| --- Log opened Thu Apr 05 00:00:22 2012 | ||
| -!- AdrianG [~amphetami@unaffiliated/amphetamine] has quit [Ping timeout: 244 seconds] | 00:09 | |
| 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 | 00:12 |
| yashgaroth | plus, robocop | 00:14 |
| delinquentme | who / what is there | 00:16 |
| kanzure | delinquentme: cheap stuff | 00:16 |
| yashgaroth | robocop | 00:16 |
| 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 | 00:17 |
| delinquentme | oodulstay | 00:18 |
| kanzure | http://www.cityfeet.com/cont/michigan-industrial-space | 00:20 |
| 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 | 00:21 |
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| 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 | 00:23 |
| skorket | http://www.cityfeet.com/Commercial/ForSale/21500-24-Mile-Macomb-MI-48042-2371006.aspx | 00:24 |
| skorket | and on and on | 00:24 |
| skorket | I mean, you could almost just squat on some the real estate. Detroit is pretty deserted | 00:25 |
| kanzure | i'm tempted to just rent out 20k sqft and just chill out in the middle while i write my code | 00:29 |
| 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 | 00:45 |
| jrayhawk | git:// as a protocol doesn't support authentication | 00:47 |
| kanzure | welp. okay. | 00:48 |
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| jrayhawk | [url "jrayhawk@piny.be:/srv/git/"] | 00:49 |
| jrayhawk | pushInsteadOf = git://piny.be/ | 00:49 |
| 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/ | 00:50 |
| 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 | 00:51 |
| jrayhawk | is there an underground portion | 00:52 |
| kanzure | detroit usually includes basements yes | 00:52 |
| 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 | 00:53 |
| 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. | 00:54 |
| 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 | 00:55 |
| jrayhawk | although it would get rendered as a giant block of <pre> text inside the page template | 00:56 |
| kanzure | did we disable anonymous editing for a reason? | 00:56 |
| 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. | 00:57 |
| 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. | 00:58 |
| kanzure | okay. | 00:59 |
| 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 | 01:00 |
| 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 | 01:01 |
| jrayhawk | eh | 01:07 |
| jrayhawk | anonymous user registration with optional moderator approval is supported, even | 01:09 |
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| jrayhawk | re: real estate: i would suggest getting something with FTTP pre-installed since that can get pricy | 01:12 |
| kanzure | "buy now and get your very own homeless man!" | 01:13 |
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| kanzure | http://biocurioussafety.pbworks.com/w/page/51594301/General%20Lab%20Policies | 01:51 |
| 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 |
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| yashgaroth | wait you have to put your phone number on everything? seems silly | 01:55 |
| 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? | 01:56 |
| kanzure | http://biocuriousmembers.pbworks.com/w/page/50477380/Reagent%20Store | 01:57 |
| * kanzure sleeps | 01:57 | |
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| 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? | 05:47 |
| diginet | *shotgun | 05:48 |
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| 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? | 06:08 |
| audy | diginet only by chance | 06:19 |
| 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 | 06:21 |
| 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 | 06:34 |
| 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 | 06:41 |
| 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 | 06:43 |
| 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 ? | 06:55 |
| diginet | how long does the piece of the gene need to be? | 06:56 |
| 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? | 06:59 |
| 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 | 07:00 |
| 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. ;) | 07:01 |
| 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 |
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| 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 | 07:03 |
| diginet | cool | 07:04 |
| audy | can you just order primers? | 07:04 |
| audy | do they ask questions? | 07:04 |
| 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 | 07:05 |
| gedankenstuecke | 21 bp for 5.25€ | 07:06 |
| 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 | 07:08 |
| 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 | 07:09 |
| 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 | 07:10 |
| 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 | 07:11 |
| 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 | 07:12 |
| 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 | 07:13 |
| 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 | 07:14 |
| diginet | there is good news at least | 07:15 |
| diginet | apparently both ends are flanked by non-repeating sequences which have been sequenced | 07:15 |
| diginet | so I guess see if there is a restriction enzyme which would cut at those points | 07:16 |
| kanzure | ... or you just get primers for those two | 07:17 |
| gedankenstuecke | which wouldn't be of any help if you want to get the sequence of the repeating region | 07:18 |
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| diginet | well, what process does one use for situations such as these? | 07:21 |
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| kanzure | gedankenstuecke: you would PCR out the gene in question, and then use some non-sanger sequencing method | 07:23 |
| kanzure | diginet: pyrosequencing? | 07:23 |
| 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 | 07:24 |
| 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 | 07:25 |
| gedankenstuecke | apparently the repeats are even in the protein, so this might not be of any help, but hybridisation should work | 07:26 |
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| 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) | 07:26 |
| _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 | 07:27 |
| 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. | 07:28 |
| gedankenstuecke | diginet: from which organism to which do you transfect? | 07:30 |
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| 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 :( | 07:33 |
| gedankenstuecke | and you want to bring it into e coli i guess? | 07:35 |
| gedankenstuecke | or some other bacteria | 07:35 |
| _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. ;) | 07:37 | |
| 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) | 07:38 |
| diginet | kanzure, thanks, I'm vaguely aware of what it is, but I'll make sure and read up on it more | 07:39 |
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| 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 |
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| 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? | 07:40 |
| 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 | 07:41 |
| 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 |
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| kanzure | hello DrOctothorpe | 07:42 |
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| _F7_ | I know octothorpe, he's my roomate | 07:43 |
| kanzure | sounds dangerous | 07:44 |
| diginet | how feasible is mRNA sequencing for DIYers? | 07:44 |
| kanzure | it's something that will have to be debugged pretty strongly.. | 07:45 |
| kanzure | i mean.. it's not a PCR reaction. | 07:45 |
| _F7_ | reverse transcribe? | 07:46 |
| _F7_ | After reverse transcription, it's a PCR reaction | 07:47 |
| 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 | 07:48 |
| _F7_ | Primer walk? | 07:49 |
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| gedankenstuecke | _F7_: the repeat is 9kb long | 07:53 |
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| _F7_ | Oh, Something that should be of interest to those integrating computers with their everyday carry | 07:59 |
| _F7_ | http://tideals.com/ | 07:59 |
| _F7_ | I got one a few days ago and they, surprisingly, haven't sold out | 08:00 |
| _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 | 08:02 |
| _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 | 08:04 |
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| diginet | hmm, here's an idea: apparently, the corresponding gene for the black widow has already been completely sequenced | 08:30 |
| diginet | I should just go with that | 08:31 |
| diginet | let's look up to see how its properties compare with n clavipes | 08:31 |
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| _F7_ | I've got a buddy with a severed nerve from a botched surgery. This spider silk can relink? | 08:46 |
| diginet | It is possible | 08:49 |
| diginet | If it could help someone, that's even more motivation to go through with this :) | 08:49 |
| 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/ | 08:52 |
| diginet | to be fair, Stephen Wolfram is kind of a crank | 08:56 |
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| kanzure | diginet: i guess you haven't seen fenn's lifelog or my meetlog | 08:57 |
| _F7_ | Are you doing that thing yet where you write to tags? | 09:02 |
| _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 |
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| Mokbortolan_ | that doesn't make any sense to me | 09:04 |
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| fenn | "software designed to circumvent encryption" is banned in the dmca | 09:07 |
| kanzure | is my brain a dmca violation? | 09:07 |
| 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 |
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| 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 | 09:09 |
| Mokbortolan_ | the device itself contains some patented algorithms to translate that into calorie expenditure | 09:10 |
| fenn | woo woo | 09:10 |
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| kanzure | nmz787: yo | 09:11 |
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| Mokbortolan_ | can you copyright a protocol? | 09:13 |
| 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 | 09:14 |
| 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 |
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| kanzure | within the existing paradigm and legal system that makes good sense | 09:15 |
| 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 | 09:16 |
| 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 | 09:17 |
| diginet | oh I didn't even know that | 09:20 |
| * diginet pulls foot out of mouth | 09:20 | |
| kanzure | "nc licenses considered harmful" http://www.kuro5hin.org/story/2005/9/11/16331/0655 | 09:24 |
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| Mokbortolan_ | This section might cover me: http://cyber.law.harvard.edu/openlaw/DVD/1201.html#f | 09:38 |
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| _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 | 09:53 |
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| fenn | hmm dotsies is cool, not sure if their character mapping is optimal though | 10:13 |
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| delinquentme | hurro luvlies | 10:13 |
| fenn | also, english spelling is horrid | 10:13 |
| fenn | much better to use a phonetic alphabet | 10:13 |
| 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 |
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| delinquentme | china hacking hoo? | 10:16 |
| uniqanomaly | us/europe corps govs etc | 10:16 |
| uniqanomaly | legislation is only making western citizens disadvantaged | 10:16 |
| uniqanomaly | same is true with stem cells research | 10:17 |
| uniqanomaly | retards | 10:17 |
| kanzure | CIRM seems to be doing pretty good stem cell work | 10:18 |
| kanzure | don't know what you're complaining about | 10:18 |
| 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. | 10:19 |
| 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." | 10:20 |
| uniqanomaly | ok | 10:21 |
| 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 | 10:23 |
| 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" | 10:24 |
| 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 | <uniqanomaly> legislation is only making western citizens disadvantaged | 10:25 |
| katsmeow-afk | and i agreed, and gave example | 10:26 |
| uniqanomaly | yeah ok | 10:26 |
| katsmeow-afk | "when in Rome, do as theRomans do" | 10:26 |
| 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 | 10:27 |
| 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 | 10:28 |
| 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? | 10:29 |
| uniqanomaly | yes I believe youre right | 10:30 |
| 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 | 10:33 |
| 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? | 10:34 |
| 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 | 10:35 |
| 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 | 10:36 |
| 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? | 10:37 |
| 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 | 10:38 |
| 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 | 10:39 |
| 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 | 10:40 |
| 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 | 10:41 |
| 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 | 10:42 |
| 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" | 10:43 |
| kanzure | i don't even know if a library would survive in-tact through the mail. sounds like an experiment worth doing.. | 10:44 |
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| 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 | 10:45 |
| 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 | 10:46 |
| 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 | 10:47 |
| 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 | 10:48 |
| 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 | 10:49 |
| 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 | 10:50 |
| 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 ;) | 10:51 |
| 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 | 10:52 |
| 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 | 10:53 |
| diginet | I sorry :( | 10:54 |
| diginet | I won't hold it against you :) | 10:54 |
| 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 | 10:55 |
| 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 | 10:56 |
| 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 | 10:57 |
| 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 | 10:58 |
| 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 | 10:59 |
| 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 | 11:00 |
| 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 | 11:01 |
| _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 | 11:02 |
| delinquentme | _F7_, would you like to check if duquesne has one? | 11:03 |
| delinquentme | i've got a few logins for them | 11:03 |
| diginet | _F7_ I have journal access | 11:05 |
| diginet | let me get it for you | 11:05 |
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| _F7_ | cool | 11:07 |
| fenn | ThomasEgi: cython is chipping away at the performance issue | 11:07 |
| fenn | and moore's law is chipping away at the "not enough resources" issue | 11:08 |
| 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 | 11:09 |
| 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 | 11:10 |
| 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 | 11:11 |
| diginet | or C | 11:12 |
| diginet | depending on the arch | 11:12 |
| 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 | 11:16 |
| 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. | 11:17 |
| 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 | 11:20 |
| 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 | 11:21 |
| fenn | aliens! | 11:22 |
| diginet | my favourite parody of UFO nuts ever: http://youtu.be/59zLZ6PpeSA | 11:22 |
| _F7_ | The aliens are probably communicating with his brain directly, Goertzel has been a waldo for some time now. | 11:23 |
| _F7_ | The alien telemetry device is made out of meat and has the same X-ray profile as a human brain | 11:24 |
| 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? | 11:25 |
| _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. | 11:26 |
| diginet | _F7_: I think you just asploded my brain | 11:27 |
| _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 | 11:31 |
| 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. | 11:32 |
| * 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 | 11:33 |
| 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 | 11:34 |
| 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 | 11:35 |
| _F7_ | Hackerspace crazies.. this one guy came in with a fischer price plastic donut toy thing | 11:36 |
| _F7_ | and started making 'odin coils' | 11:36 |
| _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 | 11:37 |
| _F7_ | He insists it's part of some kind of antigravity drive | 11:38 |
| ParahSailin_ | wow | 11:38 |
| _F7_ | I still have the mercury, he abandoned most of it after we told him to GTFO for flowing rivers of mercury | 11:39 |
| fenn | speaking of crazies, i accidentally recorded this conversation at noisebridge http://fennetic.net/irc/erin_full_edited.mp3 | 11:40 |
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| ParahSailin_ | [indistinct voices] | 11:50 |
| 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. | 11:51 |
| ParahSailin_ | 22 hours | 11:52 |
| 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 | 11:53 |
| 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 | 11:54 |
| 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? | 11:55 |
| katsmeow-afk | i hope they do it, i'd like to see the spin on news reports of it | 11:56 |
| 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 | 11:57 |
| 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 | 11:59 |
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| kanzure | http://www.meetup.com/HardwareStartupSF/ | 12:17 |
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| _F7_ | in this channel we type faster than most people think | 12:37 |
| katsmeow-afk | sorry, could you type that slower? i didn't catch it | 12:39 |
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| 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/ | 12:43 |
| 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? | 12:46 |
| 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 | 12:47 |
| 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. | 12:48 |
| 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 | 12:49 |
| 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 | 12:50 |
| katsmeow-afk | i think it's ipossible, given that a polar orbit is moving 90 degrees to an equatorial orbit | 12:51 |
| 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 | 12:53 |
| 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 | 12:54 |
| 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 | 12:55 |
| kanzure | lichen: are you open to relocating | 13:04 |
| lichen | yeah, depending | 13:04 |
| kanzure | kk | 13:05 |
| 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 | 13:08 |
| fenn | knapp needs to learn about the subjunctive tense | 13:09 |
| kanzure | i'm still hoping for intergalactic laser cutting/chemistry | 13:09 |
| 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 | 13:10 |
| katsmeow-afk | aim and combine pulsar beams so they are more of a continuous stream | 13:11 |
| fenn | by the time you arrive in your intergalactic chariot, the planet will have spontaneously generated and demanding compensation for "wrongful life" | 13:12 |
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| 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 | 13:15 |
| 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 | 13:17 |
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| _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 | 14:05 |
| _F7_ | To be sure, however, the electronic entity modulated Godelian Shock Input over the ships various PAs and communications devices. | 14:08 |
| Mokbortolan_ | receive when they find the... got cut off | 14:22 |
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| delinquentme | _F7_, what is this? | 14:43 |
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| 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 | 14:55 |
| 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 | 14:56 |
| fawwo | heya | 14:57 |
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| kanzure | fawwo: what brings you around? | 14:58 |
| 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 | 15:01 |
| 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" | 15:02 |
| fawwo | is that just taking all the possible encodings/character sets into account? | 15:03 |
| fawwo | *isnt | 15:03 |
| kanzure | err why would is/isnt matter in that message? | 15:04 |
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| 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 | 15:05 |
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| kanzure | le sigh http://en.wikipedia.org/wiki/List_of_organic_reactions | 15:23 |
| kanzure | aren't there supposed to be >150k reaction mechanisms | 15:23 |
| kanzure | i wonder if there's something like xpath for querying chemical structures | 15:27 |
| kanzure | smiles/frowns is just for parsing strings right? | 15:27 |
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| kanzure | wondering why i haven't written something for http://en.wikipedia.org/wiki/Retrosynthetic_analysis yet | 15:33 |
| 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 | 15:34 |
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| kanzure | weird i wonder what all this code is | 15:37 |
| kanzure | did i ever push this anywhere? geeze | 15:37 |
| 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 | 15:38 |
| kanzure | it uses smiles, smarts, frowns, and pydaylight | 15:40 |
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| kanzure | "Frowns (a now unsupported Open Source Python cheminformatics library)" | 15:44 |
| kanzure | oh. | 15:44 |
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| F71 | *frowns | 16:00 |
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| kanzure | hi queequeg | 17:13 |
| 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 | 17:18 |
| kanzure | you might consider my commits to be git spam | 17:27 |
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| queequeg | hello, a friend told me to join because i'm interested in bioengineering | 17:45 |
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| yashgaroth | okay then | 17:46 |
| kanzure | heh | 17:46 |
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| kanzure | fenn: ping? | 18:37 |
| kanzure | hi F71 | 18:41 |
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| 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. | 18:48 |
| sylph_mako | Seriously this is how I feel about a lot of transhumanist directives. Why are we in such a dang rush? | 18:49 |
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| 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 |
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| kanzure | yo gene_hacker | 18:57 |
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| fawwo | thx jrayhawk | 19:16 |
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| fenn | bold words | 19:25 |
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| fawwo | actually the "change" it talks about seems to mostly "just" be about giving people a community to be part of | 19:36 |
| fenn | you mean they're not suggesting a radical transformation in the substrate and form you are made of? | 19:37 |
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| fawwo | yez, though unfortunately I dont think that was ever on the table | 19:41 |
| strangewarp | Hey guize let's adopt green syndicalism and make thousand-year plans to be carried out by our heroic human descendents | 19:44 |
| kanzure | what | 19:46 |
| jrayhawk | a thousand year reich? | 19:46 |
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| strangewarp | [sarcasm] | 19:49 |
| sylph_mako | hah. I see. | 19:51 |
| kanzure | micro porn http://rockmaninoff.files.wordpress.com/2011/06/gc_picture-027m_albertfolchlab1.jpg | 19:51 |
| kanzure | that's not really micro is it? | 19:52 |
| fenn | if it was too micro it wouldn't blend | 19:53 |
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| kanzure | 100 microns is a dust mite. | 19:56 |
| kanzure | or the thickness of human hair. | 19:57 |
| kanzure | those features look much larger than that.. | 19:58 |
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| 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 | 20:12 |
| roksprok | obviously tremendously overpriced | 20:13 |
| roksprok | at 16000 | 20:13 |
| roksprok | but gives you something to compare to | 20:13 |
| kanzure | "2 inch focus lens kit" eh | 20:15 |
| kanzure | "Reduces beam spot size to 0.001" gah units! | 20:15 |
| 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 | 20:16 |
| 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 | 20:17 |
| 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? | 20:18 |
| 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 | 20:19 |
| kanzure | maybe they started off with absurd prices | 20:20 |
| roksprok | thanks F71 | 20:20 |
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| roksprok | i imagine they have a default of like 3 times total assembly costs | 20:20 |
| roksprok | as the CO2 lasers i've seen are all a few grand | 20:21 |
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| roksprok | and 30 watts is nothing special | 20:22 |
| roksprok | and of course hpdfo is just...their stupid trade name | 20:22 |
| roksprok | for 'more lenses!!!!!' | 20:23 |
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| 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? | 20:34 |
| jrayhawk | Makes the process more complicated and expensive. | 20:35 |
| jrayhawk | Motherboards nowadays are actually fairly deep; usually over eight layers of circuitry. | 20:36 |
| roksprok | do you know off the top of your head an estimation of how thick each layer is? | 20:37 |
| roksprok | 50 um? | 20:37 |
| 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. | 20:38 |
| 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 | 20:39 |
| roksprok | after working on it for 12 years | 20:40 |
| 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 | 20:41 |
| 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 | 20:43 |
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| roksprok | kanzure are you planning on using micado/autoCAD for your chip design? or design your own system | 20:46 |
| kanzure | my own | 20:46 |
| kanzure | i'll export to svg, dxf, step and gcode | 20:47 |
| 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? | 20:51 |
| 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 | 20:52 |
| kanzure | this site looks like a sam | 20:53 |
| kanzure | *scam | 20:53 |
| kanzure | notice the fake photo on their page | 20:53 |
| 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 | 20:54 |
| roksprok | idex corporation, who owns them, is a 1.5 billion dollar a year company | 20:55 |
| 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? | 20:56 |
| 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 | 20:57 |
| 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. | 20:58 |
| lichen | http://youtu.be/Yxfn5PFWYTk | 21:00 |
| kanzure | lichen: http://www.youtube.com/watch?v=SQq_XmhBTgg#t=40 | 21:02 |
| lichen | cool ill have to watch through this | 21:03 |
| lichen | looks pretty campy | 21:03 |
| kanzure | very much so.. | 21:03 |
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| kanzure | kla/win 6 | 21:22 |
| kanzure | fjkasdjfla | 21:22 |
| Mariu | Windows Vista ? | 21:24 |
| Mariu | win 6 reminded me of that | 21:24 |
| kanzure | irssi :| | 21:24 |
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| kanzure | klafka! | 21:26 |
| kanzure | roksprok: are you still planning to do your reagent store | 21:27 |
| klafka | kanzure! | 21:27 |
| 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 | 21:28 |
| 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 |
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| 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. | 21:30 |
| 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 | 21:31 |
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| 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 | 21:33 |
| 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 | 21:34 |
| roksprok | but yea hopefully it will continue to go ok | 21:35 |
| 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 | 21:36 |
| 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 | 21:37 |
| roksprok | a little | 21:38 |
| kanzure | http://www.neuron.yale.edu/neuron/ | 21:38 |
| roksprok | is that kind of the biggest neural simulation thing? | 21:38 |
| 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?) | 21:39 |
| 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." | 21:40 |
| 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 | 21:41 |
| kanzure | emergent... isn't that randall o'reilly's thing | 21:42 |
| kanzure | superkuh: weren't you playing with that? | 21:42 |
| 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? | 21:43 |
| roksprok | if there is one thing i need it is more people to bitch to | 21:44 |
| kanzure | archels: you too.. | 21:44 |
| 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++. | 21:45 |
| roksprok | o yea that was a while ago | 21:46 |
| roksprok | did delinquentme ever find someone to apply to ycombinator with him? | 21:51 |
| kanzure | sure.. all of us :P | 21:53 |
| 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 | 21:54 |
| 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. | 21:55 |
| roksprok | i think they funded a lab notebook site | 21:56 |
| roksprok | so they are in the 'marketing to scientists' area | 21:56 |
| 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. | 21:57 |
| 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 | 21:58 |
| 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 | 21:59 |
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| 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 | 22:00 |
| 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 | 22:01 |
| 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 | 22:02 |
| 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 | 22:03 |
| 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 | 22:04 |
| 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 | 22:05 |
| kanzure | that's probably more than 2k bp :) | 22:06 |
| juul | haha | 22:06 |
| juul | nice list though | 22:07 |
| kanzure | gut/insulin needs to happen already.. it's 2012 ffs | 22:07 |
| 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 | 22:08 |
| 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 | 22:09 |
| 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 | 22:10 |
| 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 | 22:11 |
| 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 | 22:12 |
| 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 | 22:13 |
| 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 | 22:14 |
| 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 | 22:15 |
| 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 | 22:16 |
| 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 | 22:17 |
| 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. | 22:18 |
| 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 | 22:19 |
| 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.. | 22:20 |
| 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 |
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| kanzure | yo nmz787 | 22:21 |
| juul | hehe | 22:21 |
| 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 | 22:22 |
| nmz787 | oh, nevermind | 22:25 |
| nmz787 | silicatein? | 22:26 |
| yashgaroth | heat shock response -> rfp? | 22:26 |
| yashgaroth | ooh and cold response -> bfp if that exists | 22:26 |
| kanzure | what happened to those antifreeze proteins | 22:27 |
| juul | kanzure, oooh! that's interesting | 22:31 |
| juul | put it in hela to minimize crystallization damage during freezing | 22:33 |
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| juul | yashgaroth, not a bad idea | 22:46 |
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| yashgaroth | 2kb is kind of restrictive | 22:46 |
| 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? | 22:47 |
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| juul | kanzure, hm, yeah i could ask | 22:54 |
| kanzure | jonathan cline has always looked like john schloendorn to me | 22:59 |
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| kanzure | nmz787: let's move towards nailing down the specs on the cutter | 23:03 |
| kanzure | i think we've practically finalized the xy stage plan? | 23:04 |
| nmz787 | send me the real wiki link | 23:05 |
| nmz787 | kanzure: does that mean we're buying one of the ebay items? | 23:05 |
| 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 |
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| 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 | 23:06 |
| 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. | 23:07 |
| 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 | 23:09 |
| nmz787 | well how much is mmilling? | 23:10 |
| nmz787 | i.e. for the rail support | 23:10 |
| nmz787 | oh this is more reasonable | 23:11 |
| nmz787 | http://www.thorlabs.com/NewGroupPage9.cfm?ObjectGroup_ID=159 | 23:11 |
| nmz787 | eh, not really | 23:12 |
| nmz787 | but what i'm getting at is that we at least need a sheet of aluminum with 4 holes of a parallelogram | 23:13 |
| -!- nmz787 [~Nathan@cpe-67-242-177-23.rochester.res.rr.com] has quit [Quit: Leaving.] | 23:18 | |
| -!- Mariu [Jimmy98@89.41.57.33] has quit [Ping timeout: 265 seconds] | 23:29 | |
| 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 | 23:41 |
| strangewarp | (And I hope it doesn't end up lame) | 23:42 |
| jrayhawk | you might be able to help | 23:42 |
| 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 | 23:43 | |
| strangewarp | yes!!! | 23:49 |
| * strangewarp thinks | 23:52 | |
| jrayhawk | a dangerous pasttime | 23:52 |
| strangewarp | truly, it has brought me nothing but an exotic goal system and an arts degree | 23:53 |
| kanzure | lesswrong is considered harmful to your health | 23:54 |
| kanzure | clop clop | 23:54 |
| --- Log closed Fri Apr 06 00:00:23 2012 | ||
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