicron? | 19:26 |
| davidad | Good luck with that... | 19:26 |
| nmz787 | spot size of ~1 micron | 19:27 |
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| nmz787 | i think we just need a plano convex lens | 19:27 |
| kanzure | well. yeah, not submicron. but 1 micron would be great. | 19:27 |
| roksprok_ | honestly i can't imagine what high-throughput patch-clamp would look like....a porcupine | 19:27 |
| davidad | gotcha | 19:27 |
| juul | \ | 19:27 |
| davidad | yeah, pretty much...I doubt one could get more than a dozen good signals at once | 19:27 |
| davidad | and even that would be insane | 19:28 |
| nmz787 | can't you have a pH indicator fluorophore to see the neural transduction along the neuron? | 19:28 |
| roksprok_ | it would make for an awesome science/nature cover photo though | 19:28 |
| nmz787 | what flows into the cell K+ right? | 19:29 |
| davidad | K, Na, Cl, some Ca are all involved | 19:29 |
| kanzure | nmz787: you can do all sorts of things.. some people do azobenzene or gfp in the ion channels | 19:29 |
| davidad | but yeah pHluorin is a possibilty | 19:29 |
| nmz787 | so its mostly a pH increase? in the cell...? I guess you'd have to have a really sensitive dye | 19:30 |
| kanzure | there are also voltage sensitive dyes | 19:30 |
| nmz787 | is that not the same here? | 19:30 |
| davidad | <http://www.jneurosci.org/content/23/2/373.full> - synapto-pHluorin | 19:31 |
| davidad | not the same | 19:31 |
| nmz787 | lewis acid vs bronsted | 19:31 |
| kanzure | "Synaptic Activity of the AFD Neuron in Caenorhabditis elegans Correlates with Thermotactic Memory" | 19:31 |
| davidad | but yeah there are a lot of things to try...once I learn how to transform worms... hopefully some of them will work :) | 19:31 |
| kanzure | electroporation? | 19:32 |
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| davidad | of what, the cuticle? | 19:32 |
| kanzure | the whole organism why not :P | 19:32 |
| davidad | :P | 19:32 |
| davidad | no, transformation happens by microinjection into the gonad | 19:32 |
| roksprok_ | may i ask if success would be the ability to predict which neurons would fire depending on which are stimulated? | 19:33 |
| roksprok_ | and so on and so on.... | 19:33 |
| davidad | that's a great question | 19:33 |
| davidad | C. elegans in particular is difficult to think about digitally | 19:34 |
| davidad | because it uses graded potentials | 19:34 |
| davidad | rather than action potentials | 19:34 |
| davidad | so, we can't pretend that there is a neat sequence of states with each state taking a value on a 302-dimensional hypercube and some transition probabilities between each pair of states | 19:34 |
| roksprok_ | >:-0 did not know that | 19:34 |
| davidad | I think this is a good thing because I suspect even the mammalian brain does not do a whole lot of "digital" computation, at least not in the way we are inclined to think about it | 19:35 |
| davidad | instead, we have to think about the C. elegans nervous system as a dynamical system | 19:35 |
| davidad | with some attractors, and some energy barriers between those attractors | 19:36 |
| davidad | and lots of interacting feedback loops | 19:36 |
| kanzure | and phase transitions? | 19:36 |
| davidad | bifurcations to be sure, though they may not meet the statmech criteria as "phase transitions" precisely | 19:36 |
| kanzure | i think this is what amit wrote about | 19:37 |
| davidad | but the goal is to sort of figure out what state space really looks like, where the trajectories are, and how to map that space to observables like behavior and activation levels | 19:37 |
| kanzure | Modeling brain function: the world of attractor neural networks. 1989 | 19:37 |
| roksprok_ | would it be possible to get the....are they called evolution rules? | 19:37 |
| davidad | if you're referring to learning, plasticity or development, I'm explicitly leaving those out for the scope of my PhD | 19:38 |
| nmz787 | davidad: can they do two photon with a DMD chip? | 19:39 |
| roksprok_ | do c. elegans have much plasticity? | 19:39 |
| davidad | nmz787: not that I'd heard of. google turns up http://link.aip.org/link/doi/10.1117/12.874681 | 19:40 |
| davidad | roksprok_: not much, but some. there's certainly no adult neurogenesis and little if any rewiring, but synaptic strengths can certainly be modified | 19:40 |
| davidad | for instance, they can learn attractions to previously neutral odors | 19:41 |
| nmz787 | sounds about what i was looking for | 19:41 |
| nmz787 | davidad: how would you use two-photon microscopy without something like that DMD paper for the zebrafish... seems like it would be moving around too much to use a single focus | 19:42 |
| nmz787 | i.e. you need a movie of more than 1 pixel | 19:43 |
| davidad | nmz787: you paralyze it | 19:43 |
| davidad | hasn't been published yet, but look for "Brain-wide neural dynamics at single-cell resolution during motor adaptation in larval zebrafish" coming out in Nature later this year by Ahrens et al | 19:44 |
| nmz787 | by stopping neurons, or cutting muscle? | 19:44 |
| davidad | no effect on neurons, it's a toxin that is highly specific to muscle cells, from some African snake's venom | 19:45 |
| roksprok_ | have you heard of randall koene/substrate independent minds? if so....are you optomistic or is he seen as a bit of a kook by the academic community | 19:46 |
| davidad | randal is a friend | 19:47 |
| davidad | personally I believe he has exactly the right fundamental ideas | 19:47 |
| kanzure | roksprok_: everyone knows randal in here | 19:47 |
| davidad | however, I'm pretty shy about talking in that way in the academic world | 19:48 |
| davidad | as is Ken Hayworth, whose desk I sat next to for a couple months | 19:48 |
| roksprok_ | very cool....i found his stuff really inspiring | 19:48 |
| davidad | yeah...we were both very happy to find someone else who "gets it" | 19:48 |
| davidad | incidentally, ed boyden also gets it, as you may be able to tell | 19:48 |
| davidad | but most scientists don't | 19:49 |
| roksprok_ | did Ken do the brain slicer? | 19:49 |
| davidad | yes, that's right | 19:49 |
| kanzure | davidad: have you talked with todd/3scan lately | 19:49 |
| davidad | not since SfN in November | 19:49 |
| kanzure | iirc they finally got a space | 19:49 |
| davidad | cool | 19:49 |
| kanzure | damn so i've never been to Society for Neuroscience | 19:50 |
| kanzure | kinda missing out | 19:50 |
| davidad | it's quite a thing | 19:50 |
| davidad | I think it's the largest event of any kind I've ever been to | 19:51 |
| davidad | larger than a baseball game, or a rock concert | 19:51 |
| davidad | not as large as a presidential inauguration, but I've never been to one of those | 19:51 |
| roksprok_ | was it around 30,000 people or more? | 19:51 |
| davidad | 32,357 | 19:52 |
| roksprok_ | wow | 19:52 |
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| davidad | it's an interesting phenomenon | 19:53 |
| davidad | neuroscience is a small enough field that they can manage to basically get everyone at a single conference | 19:53 |
| davidad | but only just | 19:53 |
| davidad | so it's one of the largest conferences around | 19:53 |
| diginet | sounds like a party | 19:54 |
| roksprok_ | i am suprised the 'anthropology of scientists' haven't written a bunch about it | 19:54 |
| davidad | in computer science, for instance, there is no Society for Computer Science conference that every computer scientist goes to | 19:54 |
| yashgaroth | I think it is the largest...AACR is maybe half that number | 19:54 |
| davidad | just a lot of small conferences with a thousand or two attendees | 19:54 |
| roksprok_ | do you think that helps people stay focused on the 'bigger picture' and work together to solve problems or do people kinda hang out with their niche | 19:55 |
| davidad | it's certainly a lot of fun to walk around the exhibit hall because it's like walking around the entire field of neuroscience | 19:56 |
| davidad | but when you leave sfn, you don't really stay in touch with people who weren't in your specific area | 19:56 |
| davidad | so I don't think it has any lasting effect | 19:56 |
| roksprok_ | ah...i see | 19:57 |
| roksprok_ | is ed boyden your advisor? or does that not happen till later | 19:59 |
| davidad | I'm actually at both MIT and Harvard right now | 20:01 |
| davidad | I'm a PhD student at Harvard and a Research Affiliate at MIT | 20:01 |
| davidad | Ed is my advisor at MIT | 20:01 |
| davidad | my advisor at Harvard is going to be Sharad Ramanathan, if all goes according to plan | 20:01 |
| kanzure | aha so ed is sponsoring you.. hell yeah | 20:01 |
| davidad | exactly :) | 20:02 |
| kanzure | well i don't think i'd pick anyone else | 20:02 |
| roksprok_ | very cool...hope things do go according to plan | 20:02 |
| davidad | thanks! | 20:02 |
| roksprok_ | is ramanathan the connectome guy? | 20:02 |
| kanzure | no that's seung | 20:03 |
| kanzure | sebastien seung | 20:03 |
| kanzure | sebastian | 20:03 |
| davidad | I know seung, he's cool | 20:03 |
| davidad | but he's fallen into the kurzweil trap | 20:03 |
| kanzure | being a grumpy old man watching the stock market? | 20:04 |
| davidad | err | 20:04 |
| davidad | no, not that one ~_^ | 20:04 |
| davidad | rather, he does too much writing and public speaking and pandering to the lay public | 20:04 |
| davidad | which makes him look a lot stupider than he actually is | 20:04 |
| davidad | and commits him to oversimplifications | 20:05 |
| roksprok_ | and grand promises | 20:05 |
| davidad | indeed | 20:05 |
| kanzure | my beef with ray is summarized by the essays here: http://heybryan.org/fernhout/ | 20:05 |
| kanzure | well i guess that's not a summary. | 20:06 |
| kanzure | rather, the inevitability and commercial undertones | 20:06 |
| roksprok_ | maybe it will help increase neuroscience funding? that would at least help you all | 20:06 |
| davidad | it hasn't yet | 20:07 |
| davidad | the only funding it's increased is seung's publisher's | 20:07 |
| davidad | :P | 20:07 |
| kanzure | good business models and business might help | 20:07 |
| kanzure | fighting over research funding is vicious | 20:08 |
| davidad | yes, it is | 20:08 |
| davidad | see http://davidad.net/nelson/ | 20:08 |
| kanzure | it's like.. what, a few billion dollars a year? | 20:08 |
| nmz787 | i saw seung recently | 20:10 |
| nmz787 | he spoke at my school | 20:10 |
| roksprok_ | so i know kanzure will punch me for bringing this up...but i read davidad.net/nelson/ and the marketing/commericialization problem seems to be along the line of something i was thinking of earlier... | 20:12 |
| davidad | yeah? | 20:12 |
| roksprok_ | but what do you think of a non-profit research center that spun off for-profits? | 20:12 |
| davidad | sounds good to me | 20:13 |
| kanzure | haha | 20:13 |
| kanzure | i was telling roksprok_ that he would have to find funding somehow | 20:13 |
| kanzure | by writing grants or something | 20:13 |
| kanzure | which isn't a steady stream of income | 20:13 |
| davidad | to be fair, it only has to be bootstrapped to profitability | 20:13 |
| roksprok_ | and hopefully being funded by the equity in those for-profits, with some going to the researchers/internal people who worked on it to encourage practical research | 20:13 |
| davidad | hopefully ~10 years | 20:14 |
| kanzure | bootstrapping means 5-15 years | 20:14 |
| kanzure | yes | 20:14 |
| davidad | that's the sort of thing that can be achieved with a few wealthy individuals | 20:14 |
| davidad | I have a meeting with Peter Thiel in 3 weeks on exactly this subject | 20:14 |
| kanzure | haha. throw in a good word for us! | 20:14 |
| kanzure | ah that's right you also missed 20under20 | 20:15 |
| kanzure | i was a little sad about that | 20:15 |
| davidad | I didn't miss it, per se | 20:15 |
| kanzure | oh you're like one year younger than me i think | 20:15 |
| davidad | I considered it, and talked to people at the foundation about it | 20:15 |
| roksprok_ | i also think it would help with the innovator's dilemma....as the for-profits would not be the ones deciding wether or not to commercialize stuff | 20:15 |
| davidad | we concluded that I'm in a unique position where being in academia is actually probably a good thing | 20:15 |
| davidad | so I didn't apply | 20:16 |
| davidad | figured the money is better used on people who are "worse off" in some sense | 20:16 |
| kanzure | not surrounded by.. say.. marvin mensky, ed boyden, sebastian seung, sharad ramanathan.. | 20:17 |
| davidad | right | 20:17 |
| kanzure | *minsky | 20:17 |
| kanzure | oh and those other fablab people heh | 20:17 |
| roksprok_ | and i'm pretty sure phd funding is more than 100,000 | 20:17 |
| roksprok_ | or whatever 20under20 fellows get | 20:17 |
| davidad | no, actually | 20:18 |
| davidad | being a phd student is not very lucrative | 20:18 |
| kanzure | $40k/year aww yeah | 20:18 |
| davidad | almost 40k, heh | 20:19 |
| roksprok_ | well...i assume you will be there more than three years... | 20:19 |
| davidad | well, sure | 20:20 |
| davidad | but the thiel fellowship is two years | 20:20 |
| roksprok_ | oh i did not know that | 20:20 |
| davidad | and income is best measured in dollars per unit time, not total dollars | 20:20 |
| roksprok_ | true | 20:20 |
| roksprok_ | are you planning on staying in academia then? or too early to say? | 20:21 |
| roksprok_ | i mean....working towards tenure | 20:21 |
| davidad | not unless I am beat over the head with offers | 20:21 |
| davidad | like, if Stanford asks me nicely to be a professor and says I only have to teach one class a year and can do whatever I want | 20:22 |
| davidad | well, fine | 20:22 |
| davidad | but that is not very likely | 20:22 |
| roksprok_ | starting a company/commercializing your research or getting funding from elsewhere? | 20:22 |
| davidad | my goal is to fix research as an institution | 20:23 |
| davidad | to create the next Bell Labs | 20:23 |
| davidad | whatever that may be | 20:23 |
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| roksprok_ | laudable....but very difficult! | 20:23 |
| davidad | it's a long-term goal! | 20:24 |
| davidad | :) | 20:24 |
| davidad | and having Peter Thiel on board helps >.> | 20:24 |
| roksprok_ | yes...and if you succeed it will be truly world changing | 20:25 |
| davidad | right | 20:25 |
| davidad | what about you? | 20:25 |
| davidad | it sounds like you may have a similar goal | 20:25 |
| kanzure | davidad: have you seen my pitch deck http://diyhpl.us/~bryan/nucleic/su-slides.pdf | 20:26 |
| davidad | but maybe it was just something you were daydreaming about :) | 20:26 |
| davidad | kanzure: nope | 20:26 |
| roksprok_ | so this may be an odd question...but i know Thiel funds the singularity institute, and they don't seem to look to highly on things that accellerate AI/brain emulation...would Thiel fund something that would do that? or does he agree with FAI or nothing? | 20:26 |
| davidad | I have Eliezer's approval on safety concerns. | 20:27 |
| davidad | He's not worried about superintelligent worms. | 20:27 |
| davidad | Mice, maybe, but that's a ways off | 20:27 |
| davidad | Thiel recognizes that brain emulation is underaddressed in his current portfolio | 20:28 |
| davidad | so he's actually more interested in funding it than other approaches which he kind of has covered already in some sense | 20:28 |
| roksprok_ | davidad: i would like to see 'minds', 'cognition' and 'consiousness' become something as editable/fungible/understood as thermodynamics/circuits/ect.... | 20:28 |
| davidad | absolutely! | 20:29 |
| roksprok_ | very good to know! i know he is probably aware, but Ted Berger has done awesome stuff towards 'replacement parts for the brain' he calls it | 20:29 |
| delinquentme | davidad, who are you? | 20:30 |
| delinquentme | one of the 20 under 20? | 20:30 |
| kanzure | davidad: btw, i hear halcyon is liquidating | 20:30 |
| delinquentme | a alex and all those kids? | 20:30 |
| davidad | http://lmgtfy.com/?q=davidad | 20:30 |
| kanzure | delinquentme: call now? | 20:30 |
| davidad | kanzure: really? I hadn't heard that | 20:31 |
| kanzure | davidad: people are taking equipment off their hands haha | 20:31 |
| roksprok_ | their website is wiped | 20:31 |
| delinquentme | cool | 20:31 |
| katsmeow-afk | kanzure has been announcing that in here for a week now | 20:31 |
| davidad | haha | 20:31 |
| delinquentme | kanzure, im all kinds of pissy right now | 20:31 |
| davidad | well, it's news to me | 20:31 |
| delinquentme | busted website wont parse correctly | 20:31 |
| kanzure | delinquentme: show me | 20:32 |
| kanzure | delinquentme: consider using webkit to parse it | 20:32 |
| delinquentme | http://www.lww.com/webapp/wcs/stores/servlet/CatalogSearchResultCmd?storeId=11851&catalogId=9012052&langId=-1&searchTerm=journal#docType=0&pageSize=300&storeId=11851&langId=-1&catalogId=9012052&searchTerm=journal&resultCatEntryType=&beginIndex=0&sType=&searchTermScope=&facetFields=%2CpublicationDate_facet%2CpubFrequency_facet%2CauthorNames_facet%2Cprimary&filterValue=productType_facet%3A%22Journal++++++++++++++++++++++++++ | 20:32 |
| delinquentme | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++%22%7C%22Journal+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | 20:32 |
| delinquentme | ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++%22&sortBy=productNameSort+asc | 20:32 |
| delinquentme | that | 20:32 |
| kanzure | the fuck is that url | 20:32 |
| delinquentme | ( not kidding ) | 20:32 |
| delinquentme | is a site-generated URL | 20:32 |
| delinquentme | one of the fields in there specs 300 entries | 20:32 |
| kanzure | &sortBy=productNameSort+as <---- can probably be attacked with sql injection | 20:33 |
| kanzure | &sortBy=productNameSort+asc | 20:33 |
| davidad | o_O | 20:33 |
| delinquentme | yeah hence &pageSize=300 | 20:33 |
| kanzure | davidad: we are forming 'science liberation front' | 20:33 |
| davidad | uh oh | 20:33 |
| kanzure | davidad: http://diyhpl.us/~bryan/irc/ezproxy.py | 20:34 |
| delinquentme | davidad, but yeah its cool we've got a legit scientist whos onboard w the Theil opz | 20:34 |
| davidad | pirating articles, are we? | 20:34 |
| delinquentme | nah just indexing | 20:34 |
| kanzure | davidad: ALL of them | 20:34 |
| davidad | lol | 20:34 |
| delinquentme | thus far its totally legal :D | 20:34 |
| kanzure | yep. | 20:34 |
| delinquentme | kanzure, I also tried feeding that URL into a bit.ly to see if there was something w weird encoding | 20:34 |
| delinquentme | ( didnt help ) | 20:35 |
| kanzure | why is this not parsing ? | 20:35 |
| kanzure | are you saying the url is broken | 20:35 |
| kanzure | or the html is bad | 20:35 |
| delinquentme | so I can open up the page. however all the IDs that im seeing in browser | 20:36 |
| delinquentme | are of different values in mechanize / noko | 20:36 |
| delinquentme | so yeah a webkit might be the answer | 20:36 |
| kanzure | maybe it's a POST | 20:36 |
| kanzure | and not a GET? | 20:36 |
| delinquentme | true! | 20:37 |
| davidad | kanzure, it looks like they decided to leave the sequencing business because Oxford Nanopore | 20:37 |
| davidad | so it makes sense that they're getting rid of TEMs and such | 20:37 |
| kanzure | davidad: yeah but that also sounds crazy | 20:37 |
| davidad | they're going to focus on synthesis instead | 20:37 |
| davidad | watch out ;P | 20:37 |
| kanzure | what | 20:37 |
| delinquentme | IDK right now im just gonna press on w maney | 20:37 |
| kanzure | synthesis. fuck them. | 20:37 |
| davidad | lol | 20:37 |
| kanzure | oh well | 20:37 |
| delinquentme | davidad, they're doing synth now? | 20:37 |
| kanzure | they probably won't do it open source | 20:37 |
| kanzure | so i'm safe | 20:37 |
| davidad | http://pandodaily.com/2012/02/22/new-competitive-threat-forces-halcyon-molecular-to-accelerate-its-game-plan/ | 20:38 |
| davidad | most recent update I can find | 20:38 |
| kanzure | see, when i talked with them they told me their game plan was "SEQUENCE EVERYTHING" | 20:38 |
| kanzure | "and if someone gets cheap sequencing before us, then we will focus on selling microscopes" | 20:38 |
| kanzure | by 'talked with' i mean "interviewed with" | 20:39 |
| kanzure | so i'm a little annoyed they lied to me | 20:39 |
| delinquentme | im a little bitter this is public information and I've not heard about it | 20:39 |
| delinquentme | << semi halcyon fanboy | 20:39 |
| delinquentme | 3/4ths | 20:39 |
| davidad | halcyon plays it secretive all right | 20:39 |
| delinquentme | tis the pivot no? | 20:39 |
| kanzure | ah no that was just what elon was saying | 20:40 |
| kanzure | i spoke with some others and they say that elon was in panic mode | 20:40 |
| kanzure | so i'm not convinced they are doing gene synthesis. pandodaily is not a reliable source anyway. | 20:40 |
| kanzure | panicy invester + pandodaily => not trustable | 20:40 |
| kanzure | *investor | 20:40 |
| yashgaroth | I don't see how reading sequences via TEM translates into synthesis | 20:41 |
| davidad | it doesn't! | 20:41 |
| davidad | thus wiping their website and selling their TEMs | 20:41 |
| davidad | it's effectively a reboot of the business | 20:41 |
| yashgaroth | but then they'll just be another phosphoramidite company | 20:41 |
| davidad | knowing halcyon, they'll never be "just another" anything | 20:42 |
| kanzure | yashgaroth: nah they could be doing whatever gen9bio is doing | 20:42 |
| yashgaroth | fair enough | 20:42 |
| kanzure | or whatever i'm doing | 20:42 |
| kanzure | davidad: ah but they told me they wanted to *sell* microscopes as a business | 20:43 |
| kanzure | not as a liquidation event | 20:43 |
| kanzure | like they wanted to manufacture ad sell them. | 20:43 |
| kanzure | that was coming from michael andregg | 20:43 |
| davidad | yeah that doesn't make any sense really | 20:44 |
| kanzure | this is why i chose not to work for them | 20:44 |
| katsmeow-afk | was there supposed to be a book at http://blog.davidad.net/post/8483102117/the-problem-with-agi ? | 20:44 |
| davidad | fair enough | 20:44 |
| roksprok_ | one of their application questions was 'how would you build an electron microscope in a 1mm cube?' | 20:44 |
| kanzure | no it wasn't 1mm cube was it? it was just in general? | 20:44 |
| davidad | katsmeow: nope, that's just an image. ben said it at AGI-11 and it resonated with me, so I typeset it. | 20:45 |
| roksprok_ | i thought i remember there was a space constraint...but the website is dead so .... | 20:45 |
| * davidad shrugs | 20:45 | |
| katsmeow-afk | oh | 20:45 |
| kanzure | ben goertzel is very anti-SIAI | 20:45 |
| kanzure | that's about his one redeeming quality | 20:45 |
| davidad | the funny thing is, people like us spend so much time with people who share our mindsets, that we forget how much we have in common | 20:46 |
| davidad | imagine for example a debate between Ben Goertzel and David Chalmers | 20:46 |
| davidad | whose side would you be on then? | 20:46 |
| kanzure | about what | 20:46 |
| davidad | consciousness | 20:46 |
| kanzure | i don't believe in that | 20:46 |
| kanzure | and iirc both of them do | 20:46 |
| kanzure | so neither of them | 20:46 |
| davidad | lol | 20:46 |
| davidad | fine | 20:46 |
| kanzure | game over? :) | 20:46 |
| kanzure | davidad: hey you should be all for anti-consciousness | 20:47 |
| delinquentme | YIL the CEO of koenigsegg started when he was 22 years old , with no engineering background and protoyped his first car with parts from supplier sponsors | 20:47 |
| davidad | I am anti-consciousness | 20:47 |
| kanzure | davidad: instead of modeling the brain as conscious, you model it as a non-linear system | 20:47 |
| roksprok_ | such an iconoclast... | 20:47 |
| delinquentme | bad ass right? | 20:47 |
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| davidad | delinquentme: indeed! | 20:47 |
| davidad | yeah, I don't believe in consciousness either | 20:47 |
| delinquentme | supplier-effing-sponsored | 20:48 |
| kanzure | it causes more problems than it's worth | 20:48 |
| davidad | I'm aligned with Daniel Dennett | 20:48 |
| delinquentme | consiousness? | 20:48 |
| davidad | Chalmers particularly pisses me off | 20:48 |
| davidad | Goertzel doesn't really piss me off about anything, he seems to have mostly the right ideas | 20:48 |
| davidad | I don't think his project is going anywhere, but I have no problem with that | 20:48 |
| kanzure | eh. goertzel threatened legal action against me so i had to cut him off. | 20:48 |
| davidad | oh dear :/ | 20:49 |
| kanzure | my thoughts too. | 20:49 |
| davidad | why? | 20:49 |
| davidad | that is, what was he threatening to act on? | 20:49 |
| kanzure | he was angry when i didn't renew a software contract for hplusmagazine | 20:49 |
| davidad | ah. | 20:49 |
| davidad | I may regret joining H+... | 20:49 |
| kanzure | you definitely will | 20:49 |
| kanzure | i do! | 20:49 |
| davidad | I've already gotten various people I don't know adding me on facebook and asking me to vote for them | 20:50 |
| kanzure | ah yeah i hate that | 20:50 |
| kanzure | i was involved as director of r&d for about a year | 20:50 |
| roksprok_ | what are the votes for....board of directors or something? | 20:50 |
| kanzure | they are going nowhere | 20:50 |
| kanzure | it's just not worth the effort | 20:50 |
| davidad | roksnprok_: yes | 20:50 |
| davidad | whoa where'd that 'n' come from | 20:50 |
| davidad | anyway yeah, I agree | 20:50 |
| kanzure | tab completion? | 20:50 |
| roksprok_ | kanzure may i ask if your parting was amicable? | 20:50 |
| kanzure | roksprok_: it was not | 20:50 |
| kanzure | again- threats of legal action for silly things | 20:51 |
| davidad | I only joined to vote for Tom McCabe, who I actually like | 20:51 |
| kanzure | i just don't want to deal with that drama | 20:51 |
| davidad | bleh. | 20:51 |
| kanzure | what's it going to get me? hplusmagazine? why are they doing a blog anyway | 20:51 |
| kanzure | oh yeah we're going to publish in the one dying media | 20:51 |
| kanzure | magazines! OF COURSE! | 20:51 |
| davidad | I thought the magazine was pretty cool | 20:51 |
| kanzure | and then pay $10,000/mo for an editor to spam reddit/digg about it | 20:51 |
| kanzure | it's offline | 20:52 |
| davidad | having a physical magazine made the whole memespace feel more legit somehow | 20:52 |
| roksprok_ | it is not printing anymore...is it? | 20:52 |
| kanzure | oh nope it's back | 20:52 |
| kanzure | roksprok_: nope | 20:52 |
| kanzure | it's just a bunch of populist drivel :( | 20:52 |
| davidad | true | 20:52 |
| kanzure | anyway. let's get back to intergalactic superlasers | 20:52 |
| davidad | I didn't like _reading_ the magazine, I just liked holding it :P | 20:52 |
| Mariu | ^^ | 20:52 |
| kanzure | haah | 20:52 |
| kanzure | fair enough | 20:53 |
| delinquentme | kanzure, ingenta connect? | 20:55 |
| delinquentme | they | 20:55 |
| delinquentme | 've got to be brand new | 20:55 |
| delinquentme | they're another aggregatorrrrr | 20:55 |
| kanzure | huh? no i think ingenta is at least 10 years old | 20:55 |
| delinquentme | and i've got a head ache from staring | 20:55 |
| delinquentme | their shit looks really clean for being that old | 20:56 |
| delinquentme | surprising | 20:56 |
| davidad | yeah I remember using ingenta in college (i.e. pre-2005) | 20:56 |
| delinquentme | i might be able to knock a few more of these out w that | 20:57 |
| delinquentme | im about half way | 20:57 |
| delinquentme | meh | 20:57 |
| davidad | kanzure: you don't have genscript listed as a competitor? | 20:57 |
| delinquentme | lololol http://www.technologyreview.com/blog/editors/27734/?p1=A2 | 20:58 |
| kanzure | davidad: doh | 20:58 |
| kanzure | well i also dont have dna2.0 | 20:58 |
| kanzure | i'm just selling devices | 20:58 |
| kanzure | not a service | 20:58 |
| delinquentme | TIL ycomb 'me too' startups happen @ the country level too | 20:58 |
| kanzure | davidad: also i'm self-funding it so far | 20:59 |
| davidad | delinquentme: that's pretty nifty | 21:00 |
| delinquentme | kanzure, u saw my shit about koenigsegg | 21:03 |
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| delinquentme | while microfluidics != headers | 21:03 |
| delinquentme | its an option | 21:03 |
| kanzure | suppliers? | 21:03 |
| delinquentme | yeah | 21:03 |
| kanzure | suppliers of what ? | 21:03 |
| delinquentme | IMO its a really fucking good option too | 21:03 |
| delinquentme | ah well | 21:04 |
| davidad | supplies of reagents, maybe? | 21:04 |
| delinquentme | you know for ahem | 21:04 |
| delinquentme | protptyping | 21:04 |
| delinquentme | derrr | 21:04 |
| kanzure | davidad: why would they want to support something that reduces the dependence on reagents, heh | 21:04 |
| delinquentme | fingers | 21:04 |
| kanzure | delinquentme: i'm still not sure what supplier you are talking about | 21:04 |
| davidad | microfluidic synthesis doesn't reduce dependence on reagents, does it? | 21:04 |
| kanzure | davidad: way less volume | 21:05 |
| kanzure | also, i want to do protein purification on a chip eventually | 21:05 |
| davidad | fair enough | 21:05 |
| kanzure | and possibly use nano sieves to not lose the enzymes after each reaction | 21:05 |
| delinquentme | yeah but lower vol / reaction only means just that | 21:05 |
| delinquentme | lower use per reactions | 21:05 |
| delinquentme | http://www.technologyreview.com/biomedicine/37204/ << forgot about this | 21:06 |
| delinquentme | ehhhh quakes lab again | 21:07 |
| delinquentme | Y ACADEMIA U SO INBRED | 21:07 |
| kanzure | what's wrong with quake? his work tends to be solid | 21:07 |
| kanzure | also pdms membrane/pressure valves | 21:07 |
| kanzure | and he did the first microfluidic sanger sequencer iirc | 21:07 |
| kanzure | ah fluidigm is quake. didn't know that.. | 21:08 |
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| delinquentme | nothing wrong with it | 21:10 |
| delinquentme | just nedz more | 21:10 |
| kanzure | http://www.fluidigm.com/chips-kits.html | 21:10 |
| kanzure | "EP1 System is also compatible with the world’s first reusable chips for SNP genotyping which will ultimately drive costs to one cent per genotype." | 21:10 |
| kanzure | wonder why no generic sequencer is being commercialized there | 21:11 |
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| davidad | cheers folks | 21:18 |
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| delinquentme | between u and me kanzure ( and all the other cool kids here ) | 21:19 |
| delinquentme | this is something I want to get good at | 21:19 |
| delinquentme | suppliers are in industry | 21:19 |
| kanzure | here's their form 10-Q | 21:19 |
| kanzure | http://files.shareholder.com/downloads/ABEA-5TB8PR/1789707350x0xS1193125-11-311107/1162194/filing.pdf | 21:19 |
| kanzure | $82 mil in assets | 21:19 |
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| kanzure | $28 mil in product revenue ending 2011 | 21:21 |
| delinquentme | qualifies as fucking incredible huh | 21:22 |
| delinquentme | sac | 21:22 |
| delinquentme | needs | 21:22 |
| delinquentme | hit | 21:22 |
| delinquentme | later! | 21:22 |
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| kanzure | huh it had a $77 mil IPO? that's sorta small | 21:25 |
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| kanzure | "Product margin: 67%" | 21:29 |
| klafka | what is that? | 21:34 |
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| kanzure | net losses of 218 million | 21:39 |
| kanzure | klafka: reading fluidigm's form 10-Q http://files.shareholder.com/downloads/ABEA-5TB8PR/1789707350x0xS1193125-11-311107/1162194/filing.pdf | 21:40 |
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| kanzure | what?? "Our performance is substantially dependent on the performance of our senior management and key scientific and technical personnel, particularly Gajus V. Worthington, our President and Chief Executive Officer. We do not maintain fixed term employment contracts with any of our employees" | 21:48 |
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| Mokbortolan_ | uhh | 22:03 |
| Mokbortolan_ | fixed-term employment contracts = we will pay you for 1 year | 22:03 |
| Mokbortolan_ | so, like, regular salaried employees, I think | 22:03 |
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| kanzure | Mokbortolan_: ah so it's probably at-will | 22:07 |
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| kanzure | wow this is endless: | 23:11 |
| kanzure | http://addyosmani.github.com/backbone-fundamentals/ | 23:11 |
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