--- Log opened Thu Apr 05 00:00:22 2012 00:09 -!- AdrianG [~amphetami@unaffiliated/amphetamine] has quit [Ping timeout: 244 seconds] 00:12 < kanzure> hmm maybe i can convince fenn and nmz787 to move to detroit 00:12 < kanzure> 10k sqft for $1k/mo and all the industrial equipment you can dream of 00:14 < yashgaroth> plus, robocop 00:16 < delinquentme> who / what is there 00:16 < kanzure> delinquentme: cheap stuff 00:16 < yashgaroth> robocop 00:17 < skorket> kanzure, if you wanted to get a diy bio thing going in detroit, I might even be convinced 00:17 < kanzure> skorket: are you in the area? you should meet tim schmidt 00:17 < skorket> ah, sadly, I'm in upstate NY (Ithaca) but thinking of moving 00:17 < skorket> Boston is top of my list 00:17 < delinquentme> night time 00:18 < delinquentme> oodulstay 00:20 < kanzure> http://www.cityfeet.com/cont/michigan-industrial-space 00:21 < kanzure> http://www.cityfeet.com/Commercial/ForLease/1215-Lipsey-Drive-Charlotte-MI-48813-17487695L17487695L1.aspx 00:21 < kanzure> 30k sq ft for $1750/mo? 00:21 < skorket> kanzure, for that type of money you could buy a whole block in some neighborhoods 00:23 -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has quit [Quit: Leaving.] 00:23 < kanzure> so $600/mo for 10k sq ft on that last one 00:23 < skorket> http://www.cityfeet.com/Commercial/ForSale/4940-DELEMERE-AVE-ROYAL-OAK-MI-48073-2419396.aspx 00:24 < skorket> http://www.cityfeet.com/Commercial/ForSale/21500-24-Mile-Macomb-MI-48042-2371006.aspx 00:24 < skorket> and on and on 00:25 < skorket> I mean, you could almost just squat on some the real estate. Detroit is pretty deserted 00:29 < kanzure> i'm tempted to just rent out 20k sqft and just chill out in the middle while i write my code 00:45 < jrayhawk> If you're dissatisfied with PSU's network, your other vserver actually has fairly diverse and stable peering 00:45 < kanzure> i'm more curious about fenn's odd git issue 00:47 < jrayhawk> git:// as a protocol doesn't support authentication 00:48 < kanzure> welp. okay. 00:49 -!- _0bitcount [~ulises11@213.37.203.109.dyn.user.ono.com] has joined ##hplusroadmap 00:49 < jrayhawk> [url "jrayhawk@piny.be:/srv/git/"] 00:49 < jrayhawk> pushInsteadOf = git://piny.be/ 00:50 < jrayhawk> err, [url "jrayhawk@piny.be:/srv/git/"] pushInsteadOf = git://piny.be/ 00:50 < jrayhawk> huh, man, rxvt does not want to copy that properly 00:50 < jrayhawk> [url "gnusha.org:/srv/git/"] pushInsteadOf = git://gnusha.org/ 00:51 < jrayhawk> beh, fuck it, you get the idea 00:51 < jrayhawk> that should go into ~/.gitconfig or git config --global 00:51 < kanzure> jrayhawk: would you settle for less than a missile silo if it means 30k sqft 00:52 < jrayhawk> is there an underground portion 00:52 < kanzure> detroit usually includes basements yes 00:53 < jrayhawk> when i think detroit, i think civil unrest, class warfare, and fires 00:53 < jrayhawk> sounds like fun to me 00:53 < kanzure> so.. right up your alley? 00:53 < kanzure> yep ok 00:54 < jrayhawk> re: projects/laser_etcher: Ikiwiki, unfortunately, does not have a general purpose file editor. 00:54 < kanzure> giant textbox? 00:54 < jrayhawk> Somebody might've made one of those by now and I guess I could support that, too. 00:55 < kanzure> eh. 00:55 < jrayhawk> if you were to rename that to projects/laser_etcher.mdwn you could edit it fine, or if one of us were to enable the 'txt' plugin and rename it to projects/laser_etcher.txt then that would also work 00:56 < jrayhawk> although it would get rendered as a giant block of
text inside the page template 00:56 < kanzure> did we disable anonymous editing for a reason? 00:57 < jrayhawk> "anonymous" has never been a usecase I've wanted to support since I hate turing tests; anonymous user registration and world write access is supported, though. 00:58 < jrayhawk> And there's an 'export this repo as writable through git-daemon' git config that you could use; I haven't seen if spammers hit git:// at all. 00:59 < kanzure> okay. 01:00 < jrayhawk> Joey Hess made some impressive pre-receive hook that checks to see if a given ref update would involve objects outside of allowed directories that makes that slightly safer 01:01 < jrayhawk> so, for instance, git://git.ikiwiki.info/ allows you to write commits against everything in doc/ 01:01 < jrayhawk> (and you're encouraged to mess about in doc/sandbox/ if you want to enjoy the novelty of that) 01:01 < kanzure> "allowed directories" sounds like a hack on top of the already brittle permissions system 01:07 < jrayhawk> eh 01:09 < jrayhawk> anonymous user registration with optional moderator approval is supported, even 01:12 -!- delinquentme [~asdfasdf@c-67-163-157-246.hsd1.pa.comcast.net] has quit [Ping timeout: 246 seconds] 01:12 < jrayhawk> re: real estate: i would suggest getting something with FTTP pre-installed since that can get pricy 01:13 < kanzure> "buy now and get your very own homeless man!" 01:14 -!- diginet [~diginet@ppp-70-246-16-75.dsl.hstntx.swbell.net] has quit [Ping timeout: 252 seconds] 01:51 < kanzure> http://biocurioussafety.pbworks.com/w/page/51594301/General%20Lab%20Policies 01:54 < yashgaroth> looks standard 01:54 < kanzure> probably 01:54 < kanzure> just odd that they don't link to any of that from their site 01:54 -!- _0bitcount [~ulises11@213.37.203.109.dyn.user.ono.com] has quit [Quit: Leaving] 01:55 < yashgaroth> wait you have to put your phone number on everything? seems silly 01:56 < kanzure> oh i guess they link to http://biocuriousmembers.pbworks.com/w/page/46478291/FrontPage 01:56 < kanzure> https://groups.google.com/group/biocurious-printer-hacking 01:56 < kanzure> "Participants: Patrik D'haeseleer, Aaron Vollrath, Raghuvir Sengupta, Gregory Costanza, Ari, Serban Ciotlos, Jessabella, Coila, Gerald Witters, Eri Gentry, Kevin Bjorke, Michael Scroggins, Vineeth, Jing Luo, Cameron Clarke, Jonathan Reyles (+non-locals: Bryan Bishop, Lee Nelson, Elizabeth Amaral)" 01:56 < kanzure> so nice of them to include me? 01:57 < kanzure> http://biocuriousmembers.pbworks.com/w/page/50477380/Reagent%20Store 01:57 * kanzure sleeps 01:58 -!- yashgaroth [~f@cpe-66-27-117-179.san.res.rr.com] has quit [Quit: same] 02:12 -!- diginet [~diginet@ppp-70-246-16-75.dsl.hstntx.swbell.net] has joined ##hplusroadmap 02:15 -!- diginet [~diginet@ppp-70-246-16-75.dsl.hstntx.swbell.net] has quit [Read error: Connection reset by peer] 02:18 -!- diginet [~diginet@ppp-70-246-16-75.dsl.hstntx.swbell.net] has joined ##hplusroadmap 03:03 -!- ThomasEgi [~thomas@pppdyn-58.stud-ko.rz-online.net] has joined ##hplusroadmap 03:03 -!- ThomasEgi [~thomas@pppdyn-58.stud-ko.rz-online.net] has quit [Changing host] 03:03 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 03:23 -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has joined ##hplusroadmap 03:27 -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has quit [Ping timeout: 246 seconds] 03:46 -!- Mariu [Jimmy98@89.41.57.33] has quit [] 03:47 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has quit [Ping timeout: 252 seconds] 04:16 -!- bkero [~bkero2@osuosl/staff/bkero] has quit [Ping timeout: 265 seconds] 04:18 -!- ferrouswheel [~joel@li159-85.members.linode.com] has quit [Ping timeout: 252 seconds] 04:18 -!- capiscuas [~capiscuas@ppp-58-8-213-19.revip2.asianet.co.th] has quit [Quit: Leaving] 04:32 -!- ferrouswheel [~joel@li159-85.members.linode.com] has joined ##hplusroadmap 04:33 -!- bkero [~bkero2@li280-127.members.linode.com] has joined ##hplusroadmap 04:34 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 04:46 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 04:52 -!- sylph_mako [~mako@118-92-207-0.dsl.dyn.ihug.co.nz] has quit [Ping timeout: 276 seconds] 05:02 -!- rdb [~rdb@panda3d/developer/rdb] has quit [Quit: leaving] 05:07 -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has joined ##hplusroadmap 05:37 -!- capiscuas [~capiscuas@ppp-58-8-213-19.revip2.asianet.co.th] has joined ##hplusroadmap 05:38 -!- capiscuas [~capiscuas@ppp-58-8-213-19.revip2.asianet.co.th] has quit [Client Quit] 05:47 < diginet> so, sorry for the potentially stupid question, but what is the best non-shutgown method for isolating a selection of DNA (around 10 to 12 kbases) to sequence? 05:48 < diginet> *shotgun 05:52 -!- ThomasEgi [~thomas@pppdyn-58.stud-ko.rz-online.net] has joined ##hplusroadmap 05:52 -!- ThomasEgi [~thomas@pppdyn-58.stud-ko.rz-online.net] has quit [Changing host] 05:52 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 06:02 -!- gene_hacker [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has joined ##hplusroadmap 06:08 < diginet> I mean, I know about restriction enzymes, but I would think using those without first isolating the area of interest would prove difficult. Are there REs for sequences that only occur at promoters/terminators for genes? 06:19 < audy> diginet only by chance 06:21 < diginet> how is this usually done? I mean, do I have to sequence the entire genome just to get this one gene? Surely that isn't the norm 06:34 < gedankenstuecke> you can do 12 kb by sanger-sequencing with overlapping primer pairs. this is still done for some mitochondrial genomes. but this will only work if you know at least parts of the sequence 06:41 < diginet> Yeah I do know some parts of it, it's just that's there's no reliable full sequence of the gene in question 06:43 < gedankenstuecke> in this case you can start with the known-reliable parts and sequence the missing parts with sanger from there on. sanger allows for ~1kb of sequence per primer, so 12 primer (pairs if you want to sequence in both directions) should be enough 06:55 < audy> diginet what gedankenstuecke said 06:55 < audy> 1.) get a piece of the gene, 2.) PCR amplify, 3.) sanger sequencing 06:55 < audy> it can be done on the real cheap 06:55 < audy> I think sanger sequencing is ~$20 amiright, gedankenstuecke ? 06:56 < diginet> how long does the piece of the gene need to be? 06:59 < gedankenstuecke> audy: i have to admit i'm not sure, a single sequencing reaction will cost about ~$1 if you do the PCR yourself 06:59 < audy> diginet what do you want to do with said gene? 07:00 < audy> diginet oh, to design primers 07:00 < gedankenstuecke> diginet: well your primer should be between 16-25 bp long and you should keep 50-100 bp of overlap with already known sequence-parts 07:00 < diginet> well, I want to sequence the gene just to study, since as mentioned a full sequence hasn't been done yet 07:00 < gedankenstuecke> so start looking for primers at ~100bp off the end of the known-sequence parts 07:00 < diginet> right right 07:01 < diginet> but, where do I get the primers from? 07:01 < gedankenstuecke> this should still give you up to 1kb of new sequence 07:01 < diginet> the problem is the gene in question is highly repetitive 07:01 < gedankenstuecke> this probably depends on where you are located but generally you can just order them online. ;) 07:02 < gedankenstuecke> okay, this will be a problem 07:02 < gedankenstuecke> because you can't design primers in those regions 07:02 < diginet> well, that would mean there are 4^25 possible combinations, do they sell every which possible one? 07:02 < diginet> yeah, which is probably why it hasn't been sequenced 07:02 -!- Mariu [Jimmy98@89.41.57.33] has joined ##hplusroadmap 07:03 < gedankenstuecke> diginet: they will get synthesized for you 07:03 < diginet> oh right, isn't the going rate like $1 per bp or so? 07:03 < gedankenstuecke> you tell them which sequence you want and they synthesize it and ~3 days later you should have them in mail 07:04 < diginet> cool 07:04 < audy> can you just order primers? 07:04 < audy> do they ask questions? 07:05 < diginet> so, is there any research in the way of reliable DIY sequencing of repetive DNA? 07:05 < gedankenstuecke> this was the first hit for primer design with google: https://eu.idtdna.com 07:06 < gedankenstuecke> 21 bp for 5.25€ 07:08 < diginet> oh, wiw 07:08 < diginet> *wow 07:08 < diginet> good deal 07:08 < gedankenstuecke> audy: i know there are companies which deliver to non-institutional addresses with no-questions asked, but i'd guess the DIYBio-google-group can give suggestions which companies are good 07:09 < audy> diginet how repetitive is it? how long is the gene? 07:09 < gedankenstuecke> probably you can find cheaper companies or get some discount if you order lots of primers 07:09 < diginet> 10k to 12k dp, and pretty darn repetivie 07:09 < gedankenstuecke> do you ~ know how long the repeats are? 07:09 < audy> diginet you'll need to do multiple sanger runs then 07:10 < audy> diginet the repetitiveness won't be a huge problem if you use sanger 07:10 < gedankenstuecke> audy: it will 07:10 < diginet> let me look at the papers I have on it 07:10 < gedankenstuecke> it the repeats are too long you wont know how to stitch back the sanger fragments 07:10 < diginet> the repeats I think are like 3-10 bp 07:11 < diginet> brb, let me go look it up 07:11 < audy> gedankenstuecke but sanger reads are long. If you have some polymorphism in the repeat region it won't be so bad 07:11 < gedankenstuecke> audy: right, this is why I asked on how long the repeats are in total :) 07:11 < gedankenstuecke> if its < 1kb you should be fine, above you can't do it with standard sanger 07:12 < diginet> MaSp1 and MaSp2 are large proteins of about 250 to 350 kDa that share a general domain 07:12 < diginet> architecture (Sponner et al., 2005a; Ayoub et al., 2007). Both proteins contain a large, 07:12 < diginet> central, repetitive domain that consists of approximately 100 tandem copies of a 30 to 40 07:12 < diginet> amino acid repeat sequence. The consensus repeat sequences for both MaSp1 and MaSp2 07:12 < diginet> are glycine-rich and end in poly-alanine motifs (usually four to seven residues long). For 07:12 < diginet> MaSp1, the consensus repeat includes (GGX)n motifs (where X = A, L, Q, or Y) and very 07:12 < diginet> low proline content. In contrast, the MaSp2 consensus repeat has significant proline content 07:12 < diginet> and characteristic motifs such as GPG and QQ (Gatesy et al., 2001). The repetitive domains 07:12 < diginet> of different spidroins display a relatively high level of amino acid sequence variation that has been implicated in providing the elasticity and toughness that is characteristic of the 07:12 < diginet> different fibers (Hayashi & Lewis, 1998; Hayashi et al., 1999; Rising et al., 2005)." 07:12 < diginet> woops, that was weird, sorry for the bizarre formatting 07:13 < diginet> and I don't know where I got 3-10bp from 07:13 < diginet> since that's way wrong, must've been confusing that with codon repeats 07:14 < gedankenstuecke> ok, no way to solve this with sanger i'd say. the "central" repeat should measure around 9kb? 07:14 < gedankenstuecke> ~100 repeats of 30aa length = 100 repeats of 90bp length 07:15 < diginet> there is good news at least 07:15 < diginet> apparently both ends are flanked by non-repeating sequences which have been sequenced 07:16 < diginet> so I guess see if there is a restriction enzyme which would cut at those points 07:17 < kanzure> ... or you just get primers for those two 07:18 < gedankenstuecke> which wouldn't be of any help if you want to get the sequence of the repeating region 07:19 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Ping timeout: 265 seconds] 07:21 < diginet> well, what process does one use for situations such as these? 07:21 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer] 07:21 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has joined ##hplusroadmap 07:21 -!- F71 [~Adium@safekick-americas-2.consolidated.net] has joined ##hplusroadmap 07:22 -!- F71 is now known as _F7_ 07:22 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer] 07:23 < kanzure> gedankenstuecke: you would PCR out the gene in question, and then use some non-sanger sequencing method 07:23 < kanzure> diginet: pyrosequencing? 07:24 < gedankenstuecke> kanzure: how would that be of any help? you still can't assembly the fragments 07:24 < gedankenstuecke> well, you can, but you can assemble the fragments as long/short you like :D 07:25 < kanzure> gedankenstuecke: you could assemble the fragments and then do dna hybridization to test which version is right 07:25 < kanzure> also.. maybe it would be better to do mRNA sequencing or somethingw 07:26 < gedankenstuecke> apparently the repeats are even in the protein, so this might not be of any help, but hybridisation should work 07:26 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has joined ##hplusroadmap 07:26 < diginet> well, one thing I'm semi-concerned with: is it worth trying to sequence the introns as well? 07:26 < diginet> (with the eventual goal of transfection in another cell) 07:27 < _F7_> there shouldn't be introns in the mRNA 07:27 < gedankenstuecke> but in this case they already have an idea of how long the result is, so you'd need to synth. ~9kb of repeats. which you can do, but you won't learn anything interesting out of it i guess 07:27 < _F7_> I don't see any utility to sequencing them 07:28 < kanzure> stop giving me hard problems! 07:28 < diginet> yeah, you're probably right. you don't think the lacking of them could potentially negatively influence expression rates? 07:28 < kanzure> hm. 07:30 < gedankenstuecke> diginet: from which organism to which do you transfect? 07:31 -!- ThomasEgi [~thomas@pppdyn-72.stud-ko.rz-online.net] has joined ##hplusroadmap 07:31 -!- ThomasEgi [~thomas@pppdyn-72.stud-ko.rz-online.net] has quit [Changing host] 07:31 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 07:33 < diginet> Nephilia Clavipes, MaSp1 (spider silk gene, one of two) 07:33 < diginet> also, sorry in advance for spamming this channel with my inane questions :( 07:35 < gedankenstuecke> and you want to bring it into e coli i guess? 07:35 < gedankenstuecke> or some other bacteria 07:37 < _Sketch_> Wow. I don't think there's any way I can keep up with the backscroll on this channel. 07:37 < Mariu> :p 07:37 * _Sketch_ shakes his fist. Quit making so much stuff, you hooligans. ;) 07:38 < kanzure> diginet: but really. make sure you know about dna hybridization and why it might be helpful to you. 07:38 < diginet> not E. Coli won't work, it won't accomodate the entire gene without truncation (according to several papers I've read) 07:39 < diginet> kanzure, thanks, I'm vaguely aware of what it is, but I'll make sure and read up on it more 07:39 -!- gene_hacker_ [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has joined ##hplusroadmap 07:39 < kanzure> yo gene_hacker_ 07:39 < diginet> thanks so much for putting up with my ignorance guys, I really appreciate it :) 07:39 < diginet> this channel is really cool 07:39 -!- gene_hacker [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has quit [Ping timeout: 240 seconds] 07:39 -!- _0bitcount [~0bitcount@213.37.203.109.dyn.user.ono.com] has joined ##hplusroadmap 07:39 -!- gene_hacker_ is now known as gene_hacker 07:40 < gedankenstuecke> diginet: okay, anyway you should try it without the introns (but just my best guess, my microbiology-education lies back a couple of years) 07:40 < diginet> gedankenstuecke, well I know for prokaryotic cells, but what about eukaryotic? 07:41 < diginet> it sure would be EASIER to do so without introns :P 07:41 < diginet> oddly enough, some spider silk genes (not the one in Nephila though) have no introns, which is bizarre considering how long they are 07:41 < gedankenstuecke> diginet: in this case your best guess is as good as mine :P 07:41 < diginet> gedankenstuecke, I guess I could just try it would it first, see what happens 07:42 < diginet> s/with out/would out/p 07:42 < kanzure> maybe someone is already offering nanopore sequencing and you can just go be lazy and take advantage of their longer read lengths 07:42 -!- DrOctothorpe [~tesla@h254.158.185.173.static.ip.windstream.net] has joined ##hplusroadmap 07:42 < kanzure> hello DrOctothorpe 07:42 -!- DrOctothorpe [~tesla@h254.158.185.173.static.ip.windstream.net] has left ##hplusroadmap [] 07:43 < _F7_> I know octothorpe, he's my roomate 07:44 < kanzure> sounds dangerous 07:44 < diginet> how feasible is mRNA sequencing for DIYers? 07:45 < kanzure> it's something that will have to be debugged pretty strongly.. 07:45 < kanzure> i mean.. it's not a PCR reaction. 07:46 < _F7_> reverse transcribe? 07:47 < _F7_> After reverse transcription, it's a PCR reaction 07:48 < kanzure> _F7_: the actual problem he's having is that he has repeats in the gene and doesn't want to do sanger only to have an unassemblable mess 07:49 < _F7_> Primer walk? 07:51 -!- gene_hacker_ [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has joined ##hplusroadmap 07:52 -!- gene_hacker [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has quit [Ping timeout: 246 seconds] 07:52 -!- gene_hacker_ is now known as gene_hacker 07:53 < gedankenstuecke> _F7_: the repeat is 9kb long 07:56 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 07:59 < _F7_> Oh, Something that should be of interest to those integrating computers with their everyday carry 07:59 < _F7_> http://tideals.com/ 08:00 < _F7_> I got one a few days ago and they, surprisingly, haven't sold out 08:02 < _F7_> It's a microcontroller watch with onboard radios 08:02 < _F7_> You can pair it with anything using a cheap radio like a cc430 or 1111 08:04 < _F7_> It comes with a 1111 and a USB debugger/programmer that'll work for the whole 430 line 08:04 < _F7_> basically, giant nerd watch 08:28 -!- augur [~augur@206.196.185.104] has joined ##hplusroadmap 08:30 < diginet> hmm, here's an idea: apparently, the corresponding gene for the black widow has already been completely sequenced 08:31 < diginet> I should just go with that 08:31 < diginet> let's look up to see how its properties compare with n clavipes 08:44 -!- AdrianG [~amphetami@unaffiliated/amphetamine] has joined ##hplusroadmap 08:46 < _F7_> I've got a buddy with a severed nerve from a botched surgery. This spider silk can relink? 08:49 < diginet> It is possible 08:49 < diginet> If it could help someone, that's even more motivation to go through with this :) 08:52 < kanzure> http://blog.wolfram.com/2012/04/05/analyzing-your-email-with-mathematica/ 08:52 < kanzure> updated with responses.. http://blog.stephenwolfram.com/2012/03/the-personal-analytics-of-my-life/ 08:56 < diginet> to be fair, Stephen Wolfram is kind of a crank 08:56 -!- Helleshin [~talinck@cpe-174-101-208-182.cinci.res.rr.com] has joined ##hplusroadmap 08:57 < kanzure> diginet: i guess you haven't seen fenn's lifelog or my meetlog 09:02 < _F7_> Are you doing that thing yet where you write to tags? 09:03 < _F7_> I'd actually like to see one of those, if and when. 09:03 < Mokbortolan_> So, the guy who created the best hack for the BodyBugg says that logging the serial data going to it is a DMCA violation 09:03 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has joined ##hplusroadmap 09:04 < Mokbortolan_> that doesn't make any sense to me 09:04 -!- gene_hacker [~chatzilla@cpe-72-179-50-243.austin.res.rr.com] has quit [Ping timeout: 246 seconds] 09:07 < fenn> "software designed to circumvent encryption" is banned in the dmca 09:07 < kanzure> is my brain a dmca violation? 09:08 < diginet> the DMCA is insane 09:08 < fenn> if you can do rot-13 in your head, yes 09:08 < Mokbortolan_> fenn: there isn't any encryption used with this version of the bodybugg 09:08 < Mokbortolan_> at least, none that I need to crack 09:08 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has quit [Quit: Leaving.] 09:09 < Mokbortolan_> there might be some native encryption in use with the bluetooth communications, but it'd be part of the session layer, not explicitly defined by the app itself 09:09 < fenn> um, what does the bodybugg actually do? "calorie expenditure" means nothing 09:09 < Mokbortolan_> it's a data recorder 09:09 < Mokbortolan_> basically 09:09 < fenn> but what data 09:09 < Mokbortolan_> galvanic skin response, air temp, body temp, and motion 09:10 < Mokbortolan_> the device itself contains some patented algorithms to translate that into calorie expenditure 09:10 < fenn> woo woo 09:10 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has joined ##hplusroadmap 09:11 < kanzure> nmz787: yo 09:12 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has quit [Client Quit] 09:13 < Mokbortolan_> can you copyright a protocol? 09:14 < kanzure> you can copyright the expression of anything 09:14 < kanzure> you can also apparently patent certain protocols -_- 09:14 < diginet> Oh I can top that 09:15 < diginet> there was a guy who "wrote" music which transcribed the digits of Pi to music, and he tried to copyright that 09:15 < diginet> HOW DOES ONE COPYRIGHT PI!?!?! 09:15 < diginet> the stupid 09:15 < diginet> it hurts 09:15 < kanzure> or... 09:15 < kanzure> copyright is stupid 09:15 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has joined ##hplusroadmap 09:15 < kanzure> within the existing paradigm and legal system that makes good sense 09:16 < diginet> eeh I don't think it necessarily is, but the way it is right now sucks 09:16 < diginet> I think that protecting who can profit off of something is worthwhile, to an extent, but not the copying off it 09:16 < ThomasEgi> copyright law atm is more like... anti-copyright 09:16 < diginet> like, if I write a song, and people shared it fine, but I don't want people making money off of my work 09:17 < diginet> (thus creative commons, etc_ 09:17 < kanzure> creative commons is not about stopping people from profiting from your work 09:17 < kanzure> the NC variant is deeply regretted 09:20 < diginet> oh I didn't even know that 09:20 * diginet pulls foot out of mouth 09:24 < kanzure> "nc licenses considered harmful" http://www.kuro5hin.org/story/2005/9/11/16331/0655 09:33 -!- nmz787 [~Nathan@nathan-think.wireless.rit.edu] has quit [Quit: Leaving.] 09:33 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer] 09:33 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has joined ##hplusroadmap 09:38 < Mokbortolan_> This section might cover me: http://cyber.law.harvard.edu/openlaw/DVD/1201.html#f 09:46 -!- AdrianG [~amphetami@unaffiliated/amphetamine] has quit [] 09:53 < _F7_> Where do I go to peer around journal paywalls? I've got a big 'to read' list and my local library isn't very well connected. 09:53 < kanzure> search for ezproxy usernames/passwords 09:55 -!- nmz7871 [~Nathan@nathan-think.wireless.rit.edu] has joined ##hplusroadmap 10:01 -!- AdrianG [~amphetami@unaffiliated/amphetamine] has joined ##hplusroadmap 10:13 < fenn> hmm dotsies is cool, not sure if their character mapping is optimal though 10:13 -!- delinquentme [~asdfasdf@c-67-163-157-246.hsd1.pa.comcast.net] has joined ##hplusroadmap 10:13 < delinquentme> hurro luvlies 10:13 < fenn> also, english spelling is horrid 10:13 < fenn> much better to use a phonetic alphabet 10:15 < uniqanomaly> delinquentme: funny how west is creating legislation for everything and when time comes they are so fucking outraged it's china whos hacking them 10:15 < delinquentme> fonetik 10:15 < delinquentme> check 10:15 -!- nmz7871 [~Nathan@nathan-think.wireless.rit.edu] has quit [Quit: Leaving.] 10:16 < delinquentme> china hacking hoo? 10:16 < uniqanomaly> us/europe corps govs etc 10:16 < uniqanomaly> legislation is only making western citizens disadvantaged 10:17 < uniqanomaly> same is true with stem cells research 10:17 < uniqanomaly> retards 10:18 < kanzure> CIRM seems to be doing pretty good stem cell work 10:18 < kanzure> don't know what you're complaining about 10:19 < uniqanomaly> dunno, haven't bush slowed things down? 10:19 < kanzure> CIRM has a billion dollar budget for stem cell research 10:19 < katsmeow-afk> in many African countries, bribes are the same as pre-tipping a waiter in a resturant, and usa made bribes illegal, so China swooped in and made the bribes, scooping up mineral and oil rights 10:19 < uniqanomaly> embrional stem sell * 10:19 < kanzure> oops. 3 billion. 10:20 < fenn> implicitCAD also very nice 10:20 < kanzure> http://en.wikipedia.org/wiki/California_Institute_for_Regenerative_Medicine 10:20 < kanzure> "he California Institute for Regenerative Medicine (CIRM) was created by California's Proposition 71 (2004), which authorized it to issue $3 billion in grants, funded by bonds, over ten years for embryonic stem cell and other biomedical research." 10:21 < uniqanomaly> ok 10:23 < Mokbortolan_> looks like they're well on the way to massive improvements in mouse health 10:23 < delinquentme> pre tipping a waiter ? 10:23 < delinquentme> is that typical in china? 10:23 < katsmeow-afk> i said Africa 10:23 < delinquentme> Ahhhh 10:24 < katsmeow-afk> and i said "like" 10:24 < delinquentme> who in here has access to the laser cutter w 1 hour print time a month? 10:24 < delinquentme> ThomasEgi, ? was that you 10:24 < katsmeow-afk> or "the same as" 10:25 < ThomasEgi> uh.. i dont have a lasercutter. 10:25 < uniqanomaly> katsmeow-afk: usa gov/corporations cant bribe in Africa? 10:25 < ThomasEgi> wish i had one 10:25 < katsmeow-afk> but yeas, in some places in the usa, you might pre-tip the guy parking your car when you hand him the keys 10:25 < kanzure> fenn: what's up? 10:25 < katsmeow-afk> uniqanomaly, correct, notl egally 10:25 < uniqanomaly>legislation is only making western citizens disadvantaged 10:26 < katsmeow-afk> and i agreed, and gave example 10:26 < uniqanomaly> yeah ok 10:26 < katsmeow-afk> "when in Rome, do as theRomans do" 10:27 < katsmeow-afk> damn, my english teacher was right, there would be a day i'd need to know that phrase, 45 yrs after i heard it 10:28 < uniqanomaly> making own citizens disadvantaged in name of what, ideas? 10:28 < kanzure> this conversation is lame and boring 10:28 < uniqanomaly> natural selection will take care of it in future 10:29 < kanzure> i already showed you CIRM 10:29 < uniqanomaly> ok, nothing left to say 10:29 < kanzure> which pretty much invalidates your point about stem cell research not being funded? 10:30 < uniqanomaly> yes I believe youre right 10:33 < diginet> Ladies and Gentlemen, I present to you, the entire sequence MaSp1 gene of L. Hesperus (Black Widow) http://www.ncbi.nlm.nih.gov/nuccore/ef595246 10:34 < diginet> I don't know exactly how it compares to that of Clavipes, but according to the article detailing the sequencing, it is comparable 10:34 < diginet> My goal is C. darwini anyway, so this is a nice stepping stone 10:34 < katsmeow-afk> as ape dna is comparable to humans? 10:35 < diginet> Well, I'm sure it's similar, but I was more refering to the physical properties 10:35 < diginet> of the silk 10:35 < diginet> I was saying I don't know its weaker than that of N. clavipes 10:35 * katsmeow-afk nods 10:35 < kanzure> diginet: if you promise to start farming spiders then i promise to call you spiderman in here 10:35 < diginet> hahaha YES 10:36 < diginet> well, I wasn't going to farm spiders sadly, especially not black widows, but this does make the whole inserting the gene into an SF9 cell a lot of realistic 10:36 < fenn> finishing installing security cameras today 10:36 < katsmeow-afk> drat 10:36 < diginet> *a lot more 10:37 < diginet> afaik, no one has produced silk proteins from a complete gene-sequence, thus far all have used partial sequences that are missing the C-terminals, which are crucial to the properties of the silk 10:37 < fenn> so all this drop manipulation is nice, but how do we actually get ~15k unique oligos INTO the chip in the first place? 10:38 < fenn> if we make them on chip might as well just make 60-mers instead 10:38 < kanzure> transfer droplets into the chip before shipping it out to a person 10:39 < fenn> (of course droplet manipulation is good for assembly reactions, so there is value there in any case) 10:39 < fenn> how do you transfer droplet to chip 10:39 < fenn> without contamination 10:39 < diginet> be awesome 10:39 < kanzure> doesn't matter because you just form a droplet on-chip 10:39 < kanzure> dump liquid into a droplet-forming channel 10:40 < fenn> then you need 15k channels 10:40 < kanzure> uh why 10:40 < fenn> so you dont get sidewall contamination 10:40 < diginet> kanzure, this microfluidics might come in handy for another project I just remembered is in hte back of my mind 10:40 < kanzure> i thought sidewall contamination isn't a thing here? 10:40 < kanzure> and even if it is.. just wash the channel 10:40 < diginet> *microfluidics research 10:40 < fenn> for synthesis? yeah it is 10:40 < fenn> errors multiply in synthesis 10:41 < kanzure> no we're talking about loading 15,000 oligos into the storage unit 10:41 < diginet> pigment based displays! use solutions of actual pigments, would result in a display with much more vibrant and realistic colors 10:41 < kanzure> also, i meant "side wall contamination isn't an issue here because of the no-slip boundary condition" 10:41 < delinquentme> kanzure, has anyone hacker blood glucose meters to provide more complex profiling? 10:41 < kanzure> all of the microfluidics protocols call for wash steps of channels anyway. so that's standard. 10:41 < delinquentme> hacked** 10:41 < fenn> oh, so you make the droplet off chip and then load it through a tube 10:42 < kanzure> fenn: or you make the droplet on chip 10:42 < kanzure> (a special set of channels just for "initial loading") 10:42 < kanzure> everything that doesn't become the droplet goes to waste 10:42 < _F7_> all 6mers is 4096 oligos, where is 15K coming from? 10:42 < kanzure> _F7_: *shrug* just thinking big 10:43 < kanzure> also it would be nice to have a few thousand drops to store whatever genes you are playing with 10:43 < fenn> eh, 4^7 is 16384 10:43 < fenn> also backups are nice 10:43 < fenn> in case you suspect a droplet of contamination, or you lost it or something 10:43 < kanzure> "crap i contaminated my library, guess i have to reload everything" => sucks 10:43 < kanzure> or "crap i contaminated my library.. time to buy a new chip" 10:44 < kanzure> i don't even know if a library would survive in-tact through the mail. sounds like an experiment worth doing.. 10:45 -!- augur [~augur@206.196.185.104] has quit [Remote host closed the connection] 10:45 < kanzure> fenn: droplet generation http://www.youtube.com/watch?v=WzTOoyvGF5Q 10:45 < diginet> does anyone know of any useful open source genetics software? 10:45 < kanzure> diginet: it depends on what you are wanting to do 10:46 < diginet> hmm 10:46 < diginet> codon optimization? 10:46 < kanzure> do you know what the metabolism is like of your target speies? otherwise it's hard to decide what "optimized" means 10:46 < kanzure> *species 10:46 < diginet> sf9 cells 10:47 < diginet> I know that you have to know the target 10:47 < kanzure> that's what you mean by codon optimization, right? making sure the nucleotides are more in a ration suited to the organism's production/diet 10:47 < diginet> the whole point is to replace codons with synonyms that are expressed more readily by the target 10:47 < kanzure> yes ok 10:47 < _F7_> *Crap I contaminated my library, time to mail my chip back for reloading 10:47 < kanzure> look into biopython, bioruby, biojava, that stuff 10:47 < kanzure> _F7_: well ok. maybe that. 10:47 < diginet> there's a bunch of proprietary stuff with spurious claims 10:47 < diginet> is there biolisp by any chance? 10:47 < kanzure> but i imagine the per-chip costs will be... slim/negligible 10:48 < kanzure> diginet: ignore the proprietary crap 10:48 < fenn> i was thinking we can dye droplets different colors, to indicate contamination and for double checking counting 10:48 < kanzure> yes dyes are our best friends 10:48 < diginet> kanzure, I was planning to anyway, but I just meant to say, I'm highly skeptical of their claims 10:48 < kanzure> fenn: dyes can also block light to some extent for reactions that are sensitive to certain frequencies 10:49 < diginet> like, I really doubt that whichever company it was could consistently provide a 40-fold increase in expression 10:49 < fenn> what reactions are planned that use light? 10:49 < gedankenstuecke> diginet: I think you'll need to write this yourself, but it should be easy to do 10:49 < fenn> or you mean light interferes with the reaction? 10:49 < kanzure> none but sometimes light causes side-reactions. i don't think it's an issue to worry about. 10:49 < diginet> gedankenstuecke, yeah, I'm just most comfortable with lisp 10:49 < kanzure> i mean, there are certain chemical reactions where you have to think about light 10:49 < kanzure> we're not using any of those reactions (to my knowledge) 10:49 < kanzure> dyes are still a useful tool to know about 10:49 < fenn> meh. add an opaque layer to chip if it matters 10:49 < gedankenstuecke> diginet: i think you don't really need a library like biopython for this task 10:50 < diginet> gedankenstuecke, you're probably right, this is simple enough 10:50 < kanzure> gedankenstuecke: shhhh we need more biologists to be using standard open source software 10:50 < kanzure> gedankenstuecke: and to contribute back changes upstream 10:50 < kanzure> noo this could be the codon optimization module to biopython 10:50 < diginet> I hate python with a passion, so it won't be me writing it :P 10:51 < fenn> o_O 10:51 < gedankenstuecke> kanzure: we can still take the lisp-version and provide a wrapper for biopython :P 10:51 < diginet> ooohhh, what about BioAPL /kids/ 10:51 < diginet> semantic whitespaces are the scourge of satan 10:51 < gedankenstuecke> diginet: there is biohaskell if this is more your thing ;) 10:52 < katsmeow-afk> the scourge *by* satan 10:52 < diginet> oooooohhh (that is most definitely my thing) 10:52 < kanzure> oh dear. i am afraid i need to ban everyone now. 10:52 < diginet> I'm sorry :( 10:52 < kanzure> haha 10:52 < gedankenstuecke> disclaimer: i've never written a line of haskell and don't know how much functionality biohaskell provides ;) 10:52 < diginet> but I just reaaaaaaally don't like python 10:52 < kanzure> brb phone 10:52 < diginet> I'll check it out 10:53 < diginet> although, ruby is pretty bleh too 10:53 < diginet> mostly because of the oddly obnoxious ruby community 10:53 < gedankenstuecke> diginet: python and ruby are the only languages i use 10:54 < diginet> I sorry :( 10:54 < diginet> I won't hold it against you :) 10:55 < gedankenstuecke> it's just that biopython feels like the most-complete bioinformatics-lib out there 10:55 < diginet> yeah, python does, admittedly, have awesome libraries 10:56 < diginet> I'm kind of a language masochist 10:56 < diginet> two of my favourite languages are hieroglyphs, I mean APL, and 68k asm 10:56 < gedankenstuecke> but my latest job requires me to use pythons django for web-development and until now i'm craving to go back to rails 10:57 < ThomasEgi> the right language for the right job. except for web development ,high-performance-numbercrunching and systems that are very low on resources such as μC, python pretty much fits everything inbetween 10:58 < ThomasEgi> whitespace rules may take away some freedom. but force sorta-readable code even from people with no prior experience. 10:58 < diginet> Well, I'm just a weirdo, I find lispy syntax by far the most readable 10:58 < diginet> I know most people don't 10:59 < delinquentme> diginet, interesting choice of languages 10:59 < diginet> I think we can all agree that PHP is an abomination 10:59 < diginet> delinquentme, as I said, I'm odd :P 10:59 < delinquentme> hey man its programming though 10:59 < delinquentme> do it and if it works thats whats up 10:59 < diginet> yep 11:00 < delinquentme> being language-ist basically says "im not sure I made the right choice, so I need you to program in my language to validate my decision" 11:00 < delinquentme> silly humans 11:01 < delinquentme> so apparently there is a lab here @ cmu which has a few of these: http://www.motoman.com/ 11:01 < _F7_> I've been poking around ezproxy, I can't seem to find a university library with access to the Journal of Cellular and Molecular Medicine 11:02 < _F7_> I'm trying to get ahold of an article titled: Use of spider silk fibres as an innovative material in a biocompatible artificial nerve conduit 11:02 < _F7_> among other things 11:02 < gedankenstuecke> diginet: let me know if you've finished your codon-optimisation-programm. I was looking for a way to measure codon-bias some month ago and hadn't the time to code it myself :D 11:03 < delinquentme> _F7_, would you like to check if duquesne has one? 11:03 < delinquentme> i've got a few logins for them 11:05 < diginet> _F7_ I have journal access 11:05 < diginet> let me get it for you 11:05 -!- augur [~augur@206.196.171.205] has joined ##hplusroadmap 11:07 < _F7_> cool 11:07 < fenn> ThomasEgi: cython is chipping away at the performance issue 11:08 < fenn> and moore's law is chipping away at the "not enough resources" issue 11:09 < fenn> though i'm a cheap bastard and will still use a $2 chip even if it means i have to program in C 11:09 < diginet> http://dl.dropbox.com/u/58318055/j.1582-4934.2006.tb00436.x.pdf 11:09 < diginet> python still has pretty bad performance 11:09 < diginet> just sayin' 11:09 < fenn> translation of dropbox link: Use of spider silk fibres as 11:09 < fenn> an innovative material in a biocompatible 11:09 < fenn> artificial nerve conduit 11:10 < kanzure> yes.. please include titles to your links if your link sucks 11:10 < kanzure> and don't bring in a linkbot because they usually just spam all over the place 11:10 < diginet> okay, I'm sorry 11:10 < diginet> _F7_, anyway, there you go 11:10 < kanzure> don't be.. i'm just complaining 11:10 < diginet> and Moore's law is invoked way too much, I prefer Wirth's Law: software efficiency halves every 18 months, negating Moore's Law 11:11 < kanzure> your objection to python is whitespace, not resources 11:11 < diginet> hey, I can have more than one! 11:11 < fenn> well, you still can't run lisp on a microcontroller 11:11 < diginet> that's true 11:11 < diginet> but I would just asm for that 11:12 < diginet> or C 11:12 < diginet> depending on the arch 11:16 < archels> kanzure: haha I love the irony here. Two weeks ago, Ben Goertzel bans Burton from [singularity] for spouting nonsense about UFOs and "psi". Now Goertzel is talking about the same shit (and with him, the rest of the list). 11:16 < kanzure> archels: stop reading that list and unsubscribe 11:16 < kanzure> it brings no benefit anymore 11:17 < archels> Well, it keeps an updated listing of nutjobs in my inbox, so I'll know who _not_ to trust for any opinion on this stuff. 11:20 < diginet> UFOs man 11:20 < kanzure> diginet: he's referring to this guy who thinks aliens are communicating with him through a singularity implanted in his brain 11:20 < diginet> you know what cracks me up about UFOs? what does UFO stand for? Unidentified Flying Object. So apparently unidentifed=aline 11:20 < kanzure> wait, no.. chip 11:20 < diginet> *alien 11:21 < fenn> ironically a singularity is more plausible 11:21 < fenn> why would aliens use chips? come on 11:21 < kanzure> for the same reason that i have to use chips.. the technology on this planet is primitive 11:21 < fenn> but ... aliens man 11:22 < fenn> aliens! 11:22 < diginet> my favourite parody of UFO nuts ever: http://youtu.be/59zLZ6PpeSA 11:23 < _F7_> The aliens are probably communicating with his brain directly, Goertzel has been a waldo for some time now. 11:24 < _F7_> The alien telemetry device is made out of meat and has the same X-ray profile as a human brain 11:25 < kanzure> _F7_: how do my fingers telepathically know what i am thinking!!! 11:25 < kanzure> _F7_: btw it wasn't him who's schizophrenic 11:25 < fenn> proxipathy? 11:26 < _F7_> We all have a real brain, housed in the Brain Bank Cities on the far side of the moon we never see. Primarily based on your lifelong constant-threshold Frankenstein Radio Controls, especially your Eyesight TV sight-and-sound recorded by your brain, your moon-brain of the Computer God activates your Frankenstein Brain-wash Radio - lifelong inculcating conformist propaganda. 11:27 < diginet> _F7_: I think you just asploded my brain 11:31 < _F7_> I get this kind of insanity all the time at my hackerspace. Someone will come in, get the benefit of a welcoming community regarding assumed competence, and then they'll start enlisting help for replacing his computer power supply with a tesla free energy device 11:32 < ThomasEgi> since when did tesla build free energy devices. 11:32 < _F7_> and they'll insist that we need to implement a sentience scanner and that all the good science is surpressed 11:32 < kanzure> no it's a tesla-free energy device 11:32 < ThomasEgi> i mean. tesla was a genious engineer. not sume retarded free-energy-hoaxguy 11:32 < ThomasEgi> ah 11:32 < ThomasEgi> a tesla-free... now i get it. 11:33 * ThomasEgi throws that idea into the big fat bullshit pile that makes up planet earth. 11:33 < _F7_> I'll explain some basic thermodynamic as to how you can't get a free lunch regarding energy 11:33 < kanzure> i think we generally understand this 11:33 < kanzure> but 11:33 < _F7_> And they'll respond with something along the lines of "the computers tell elegant lies" 11:33 < fenn> how the hell does this chip work? http://www.youtube.com/watch?v=JvDZh8hmR84&feature=related 11:33 < kanzure> i would be more fascinated to hear your horrible stories about crazies 11:33 < kanzure> esp. in the hackerspace 11:34 < kanzure> fenn: EWOD. jonathan did this. 11:34 < ThomasEgi> _F7_, well you can get free energy lunch^ but... it takes quite some time to get even a crumb of it 11:34 < kanzure> fenn: http://88proof.com/synthetic_biology/blog/archives/tag/microfluidics 11:34 < _F7_> Yeah. I'm watching this odd migratory thing to the portland area 11:35 < kanzure> fenn: http://88proof.com/synthetic_biology/blog/archives/280 11:35 < _F7_> I think the main draw is it's sold as a retirement community for young crazy people 11:35 < _F7_> But It just looks like an area prime for geothermal to me 11:35 < kanzure> fenn: there are lots of EWOD papers in papers2/microfluidics/ 11:35 < _F7_> Cold weather and hot springs? heck yeah 11:36 < _F7_> Hackerspace crazies.. this one guy came in with a fischer price plastic donut toy thing 11:36 < _F7_> and started making 'odin coils' 11:37 < _F7_> It looked like some basic magnetic playing, wrapping them neatly in magnet wire 11:37 < _F7_> then he pulls out the 8 oz bottle of mercury 11:38 < _F7_> He insists it's part of some kind of antigravity drive 11:38 < ParahSailin_> wow 11:39 < _F7_> I still have the mercury, he abandoned most of it after we told him to GTFO for flowing rivers of mercury 11:40 < fenn> speaking of crazies, i accidentally recorded this conversation at noisebridge http://fennetic.net/irc/erin_full_edited.mp3 11:45 -!- azonenberg [~azonenber@2001:470:888b:2:206:70ff:fe01:46] has quit [Ping timeout: 245 seconds] 11:50 < ParahSailin_> [indistinct voices] 11:51 < lichen> i can barely understand this 11:51 < lichen> 22 hours 11:51 < lichen> 22 hours 11:51 < lichen> 22 hours 11:51 < jrayhawk> 22 hours? 11:51 < lichen> 22 hours. 11:51 < jrayhawk> damn. 11:51 < jrayhawk> 22 hours. 11:52 < ParahSailin_> 22 hours 11:53 < lichen> her tendency to repeat herself over and over suggests something wrong going on in her head 11:53 < katsmeow-afk> omg, on radio, a church just invited kids to be in a field Sunday, where they plan on dropping 4000 eggs from a passing plane for the kids to catch 11:53 < lichen> hahahaha 11:54 < lichen> amazing 11:54 < katsmeow-afk> sades of turkey drop WKRP 11:54 < katsmeow-afk> man 11:54 < jrayhawk> as god as my witness, i thought eggs could fly 11:54 < ParahSailin_> lol startup chile sent me an email containing the emails of all 333 applicants for this round 11:55 < jrayhawk> because of implanted alien antigravity devices 11:55 < kanzure> come be demolished by me 11:55 < kanzure> http://play.typeracer.com/?rt=zfysisivlt8f 11:55 < katsmeow-afk> they are pre-chicken, but that doesn't make them pre-flyable? 11:56 < katsmeow-afk> i hope they do it, i'd like to see the spin on news reports of it 11:57 < lichen> well that was boringish 11:57 < katsmeow-afk> (fictiona) history repeating itself for those too dumb to learn 11:57 < lichen> typing 100wpm sideways on my bed 11:57 < fenn> sorry, don't listen to it 11:57 < kanzure> lichen: http://www.seanwrona.com/typeracer/profile.php?username=kanzure 11:57 < lichen> god you play that a lot 11:59 < lichen> until im a professional stenographer i dont really see a need to go above 100wpm 11:59 < kanzure> stenography- so far- doesn't really work for coding 11:59 < katsmeow-afk> hell, humans here cannot think or speak 100wpm 12:00 -!- augur [~augur@206.196.171.205] has quit [Remote host closed the connection] 12:08 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 250 seconds] 12:13 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 12:17 < kanzure> http://www.meetup.com/HardwareStartupSF/ 12:34 -!- augur [~augur@206.196.186.226] has joined ##hplusroadmap 12:37 < _F7_> in this channel we type faster than most people think 12:39 < katsmeow-afk> sorry, could you type that slower? i didn't catch it 12:43 -!- audy is now known as octopine 12:43 < lichen> in which forbes doesnt know how to dream http://www.forbes.com/sites/alexknapp/2012/04/04/a-few-more-notes-on-the-impracticality-of-building-a-dyson-sphere/ 12:46 < katsmeow-afk> considering one cannot do 100% effcient energy-to-energy transformations, won't a Dyson sphere at a Mercury orbit be glowing hot to get rid of heat from the inefficencies? 12:47 < lichen> likely yes 12:47 < katsmeow-afk> not even considering the problems of a Dyson *sphere* as opposed toa Dyson *ring*, due to orbital mechanics problems building one 12:47 < lichen> ideally youd want more a dyson cloud 12:48 < lichen> focused around the poles 12:48 < kanzure> what happened to a dyson cloud 12:48 < kanzure> oh 12:48 < kanzure> you mentioned it. okay. 12:49 < katsmeow-afk> the bits of a cloud are all moving, which would be the problem in tying them togther to make a mesh or sphere too 12:49 < lichen> dont really need to tie them together 12:49 < katsmeow-afk> i agree 12:49 < katsmeow-afk> doesn't invalidate what i said 12:50 < lichen> true 12:50 < lichen> its possible to synchronize them to tie them together 12:50 < lichen> just annoyingly difficult 12:50 < lichen> and the tidal stresses would be pretty bad 12:51 < katsmeow-afk> i think it's ipossible, given that a polar orbit is moving 90 degrees to an equatorial orbit 12:53 < katsmeow-afk> i propose mining murcury, using solar to power it, and fling useable materials out to further sun-orbit distances (also closer to earth), and counter-fling the unuseable debris somewhere else 12:53 < lichen> everything has a use 12:54 < katsmeow-afk> do a ring, where the energy transmit to earth is done at the closest place on the ring to earth,, or move humans to the ring 12:54 < lichen> it seems like it would be more logical to leave what we dont need there 12:54 < lichen> takes energy to move it 12:55 < katsmeow-afk> yeas, but in the theme of equal and opposite reaction, you can fling both materia;s in opposite directions for the same push 12:55 < lichen> yeah 12:55 < lichen> hmm ive put off going to work rather too long 12:55 < lichen> this might be another call-in day 13:04 < kanzure> lichen: are you open to relocating 13:04 < lichen> yeah, depending 13:05 < kanzure> kk 13:08 < fenn> lol "transmitting the power back to earth" is hardly an objection 13:08 < fenn> hey guys let's vaporize earth with the total output of the sun 13:09 < fenn> knapp needs to learn about the subjunctive tense 13:09 < kanzure> i'm still hoping for intergalactic laser cutting/chemistry 13:10 < lichen> oh the day when we blast away asteroids with lasers 13:10 < katsmeow-afk> sounds wasteful 13:10 < kanzure> no no.. use a laser to move distant planets together to do chemistry 13:11 < katsmeow-afk> aim and combine pulsar beams so they are more of a continuous stream 13:12 < fenn> by the time you arrive in your intergalactic chariot, the planet will have spontaneously generated and demanding compensation for "wrongful life" 13:14 -!- sylph_mako [~mako@118-92-207-0.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap 13:15 < katsmeow-afk> humans shoot robots to distant planet to terraform it, 50 yrs later shoot humans there to colonise it, and on the way to the planet the humans pass a ship of robots headed back to earth with the same plan 13:17 < katsmeow-afk> what's somewhat depressing is the robots wave knowingly, and the humans look surprised 13:17 < katsmeow-afk> afk to do things irl 13:24 -!- sylph_mako [~mako@118-92-207-0.dsl.dyn.ihug.co.nz] has quit [Read error: Connection reset by peer] 13:33 -!- splicer [~ubuntu@c83-255-190-140.bredband.comhem.se] has quit [Ping timeout: 272 seconds] 13:42 -!- sylph_mako [~mako@118-92-207-0.dsl.dyn.ihug.co.nz] has joined ##hplusroadmap 13:45 -!- splicer [~ubuntu@c83-255-190-140.bredband.comhem.se] has joined ##hplusroadmap 13:47 -!- yashgaroth [~f@cpe-66-27-117-179.san.res.rr.com] has joined ##hplusroadmap 14:05 -!- augur [~augur@206.196.186.226] has quit [Remote host closed the connection] 14:05 < _F7_> A passing robot reaches into the vaccum of space from the unpressurized cabin and extends it's innermost manipulator from one of the many bundles of periphery around it's main body. It is it's understanding that the human-like sign language will convey, in an instant, the system of morality that evolved in the absence of the fleshy originators, and the amount of sympathy the arriving humans could expect to receive when they find the 14:08 < _F7_> To be sure, however, the electronic entity modulated Godelian Shock Input over the ships various PAs and communications devices. 14:22 < Mokbortolan_> receive when they find the... got cut off 14:25 -!- Mariu [Jimmy98@89.41.57.33] has quit [] 14:28 -!- diginet_ [~diginet@adsl-69-153-135-2.dsl.hstntx.swbell.net] has joined ##hplusroadmap 14:29 -!- Mariu [Jimmy98@89.41.57.33] has joined ##hplusroadmap 14:31 -!- diginet [~diginet@ppp-70-246-16-75.dsl.hstntx.swbell.net] has quit [Ping timeout: 265 seconds] 14:43 < delinquentme> _F7_, what is this? 14:54 -!- fawwo [~fawwo@146.247.208.211] has joined ##hplusroadmap 14:55 < delinquentme> so whats the issue with getting different languages to interface 14:55 < delinquentme> like once something is a string... thats encoded in utf8 and basically universal 14:56 < delinquentme> yes in some cases if you're wanting to pass an array things can get a little ghetto with choosing the delimeter 14:56 < delinquentme> but... if those are all documented ... isn't it a bit of a non-issue? 14:56 < fawwo> is it an issue? 14:56 < kanzure> what 14:56 < kanzure> hello fawwo 14:57 < fawwo> heya 14:57 -!- _0bitcount [~0bitcount@213.37.203.109.dyn.user.ono.com] has quit [Quit: Leaving] 14:58 < kanzure> fawwo: what brings you around? 15:01 < Mokbortolan_> delinquentme: JSON? 15:01 < fawwo> the usual I assume, strong interest into most things in the topic and to see if there's an active community for those 15:01 < lichen> its a pretty active community 15:01 < delinquentme> Mokbortolan_, like formatting is the only real issue 15:01 < delinquentme> like yes best case scenario everything is in one language 15:01 < kanzure> delinquentme: i have no idea what you are talking about 15:02 < delinquentme> but its been proven it can work ... so why hasn't it seen more adoption 15:02 < delinquentme> kanzure, im after "best practices" for intra-language programming 15:02 < delinquentme> intra species love making 15:02 < kanzure> what is "intra-language programming" 15:03 < fawwo> is that just taking all the possible encodings/character sets into account? 15:03 < fawwo> *isnt 15:04 < kanzure> err why would is/isnt matter in that message? 15:04 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer] 15:04 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has joined ##hplusroadmap 15:05 < fawwo> because one makes it a plain question without forknowledge/presuppositions and the other is more of an "elaborate" :P 15:05 < kanzure> answer accepted 15:22 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 15:23 < kanzure> le sigh http://en.wikipedia.org/wiki/List_of_organic_reactions 15:23 < kanzure> aren't there supposed to be >150k reaction mechanisms 15:27 < kanzure> i wonder if there's something like xpath for querying chemical structures 15:27 < kanzure> smiles/frowns is just for parsing strings right? 15:31 -!- _F7_ [~Adium@safekick-americas-2.consolidated.net] has quit [Quit: Leaving.] 15:33 < kanzure> wondering why i haven't written something for http://en.wikipedia.org/wiki/Retrosynthetic_analysis yet 15:34 < kanzure> "It is written in almost 100% Python with a small portion written in C++." 15:34 < kanzure> yep.. 100%? 15:34 < lichen> 50% python, 50% c++, and 50% lisp 15:37 -!- F71 [~Adium@safekick-americas-2.consolidated.net] has joined ##hplusroadmap 15:37 < kanzure> weird i wonder what all this code is 15:37 < kanzure> did i ever push this anywhere? geeze 15:38 < kanzure> apparently i wrote a tiny retrosynthesis library in python 15:38 < kanzure> in 2009 15:38 < fawwo> the things you do when youre drunk 15:38 < lichen> that seems like a pretty big thing to completely forget about 15:40 < kanzure> it uses smiles, smarts, frowns, and pydaylight 15:41 -!- strages_shop [~strages@256.makerslocal.org] has joined ##hplusroadmap 15:44 < kanzure> "Frowns (a now unsupported Open Source Python cheminformatics library)" 15:44 < kanzure> oh. 15:55 -!- strages_shop [~strages@256.makerslocal.org] has quit [Ping timeout: 240 seconds] 16:00 < F71> *frowns 16:04 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 16:33 -!- strages_shop [~strages@256.makerslocal.org] has joined ##hplusroadmap 16:46 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 252 seconds] 16:47 -!- strages_shop [~strages@256.makerslocal.org] has quit [Ping timeout: 240 seconds] 17:04 -!- queequeg [~queequeg@8-4.ptpg.oregonstate.edu] has joined ##hplusroadmap 17:13 < kanzure> hi queequeg 17:18 < jrayhawk> based on the lack of response to my question in #ikiwiki, i am going to say that git:// spam is not a problem yet 17:27 < kanzure> you might consider my commits to be git spam 17:30 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 17:31 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 17:37 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 17:37 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 17:42 -!- augur [~augur@208.58.5.87] has quit [Ping timeout: 276 seconds] 17:45 < queequeg> hello, a friend told me to join because i'm interested in bioengineering 17:45 -!- queequeg [~queequeg@8-4.ptpg.oregonstate.edu] has quit [Quit: Leaving] 17:46 < yashgaroth> okay then 17:46 < kanzure> heh 17:58 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 18:09 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 18:12 -!- F71 [~Adium@safekick-americas-2.consolidated.net] has quit [Quit: Leaving.] 18:23 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 18:31 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap 18:37 < kanzure> fenn: ping? 18:41 < kanzure> hi F71 18:46 -!- F71 [~Adium@50.15.211.25] has quit [Ping timeout: 244 seconds] 18:48 < sylph_mako> ~It does not matter how slow you go so long as you do not stop. 18:48 < sylph_mako> Someone take my flamebait. 18:49 < sylph_mako> Seriously this is how I feel about a lot of transhumanist directives. Why are we in such a dang rush? 18:51 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap 18:52 -!- gene_hacker [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has joined ##hplusroadmap 18:57 -!- gene_hacker_ [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has joined ##hplusroadmap 18:57 < jrayhawk> http://www.fastcompany.com/node/75905/print "Change or die. What if you were given that choice? [...] Here are the odds that the experts are laying down, their scientifically studied odds: nine to one. That's nine to one against you." 18:57 -!- gene_hacker [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has quit [Ping timeout: 246 seconds] 18:57 -!- gene_hacker_ is now known as gene_hacker 18:57 < kanzure> yo gene_hacker 19:16 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 19:16 < fawwo> thx jrayhawk 19:19 -!- capiscuas [~capiscuas@ppp-58-8-137-186.revip2.asianet.co.th] has joined ##hplusroadmap 19:25 < fenn> bold words 19:30 -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Quit: Leaving.] 19:36 < fawwo> actually the "change" it talks about seems to mostly "just" be about giving people a community to be part of 19:37 < fenn> you mean they're not suggesting a radical transformation in the substrate and form you are made of? 19:38 -!- azonenberg [~azonenber@2001:470:888b:2:206:70ff:fe01:46] has joined ##hplusroadmap 19:39 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 19:41 < fawwo> yez, though unfortunately I dont think that was ever on the table 19:44 < strangewarp> Hey guize let's adopt green syndicalism and make thousand-year plans to be carried out by our heroic human descendents 19:46 < kanzure> what 19:46 < jrayhawk> a thousand year reich? 19:48 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 19:49 < strangewarp> [sarcasm] 19:51 < sylph_mako> hah. I see. 19:51 < kanzure> micro porn http://rockmaninoff.files.wordpress.com/2011/06/gc_picture-027m_albertfolchlab1.jpg 19:52 < kanzure> that's not really micro is it? 19:53 < fenn> if it was too micro it wouldn't blend 19:54 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has joined ##hplusroadmap 19:56 < kanzure> 100 microns is a dust mite. 19:57 < kanzure> or the thickness of human hair. 19:58 < kanzure> those features look much larger than that.. 20:03 -!- roksprok [~Zac@74.83.205.124] has joined ##hplusroadmap 20:04 -!- augur [~augur@216-164-57-20.c3-0.slvr-ubr1.lnh-slvr.md.cable.rcn.com] has quit [Remote host closed the connection] 20:04 -!- fawwo [~fawwo@146.247.208.211] has quit [Quit: Leaving.] 20:12 < roksprok> http://www.clemson.edu/ces/crb/students/npradha/ECE495/laser_cutter_quotes/Engravers%20Network%20VLS230-30%20NC.pdf 20:12 < roksprok> ^^^ quote for the laser cutter used in nmz787's PDMS microfluidics in under 30 min paper 20:13 < roksprok> obviously tremendously overpriced 20:13 < roksprok> at 16000 20:13 < roksprok> but gives you something to compare to 20:15 < kanzure> "2 inch focus lens kit" eh 20:15 < kanzure> "Reduces beam spot size to 0.001" gah units! 20:16 < roksprok> i think they mean inches 20:16 < roksprok> laser cutter specs kind of suck 20:16 < roksprok> the one's on ebay give 'minimum character size' of 1 mm square 20:16 < roksprok> or 1000 dpi 20:17 < kanzure> this spec sheet is not very convincing :) 20:17 < kanzure> and where do these prices come from? they look made up 20:17 < roksprok> i think it is a emailed quote to someone at clemson u 20:18 < roksprok> who read the paper and wanted to try it 20:18 < kanzure> yeah but i mean, ULS came up with these numbers somehow 20:18 < roksprok> well isn't that where all prices come from? 20:18 < roksprok> being made up? 20:19 < roksprok> and if nobody buys it, cut the price 20:19 < roksprok> if everyone buys it. raise the price 20:19 < F71> roksprok you have things backwards 20:20 < kanzure> maybe they started off with absurd prices 20:20 < roksprok> thanks F71 20:20 -!- sylph_mako [~mako@118-92-207-0.dsl.dyn.ihug.co.nz] has quit [Quit: Leaving] 20:20 < roksprok> i imagine they have a default of like 3 times total assembly costs 20:21 < roksprok> as the CO2 lasers i've seen are all a few grand 20:22 -!- gene_hacker [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has quit [Ping timeout: 252 seconds] 20:22 < roksprok> and 30 watts is nothing special 20:22 < roksprok> and of course hpdfo is just...their stupid trade name 20:23 < roksprok> for 'more lenses!!!!!' 20:26 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 20:26 -!- F71 [~Adium@50.15.211.25] has quit [Ping timeout: 244 seconds] 20:29 -!- gene_hacker [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has joined ##hplusroadmap 20:33 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap 20:34 < roksprok> so is there any particular reason integrated circuits are not stacked more often 20:34 < roksprok> i know heat dissapation 20:34 < roksprok> but any other reasons? 20:35 < jrayhawk> Makes the process more complicated and expensive. 20:36 < jrayhawk> Motherboards nowadays are actually fairly deep; usually over eight layers of circuitry. 20:37 < roksprok> do you know off the top of your head an estimation of how thick each layer is? 20:37 < roksprok> 50 um? 20:38 < roksprok> I'm wondering if this is at all grounded in reality 20:38 < roksprok> Using 32 nanometer IC technology, the agent, which can fit into capillaries of the brain vasculature that supply every neuron, can have 2300 transistors. 20:39 < roksprok> from http://www.carboncopies.org/substrate-independent-minds 20:39 < roksprok> the agent has an 8 micron diameter 20:39 < roksprok> I've been looking at 'smartdust' which is a similar concept of very small independent computers and they only got 1mm cubed in 2010 20:40 < roksprok> after working on it for 12 years 20:41 < roksprok> in general, it seems that there is an area between 'robot' and 'nanorobot' that could be really useful, but I'm having trouble finding anyone actually working on it 20:41 < kanzure> robert freitas probably has written about something in between 20:41 < jrayhawk> Intel's marketing copy claims "over 20 layers" in their process as of 2009 20:43 < jrayhawk> I assume their layers are somewhat smaller than 50 micrometers 20:43 < kanzure> gene_hacker: yo, what's the longest channel you've seen pumped in microfluidics 20:44 -!- gene_hacker [~chatzilla@wireless-128-62-180-175.public.utexas.edu] has quit [Ping timeout: 246 seconds] 20:46 < roksprok> kanzure are you planning on using micado/autoCAD for your chip design? or design your own system 20:46 < kanzure> my own 20:47 < kanzure> i'll export to svg, dxf, step and gcode 20:51 < roksprok> and your own laser cutter/stepper motor rig 20:51 < roksprok> i wonder if you could just sell that 20:51 < kanzure> to who? 20:52 < roksprok> all those microfluidics companies 20:52 < roksprok> http://www.microfluidicscorp.com/ 20:52 < roksprok> there's one in the uk that i kept coming accross 20:52 < roksprok> and whomever they sell stuff to 20:53 < kanzure> this site looks like a sam 20:53 < kanzure> *scam 20:53 < kanzure> notice the fake photo on their page 20:54 < kanzure> this is probably some viagra front or something 20:54 < kanzure> "Tiny Particles, Big Results" 20:54 < roksprok> they claim that 17 of the top 20 global pharmaceutical companies are their customers 20:55 < roksprok> idex corporation, who owns them, is a 1.5 billion dollar a year company 20:56 < roksprok> i guess it could be just two guys in their basement so they can say 'we're on the cutting edge!!!!!' 20:56 < kanzure> hm? 20:57 < kanzure> i don't know what you want me to do. call them up and give them a cad file? 20:57 < roksprok> no, sell them your lasercutter/chip designer setup 20:58 < roksprok> or find out who buys it and say 'you could make your own for cheaper' 20:58 < kanzure> eh. okay. 20:58 < kanzure> we'll see. 21:00 < lichen> http://youtu.be/Yxfn5PFWYTk 21:02 < kanzure> lichen: http://www.youtube.com/watch?v=SQq_XmhBTgg#t=40 21:03 < lichen> cool ill have to watch through this 21:03 < lichen> looks pretty campy 21:03 < kanzure> very much so.. 21:07 -!- Mariu is now known as Winter 21:07 -!- Winter is now known as Mariu 21:09 -!- AdrianG [~amphetami@unaffiliated/amphetamine] has quit [] 21:14 -!- F71 [~Adium@50.15.211.25] has quit [Ping timeout: 244 seconds] 21:20 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap 21:22 < kanzure> kla/win 6 21:22 < kanzure> fjkasdjfla 21:24 < Mariu> Windows Vista ? 21:24 < Mariu> win 6 reminded me of that 21:24 < kanzure> irssi :| 21:26 -!- klafka [~klafka@c-24-23-160-52.hsd1.ca.comcast.net] has joined ##hplusroadmap 21:26 < kanzure> klafka! 21:27 < kanzure> roksprok: are you still planning to do your reagent store 21:27 < klafka> kanzure! 21:28 < klafka> behold! 21:28 < roksprok> no, biocurious has one...and many more resources and seems to be run well and is all around fine 21:28 < roksprok> i am still working on a protocols site 21:29 < roksprok> but it is more a teach-myself-python/django 21:29 < roksprok> so it is coming slowly 21:29 < kanzure> ooh ooh tell me about it 21:29 < kanzure> did you hear that protocol-online.org blocked me? 21:29 < roksprok> did you scrape too much? 21:29 -!- F71 [~Adium@50.15.211.25] has quit [Ping timeout: 244 seconds] 21:30 < kanzure> well. i think i hit "the wrong button". they had this perl script that emailed like 20,000 people if you browse to it over HTTP. anyway.. they didn't like that i guess. 21:31 < roksprok> i'm suprised there's someone behind it who cares about that stuff 21:31 < roksprok> i thought it was just kind of left over 21:31 < kanzure> me too 21:31 < roksprok> it was started in something like 99 and looks like it 21:31 < kanzure> it certainly doesn't feel like it has had any new content in the last.. 10 years 21:33 -!- klafka [~klafka@c-24-23-160-52.hsd1.ca.comcast.net] has quit [Quit: This computer has gone to sleep] 21:33 < roksprok> yea so there is opportunity for disruption there 21:33 < kanzure> roksprok: so you're learning django? 21:33 < roksprok> yea...it is actually really well-put together/documented/ an all around great framework 21:34 < kanzure> http://diyhpl.us/~bryan/irc/protocol-online/protocol_scraper.py 21:34 < kanzure> feel free to use this 21:34 < roksprok> my biggest mistake was wasting time on some django book suggested by lpthw instead of going straight to the documentation 21:34 < roksprok> thanks 21:35 < roksprok> but yea hopefully it will continue to go ok 21:36 < roksprok> i also signed up for a neurophysiology lab at a college by me 21:36 < roksprok> it surprisingly doesn't suck too much 21:36 < kanzure> is this a class? 21:36 < roksprok> yea 21:36 < kanzure> yeah, neurophysiology is nice 21:37 < roksprok> i found i actually enjoyed the tedious parts of it 21:37 < roksprok> which is good, because that's never happened before 21:37 < kanzure> have you played with NEURON yet 21:38 < roksprok> a little 21:38 < kanzure> http://www.neuron.yale.edu/neuron/ 21:38 < roksprok> is that kind of the biggest neural simulation thing? 21:39 < kanzure> it has very specific model support 21:39 < roksprok> i actually started learning python because i wanted to use pybrain 21:39 < kanzure> i thik some people are doing highly parallel stuff with it (like blue brain project might be using it?) 21:40 < roksprok> wow that's pretty impressive actually 21:40 < kanzure> *think 21:40 < kanzure> channel models: http://www.neuron.yale.edu/neuron/static/docs/chanlbild/main.html 21:40 < kanzure> "tool for creating voltage- and ligand-gated channels whose state transitions are described by kinetic schemes and/or HH-style differential equations." 21:41 < roksprok> wow i'm going to have to dive into this more....i was playing around with one called Emergent but it sucks in comparison 21:42 < kanzure> emergent... isn't that randall o'reilly's thing 21:42 < kanzure> superkuh: weren't you playing with that? 21:43 < superkuh> Yes. 21:43 < kanzure> roksprok: now you have someone to complain to about emergent 21:43 < roksprok> superkuh were you reading the computational cognitive neuroscience book? 21:44 < roksprok> if there is one thing i need it is more people to bitch to 21:44 < kanzure> archels: you too.. 21:45 < roksprok> hopefully i will never have to use emergent again thanks to NEURON 21:45 < roksprok> if its good enough for blue brain... 21:45 < superkuh> I didn't read the book. I don't believe it was out when I was playing with pdp++. 21:46 < roksprok> o yea that was a while ago 21:51 < roksprok> did delinquentme ever find someone to apply to ycombinator with him? 21:53 < kanzure> sure.. all of us :P 21:54 < roksprok> that would certainly be a fun interview 21:54 < roksprok> 60 people crammed in a conference room 21:54 < lichen> lol 21:54 < roksprok> we could just put on threatening glares and intimidate them into funding us 21:54 < roksprok> and spend all the money on food 21:55 < katsmeow-afk> "we already built it, we need funding to protect you from it" 21:55 < kanzure> they might go for funding a protocols site 21:55 < kanzure> esp. if it had some traction already. that wouldn't be hard. 21:56 < roksprok> i think they funded a lab notebook site 21:56 < roksprok> so they are in the 'marketing to scientists' area 21:57 < kanzure> the most hardwariest thing they've done is octopart, upverter, whatever wireless router company that was, possibly quartzy, scienceexchange 21:57 < kanzure> did cloudfab go through yc? i think so 21:57 < kanzure> well anyway. cloudfab has been acquired. 21:58 < roksprok> honestly i think this: 'ongoing, automatic medical diagnosis.' from his 'ambitious startup ideas' http://www.paulgraham.com/ambitious.html 21:58 < roksprok> would be amazing 21:58 < roksprok> one of my mom's coworkers just got diagnosed with stage 4 lung cancer 21:58 < roksprok> even though she lives within a mile of a machine that could of diagnosed it at stage 1 21:59 < lichen> i saw some guy made a site for connecting crohn's patients together 21:59 < roksprok> and it wasn't even like she never went to the doctor 21:59 < lichen> to share treatment information 21:59 < roksprok> did that get funded? 21:59 < lichen> it seems pretty far 21:59 < kanzure> curetogether? 21:59 < lichen> so i think so? 21:59 < kanzure> patientslikeme? 21:59 < lichen> idk let me trawl my logs 22:00 -!- juul [~juul@208.87.217.74] has joined ##hplusroadmap 22:00 < kanzure> roksprok: maybe she just doesn't go to the doctor's often enough. yearly physicals, etc. etc. 22:00 < lichen> i should have had my gut checked like 2 or 3 years ago 22:00 < lichen> havent due to laziness, lack of insurance 22:00 < kanzure> hi juul 22:00 < juul> hi kanzure 22:00 < roksprok> even yearly physicals suck, as other than tits/ass they don't check for any cancers 22:01 < kanzure> roksprok: that's why you demand a scan 22:01 < lichen> ah, here: http://crohnology.com/ 22:01 < roksprok> ideally you'd draw blood and check for a few thousand biomarkers 22:01 < roksprok> *tumor biomarkers 22:01 < kanzure> so, i'm pretty sure there was this patent that covered a cure for crohn's 22:01 < juul> i'm taking Endy's synthetic biology course, and I'll have time and funding to do a simple (2000 bp max) sensor+actuator system in either hela or e. coli 22:01 < kanzure> but since it was patented, nobody could touch it 22:01 < juul> any ideas? 22:01 < kanzure> if you want to make a quick buck, go dig up that patent 22:01 < lichen> sounds shitty kanzure 22:02 < kanzure> and then implement it and sell it to those crohnology.com people 22:02 < lichen> only reason i take nicotine is to fix my colitis 22:02 < lichen> and it works 22:02 < kanzure> (screw the patents) 22:02 < roksprok> kanzure: if people actually did that they wouldn't have enough people to read it 22:02 < Mariu> :p 22:02 < kanzure> juul: actuator? 22:02 < yashgaroth> like a chemical-responsive promoter and a gene product? 22:02 < juul> kanzure, some gene or set of genes to be expressed when the sensor senses 22:02 < kanzure> oh i see. not a motor 22:03 < kanzure> hm 22:03 < kanzure> juul: insulin-related stuff? :P 22:03 < juul> kanzure, hah why? because i'm danish?! 22:03 < juul> grrrr! :P 22:03 < kanzure> i wonder if there's any protein that can be expressed to cause the cell to become competent 22:03 < juul> i actually thought about self-dosing insulin via gut bacteria 22:04 < kanzure> oh right there is 22:04 < kanzure> ComP 22:04 < kanzure> http://diyhpl.us/~bryan/papers2/bio/ComP,%20a%20pilin-like%20protein%20essential%20for%20natural%20competence%20in%20Acinetobacter%20sp%20strain%20BD413%20-%20regulation,%20modification%20and%20cellular%20localization.pdf 22:04 < kanzure> diagram of genes for competence: 22:04 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Internalizing_DNA.pdf.B_subtilis_competence_proteins.gif 22:04 < yashgaroth> do syncytin or something 22:04 < lichen> why is that a transparent gif o.O 22:04 < lichen> badly transparent at that 22:04 < kanzure> SILENCE 22:05 < juul> kanzure, has that been verified to work in e. coli? 22:05 < kanzure> YOU WILL NOT QUESTION SCIENCE 22:05 < kanzure> juul: it turns out ecoli are sometimes naturally competent? 22:05 < lichen> i cant even read it due to grey background, lol 22:05 < juul> kanzure, yeah 22:05 < kanzure> juul: evidence.. http://diyhpl.us/~bryan/papers2/bio/Genetic%20transformation%20in%20freshwater%20-%20Escherichia%20coli%20is%20able%20to%20develop%20natural%20competence.pdf 22:05 < kanzure> more "competence proteins": 22:05 < kanzure> http://diyhpl.us/~bryan/papers2/bio/competence_proteins_ADP1.jpg 22:06 < kanzure> that's probably more than 2k bp :) 22:06 < juul> haha 22:07 < juul> nice list though 22:07 < kanzure> gut/insulin needs to happen already.. it's 2012 ffs 22:08 < lichen> the future is here, just not all futures are here yet 22:08 < kanzure> the future is already here, it's just not _HERE_ 22:08 < kanzure> it's over /there/ 22:08 < kanzure> it migrates at the speed of syrup 22:09 < lichen> that too 22:09 < roksprok> ok so some famous scifi author had a quote 'the future is already here it just isn't equally distributed' 22:09 < roksprok> what does that mean? 22:09 < kanzure> s/equally/evenly 22:09 < roksprok> does it mean....the first world is in the future and the third world isn't? 22:09 < kanzure> no 22:09 < katsmeow-afk> means some people have cell phones, and some don't 22:09 < strangewarp> roksprok: Bruce Sterling I think 22:10 < kanzure> it means "some stuff is in a lab and you don't have it" 22:10 < roksprok> or the future is scattered in various labs and just not availible? 22:10 < roksprok> o ok that makes sense 22:10 < strangewarp> some stuff is in labs, some stuff is available for only the ultra-rich, some stuff is banned in most countries 22:10 < strangewarp> etc. 22:10 < kanzure> ok what stuff is only available to ultrarich? 22:10 < kanzure> prove that 22:10 < roksprok> spaceflight? 22:10 < katsmeow-afk> sure, goto Somalia and see how many have the newest cell phones 22:11 < kanzure> somalia has lots of cell phones 22:11 < strangewarp> heroic levels of medical treatment 22:11 < kanzure> roksprok: maybe. arguably not even the ultrarich can do it. heh.. just the ultrarich+ultrasmart 22:11 < roksprok> i feel like you are setting the bar super high if you want Somalia to have stuff for it to be evenly distributed 22:12 < kanzure> why are we discussing this quote? 22:12 < lichen> learn: definition of 'evenly' 22:12 < roksprok> kanzure: or extremely lucky air force people 22:12 < roksprok> i have been wondering about it for years 22:12 < kanzure> roksprok: haha .. i dunno if having eight PhDs has anything to do with luck 22:12 < roksprok> when i searched i just got crap 22:13 < strangewarp> I thought Sterling was a bit wibbly on some issues, like his inexplicable position on human-equivalent AI (impossibru!) 22:13 < roksprok> so i thought i'd ask in here as i assumed you all were familiar with it 22:13 < lichen> id heard the quote 22:13 < lichen> and its true to a fair degree 22:13 < kanzure> i truly hope it's not some "social justice" stuff 22:13 < lichen> just because the military has exoskeletal suits doesnt mean theyre replacing wheelchairs yet 22:13 < kanzure> because frankly he's just adding to the problem if his hardware isn't open source 22:14 < roksprok> does he even have hardware? 22:14 < kanzure> probably not. 22:14 < kanzure> what a slacker 22:14 < kanzure> juul: what are your other options? 22:14 < roksprok> at least he isn't discussing ethics 22:14 < juul> other options? 22:14 < strangewarp> I think it's the observation that the conditions exist where scientific developments would kick off more powerful trends in social justice, if anything.. because if that isn't what Sterling meant, I've overestimated him 22:15 < kanzure> juul: genes you might pick 22:15 < roksprok> * stops distracting kanzure and juul with misunderstood scifi quotes 22:15 < kanzure> roksprok: how far along is your django site 22:16 < juul> LSD-producing gut-colonizing e. coli that triggers on something uncommon, cheap and accessible? 22:16 < juul> :) 22:16 < kanzure> oxygen? 22:16 < kanzure> oh, uncommon 22:17 < roksprok> kanzure: not far at all 22:17 < roksprok> i would not count on me doing anything 22:17 < roksprok> successfully that is 22:17 < juul> i don't really know to be honest, i'm trying to find something non-obvious that i could actually implement and that would also be useful 22:18 < kanzure> would you have gone for competence proteins, if they were smaller genes? 22:18 < lichen> if you could make bacteria that produce lsd 22:18 < lichen> that would be an impressive feat of its own 22:18 < lichen> much easier than the ochem synthesis it requires right now 22:18 < strangewarp> Sterling's most recent essay on the New Aesthetic was some amazing brain food though - with a couple inexplicable paragraphs in the middle claiming that AI is an impossible dream, so.. that might indicate he believes scientists will curl around to conventional social justice, instead of building up further objective advancements. Which would mean his earlier quote was, in fact, about social-justice-above-all-else bullpucky. 22:18 < kanzure> i think someone finally did a canabis pathway 22:18 < juul> kanzure, possibly, if no-one has done so before 22:18 < juul> lichen, true 22:18 < kanzure> strangewarp: disappointing. 22:19 < strangewarp> yeah x_x 22:19 < roksprok> kanzure this is where your dna synthesizer comes in 22:19 < roksprok> biosynthetic pathway design 22:19 < kanzure> yeah juul is completely constrained by budget here 22:19 < kanzure> but i'm sure he would be happy to use anything of any length 22:20 < juul> yeah it's actually a time-constraint 22:20 < kanzure> oh. what? 22:20 < kanzure> 2k bp is a time constraint? 22:20 < juul> DNA 2.0 can't guarantee more than 2000 bp in less than two weeks 22:20 < kanzure> lovely.. 22:21 < juul> and it's only a ten week project 22:21 < kanzure> so.. basically two rounds of debugging at once 22:21 < kanzure> so.. you should have 1/4th of a single variable to debug around 22:21 < kanzure> heh 22:21 -!- nmz787 [~Nathan@cpe-66-66-101-35.rochester.res.rr.com] has joined ##hplusroadmap 22:21 < kanzure> yo nmz787 22:21 < juul> hehe 22:22 < nmz787> yo 22:22 < kanzure> nmz787: juul is trying to figure out what to spend 2k bp on for endy's class 22:22 < kanzure> to express in ecoli 22:22 < nmz787> oh 22:22 < nmz787> i have some ideas 22:22 < nmz787> lemme check the lengths 22:22 < juul> it should be something that has an interesting trigger 22:22 < juul> but i guess that can be added on 22:25 < nmz787> oh, nevermind 22:26 < nmz787> silicatein? 22:26 < yashgaroth> heat shock response -> rfp? 22:26 < yashgaroth> ooh and cold response -> bfp if that exists 22:27 < kanzure> what happened to those antifreeze proteins 22:31 < juul> kanzure, oooh! that's interesting 22:33 < juul> put it in hela to minimize crystallization damage during freezing 22:33 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has quit [Read error: Connection reset by peer] 22:33 -!- _Sketch_ [~Sketch@71-91-221-175.dhcp.stls.mo.charter.com] has joined ##hplusroadmap 22:36 -!- nmz787 [~Nathan@cpe-66-66-101-35.rochester.res.rr.com] has quit [Quit: Leaving.] 22:41 -!- F71 [~Adium@50.15.211.25] has joined ##hplusroadmap 22:41 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 22:46 < juul> yashgaroth, not a bad idea 22:46 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 22:46 < yashgaroth> 2kb is kind of restrictive 22:47 < kanzure> what about making some primers and grabbing something out of human dna 22:47 < kanzure> or whatever genomes you have handy 22:47 < kanzure> i guess this is drew's lab.. he probably has interesting things stashed away? 22:49 -!- augur [~augur@208.58.5.87] has quit [Remote host closed the connection] 22:50 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 22:50 -!- augur [~augur@208.58.5.87] has quit [Read error: Connection reset by peer] 22:51 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 22:54 < juul> kanzure, hm, yeah i could ask 22:59 < kanzure> jonathan cline has always looked like john schloendorn to me 23:03 -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has joined ##hplusroadmap 23:03 < kanzure> nmz787: let's move towards nailing down the specs on the cutter 23:04 < kanzure> i think we've practically finalized the xy stage plan? 23:05 < nmz787> send me the real wiki link 23:05 < nmz787> kanzure: does that mean we're buying one of the ebay items? 23:06 < kanzure> well. i haven't really thought about this yet. 23:06 < kanzure> buying stuff on ebay is not highly repeatable. but i don't know if we need this to be repeatable. 23:06 < nmz787> kanzure: do we want to build a sustainable design (i.e. sustainable parts supply if we want to sell these things, or expect others to replicate with our OSHW designs) 23:06 -!- capiscuas [~capiscuas@ppp-58-8-137-186.revip2.asianet.co.th] has quit [Remote host closed the connection] 23:06 < kanzure> no clue.. 23:06 < nmz787> ok so we're on the same wavelength 23:06 < kanzure> i think a reusable design would be nice to have but it's not mandatory at this point 23:07 < nmz787> we should thing about rails and screws then 23:07 < nmz787> getting pricing on those to compare 23:07 < kanzure> fenn might chirp in and say a reusable design is easy enough.. if it's not much more of a pain in the butt for him, i'd say go for it. 23:09 < nmz787> http://www.thorlabs.com/NewGroupPage9.cfm?ObjectGroup_ID=1257 23:09 < nmz787> it has a spec sheet though, which /is/ nice 23:09 < kanzure> spec sheets! what luxury 23:09 < nmz787> lol 23:10 < nmz787> well how much is mmilling? 23:10 < nmz787> i.e. for the rail support 23:11 < nmz787> oh this is more reasonable 23:11 < nmz787> http://www.thorlabs.com/NewGroupPage9.cfm?ObjectGroup_ID=159 23:12 < nmz787> eh, not really 23:13 < nmz787> but what i'm getting at is that we at least need a sheet of aluminum with 4 holes of a parallelogram 23:18 -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has quit [Quit: Leaving.] 23:29 -!- Mariu [Jimmy98@89.41.57.33] has quit [Ping timeout: 265 seconds] 23:41 < strangewarp> oh hell 23:41 < strangewarp> Yvain on LessWrong seems to be working on a massive exploration of a resimulation issue I'd been thinking about for months 23:41 < strangewarp> I hope he takes it to its logical conclusion 23:42 < strangewarp> (And I hope it doesn't end up lame) 23:42 < jrayhawk> you might be able to help 23:43 < strangewarp> I'll poke him if it digresses without hitting the big point I had some insight on, but.. it looks like it might cover that already 23:43 * strangewarp reads the rest 23:49 < strangewarp> yes!!! 23:52 * strangewarp thinks 23:52 < jrayhawk> a dangerous pasttime 23:53 < strangewarp> truly, it has brought me nothing but an exotic goal system and an arts degree 23:54 < kanzure> lesswrong is considered harmful to your health 23:54 < kanzure> clop clop --- Log closed Fri Apr 06 00:00:23 2012