| --- Log opened Thu Mar 15 00:00:52 2012 | ||
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| strangewarp | I just found a value of resistor that I didn't expect I would already have | 05:23 |
|---|---|---|
| strangewarp | and I said | 05:23 |
| strangewarp | "ohm my gosh." | 05:23 |
| * strangewarp nerd smile | 05:23 | |
| rdb | what value? negative 0.001*omega*sqrt(-1) ohm? | 05:31 |
| strangewarp | 220 ohm, didn't think I had any extras laying around | 05:34 |
| strangewarp | Lo and behold, a baggie of them was in the pile of parts I accumulated when I was a noob | 05:34 |
| rdb | by coincidence, I found a 22 kOhm part lying on the floor that I don't remember using, yesterday | 05:36 |
| strangewarp | woot | 05:36 |
| rdb | not sure why I would need a 1206-sized 22 kOhm resistor, but whatevs | 05:36 |
| strangewarp | Those are the ultra-tiny ones? | 05:37 |
| strangewarp | (still sort of a noob here, just not a blatant one anymore) | 05:37 |
| rdb | 1206 may be tiny to some, but you won't find resistors larger than that these days :-p | 05:38 |
| strangewarp | oh ;x | 05:38 |
| rdb | 1206 > 0805 > 0603 > 0402 > 0201 > 01005 | 05:38 |
| strangewarp | ahh, that's what threw me off, there was a recent post on Hack A Day about soldering 0400/0200 parts by hand or something | 05:39 |
| strangewarp | and the memory of skimming over it made my brain go "gleep?" | 05:40 |
| rdb | I somehow doubt xx00 parts exist... they would be infinitely thin xD | 05:41 |
| rdb | the convention is xxyy where xx is the length in mils, and yy is the width | 05:41 |
| strangewarp | OH right, duh | 05:41 |
| strangewarp | It was 0402 | 05:41 |
| rdb | must've been 0402/0201 | 05:41 |
| rdb | yeah | 05:41 |
| strangewarp | yeah, thsoe | 05:41 |
| strangewarp | those, even. derp | 05:42 |
| rdb | tbh I still have some trouble soldering 0603 | 05:43 |
| rdb | haven't dared to try smaller | 05:43 |
| Vicarious | hi | 05:43 |
| rdb | hi Vicarious | 05:43 |
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| rdb | how's life? | 05:46 |
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| chris_99 | http://www.bbc.co.uk/iplayer/episode/b01dlglq/Horizon_20112012_Out_of_Control/ | 08:19 |
| chris_99 | on the brain | 08:19 |
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| thylane | http://www.sciencedaily.com/releases/2012/03/120314142843.htm | 09:03 |
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| thylane | http://scienceworld-frontiers.blogspot.com/2012/03/cultural-ratchet-present-in-humans.html | 10:21 |
| Mokbortolan_ | can someone please explain to me the process for making diamonds from cremains? | 10:21 |
| Mokbortolan_ | from what I read, what little carbon is found in cremains is in the form of carbonates | 10:22 |
| thylane | Mokbortolan_ Did you read my link yet? | 10:25 |
| Mokbortolan_ | yes | 10:25 |
| Mokbortolan_ | but it didn't really go into specifics | 10:26 |
| Mokbortolan_ | ohw ait, wrong room :p | 10:26 |
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| Mokbortolan_ | that's really interesting | 10:27 |
| Mokbortolan_ | I bet there's a fundamental difference in how humans and apes store memories | 10:27 |
| Mokbortolan_ | maybe a slightly tweaked protein that results in cultural accumulation | 10:27 |
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| thylane | I was over thinking the article, until I realized they siad human children can do ratcheting | 10:36 |
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| kanzure | there is a pleasing number of results for the search "against antibiotic resistance" | 11:27 |
| kanzure | i think that means anti-antiantibiotics | 11:27 |
| kanzure | shouldn't it just be "against biotics" | 11:28 |
| archels | anti-evolution in bacteria? | 11:28 |
| kanzure | for example there's the "swedish strategic programme against antibiotic resistance" | 11:29 |
| archels | a bacteria evolves a mutation that makes it immune to a certain antibiotic or class thereof | 11:30 |
| kanzure | sure | 11:30 |
| archels | What strategies are there to prevent this? | 11:31 |
| archels | I mean, you can't really *prevent* it, can you? | 11:31 |
| kanzure | man the soviet union knew how to pick good names | 11:39 |
| kanzure | "Department of the Mobilisation of Scientific Forces" | 11:39 |
| archels | pubmed for those keywords: Results: 1 to 20 of 19763 | 11:40 |
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| archels | Got a paper suggestion for me, kanzure? | 11:40 |
| kanzure | are you looking for antibiotic resistance evidence? | 11:40 |
| archels | No, I just want to know about the mechanisms, or directions of research that go towards preventing antibiotic resistance. | 11:41 |
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| archels | A one-sentence summary might also do. ;) | 11:42 |
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| thylane | http://www.youtube.com/user/SingularitySummits | 12:03 |
| thylane | http://www.youtube.com/user/SingularitySummits | 12:03 |
| Mariu | thanks thylane | 12:07 |
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| kanzure | hrm a panda3d developer | 12:18 |
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| roksprok | anyone familiar with 'the cure is now' www.thecureisnow.org? | 12:19 |
| kanzure | yes | 12:19 |
| kanzure | they asked me to be on their board of advisors :/ | 12:19 |
| roksprok | are you? | 12:19 |
| roksprok | it seems like someone who knows about diybio could save them thousands of dollars | 12:19 |
| kanzure | no not yet i forgot to send in some info they wanted | 12:19 |
| kanzure | they are not interested in saving thousands of dollars | 12:19 |
| roksprok | http://www.thecureisnow.org/index.php/organization/projected-expenses/129 | 12:20 |
| roksprok | 5000 for a microcentrifuge? | 12:20 |
| kanzure | i was asking around with them trying to figure out how 'lean' they are willing to be | 12:20 |
| kanzure | it turns out that they are very much interested in traditional institutional science | 12:20 |
| roksprok | bummer | 12:21 |
| roksprok | that already exists | 12:21 |
| kanzure | yep.. yet another NPO doing the same sorta thing | 12:21 |
| kanzure | this is why i haven't considered them a priority | 12:21 |
| roksprok | there are thousands of traditional institutions spending billions of dollars on alzheimers | 12:21 |
| roksprok | what do they think they are going to change? | 12:21 |
| kanzure | roksprok: you might be interested in this http://diyhpl.us/wiki/transcripts/open-science-summit-2010/scott-johnson-myelin-repair-foundation/ | 12:21 |
| kanzure | ".. is that basic science is pretty random. There's no research plan. No disease organization actually has a research plan. They put out a request for proposals, they peer review those, and those that get the highest ratings, that's what gets funded. " | 12:23 |
| kanzure | "Most academics would say that it should be random, since you can't know where they are going. Well, in some cases you want to be outcome directed." | 12:23 |
| kanzure | in non-profits there is no selection pressure to have the best team with the best skills | 12:24 |
| kanzure | most philanthropists just dump money wherever | 12:24 |
| kanzure | this is also somewhat the case for the singularity-related nonprofits | 12:25 |
| roksprok | scott johnson doesn't happen to have a website, or was this talk taped? | 12:25 |
| roksprok | i'd kind of like to ask for the diagrams | 12:25 |
| kanzure | the talk was from open science summit 2010 | 12:25 |
| kanzure | which i think uploaded videos to justin.tv or something stupid | 12:25 |
| roksprok | k i'll find them | 12:25 |
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| kanzure | i actually have those videos aggregated on hplusvideo | 12:26 |
| kanzure | i don't think i remembered to turn on my server tho | 12:26 |
| kanzure | if you bug me enough i'll redeploy it haha | 12:26 |
| roksprok | hah i don't think its worth bugging you if its available elsewhere | 12:27 |
| kanzure | on the contrary | 12:27 |
| roksprok | just means less reddit/metafiler time-wasting for me | 12:28 |
| kanzure | ok i've turned it on | 12:28 |
| kanzure | http://diyhpl.us:9001/ | 12:28 |
| jrayhawk | you can add that to /etc/rc.local | 12:28 |
| kanzure | for thumbnails: http://diyhpl.us:9001/random | 12:29 |
| kanzure | jrayhawk: honestly if i was serious about this i would use wsgi | 12:29 |
| kanzure | i'm just running the "DO NOT EVER USE THIS IN PRODUCTION" dev server | 12:29 |
| kanzure | also.. /random is written poorly. i keep pinging the poor embed.ly servers for the same info over and over again | 12:30 |
| roksprok | are you going to keep this turned on for the next few days? | 12:31 |
| kanzure | yes | 12:31 |
| roksprok | cool | 12:31 |
| kanzure | it usually only goes offline when jrayhawk has to reboot the server | 12:31 |
| kanzure | again it's just some prototype site thingy that i haven't been taking too seriously :| | 12:31 |
| jrayhawk | if i happen to have motivation cycles to spare, would you want that shoved into apache | 12:32 |
| roksprok | well it gives links to the videos, thats all i desire | 12:32 |
| kanzure | jrayhawk: yeah okay | 12:32 |
| kanzure | might as well | 12:32 |
| archels | kanzure: no papers on your archive on preventing antibiotic resistance then? | 12:33 |
| jrayhawk | i am sad there is no more minx mandate | 12:33 |
| jrayhawk | that was good comedy | 12:33 |
| kanzure | archels: i don't think you can prevent it | 12:33 |
| kanzure | but you can fight it | 12:34 |
| kanzure | you can prevent it in extreme circumstances (like, you want to prevent it /with respect to/ a known population) | 12:34 |
| chris_99 | that doesn't seem to be loading for me | 12:35 |
| kanzure | chris_99: /random will take a few moments | 12:35 |
| chris_99 | aha | 12:35 |
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| kanzure | because i was being a dork when i wrote it | 12:35 |
| chris_99 | what language is it running in? | 12:35 |
| kanzure | python/django | 12:35 |
| chris_99 | aha cool | 12:35 |
| kanzure | it takes a while because each video is displayed by pinging embed.ly | 12:35 |
| kanzure | instead of storing the information in the model | 12:35 |
| chris_99 | ah | 12:35 |
| archels | kanzure: alright, I wasn't sure there was some biotechnological method that I wasn't aware of. | 12:37 |
| kanzure | roksprok: if you have suggestions for this site, let me know | 12:37 |
| kanzure | i don't know what to do with it really | 12:37 |
| roksprok | i think its good as is, but i am just using it like your directory of papers | 12:39 |
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| roksprok | does steel know about it? maybe he could add the vids to his transhumani wiki | 12:40 |
| roksprok | well use it as a resource for finding relevant vids | 12:40 |
| Steel2 | which vids | 12:41 |
| roksprok | diyhpl.us:9001 | 12:41 |
| kanzure | i don't really care if he knows | 12:41 |
| kanzure | why is he starting a competing wiki now? | 12:42 |
| kanzure | fuck | 12:42 |
| roksprok | list of vids like kanzure's lists of papers | 12:42 |
| roksprok | i've often thought that wikis generally lacked vids | 12:46 |
| roksprok | of relevant talks | 12:46 |
| roksprok | kanzure do you work out of your apartment? or the austin hackerspace? or someplace else | 12:51 |
| roksprok | if you don't mind me asking | 12:52 |
| kanzure | roksprok: i work wherever | 13:08 |
| kanzure | i don't work at the hackerspace much | 13:09 |
| kanzure | mostly because they moved a bit further north and the closer one gets too hot during the day | 13:09 |
| roksprok | are you at the stage of doing lots of chemsitry stuff with your dna synthesis project? | 13:11 |
| roksprok | or still in the microfluidics design stage | 13:11 |
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| kanzure | just design stage.. i want to wait on the chemistry until i figure out where i will physically be in a month | 13:12 |
| lichen | that cure ise now link is interesting | 13:12 |
| kanzure | i don't want to setup multiple labs.. it is more efficient to just have one place | 13:12 |
| lichen | is* | 13:12 |
| roksprok | what are your options? | 13:12 |
| kanzure | but this is somewhat dependent on whether or not certain people are going to be available | 13:13 |
| kanzure | well if singularityu says yes then i will be using triplering's facilities | 13:13 |
| kanzure | if they say no then i need to figure out whether or not i am going to sf | 13:13 |
| lichen | are there many places like the cure is now around? | 13:13 |
| kanzure | "the cure is now" isn't particularly special :x | 13:13 |
| kanzure | there are many disease-related nonprofits | 13:13 |
| lichen | mhmm | 13:14 |
| lichen | well i was looking at their focii and it includes specifically h+ things | 13:14 |
| lichen | beyond just disease | 13:14 |
| thylane | I think medicine as a whole is transitioning into "personalized medicine" http://www.thecureisnow.org/index.php/our-strategy/philosophy-of-tcin/personalized-medicine | 13:14 |
| lichen | given that i'm rather more of a comp sci person in background i'm interesting in finding places where i can be useful | 13:14 |
| kanzure | lichen: what sort of comp sci background | 13:14 |
| lichen | general at this point, im young and breaking into the industry | 13:15 |
| kanzure | ok i have no idea what that means | 13:15 |
| lichen | i have experience more in games and graphics output | 13:15 |
| kanzure | are you able to write code? | 13:15 |
| lichen | yeah | 13:15 |
| kanzure | ok so does that mean CUDA? | 13:15 |
| lichen | c/c++/asm at this point | 13:15 |
| lichen | but i could pick up cuda | 13:15 |
| kanzure | or some other gfx output | 13:15 |
| kanzure | ok i see | 13:15 |
| lichen | im planning on learning shader design soon anyways | 13:15 |
| kanzure | are you employed | 13:15 |
| lichen | yeah, but unrelated | 13:15 |
| lichen | im looking for a job in the field at this point | 13:15 |
| kanzure | where are you? | 13:16 |
| lichen | portland, oregon | 13:16 |
| kanzure | okay | 13:17 |
| kanzure | thylane: then you would probably geek out about 'pink army' | 13:18 |
| thylane | I know a woman who obviously WANTS 'personalized medicine', but there are clinics and doctors offices that somewhat "reject" it in certain ways | 13:18 |
| thylane | I think its because they are so entrenched in statistical medicine | 13:19 |
| kanzure | complaining about it will not help her | 13:19 |
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| kanzure | visual transistor-level simulation of 6502 http://visual6502.org/ | 13:49 |
| kanzure | http://visual6502.org/JSSim/index.html | 13:52 |
| ThomasEgi | that page is pretty awesome | 13:54 |
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| kanzure | sciencehackday chicago http://sciencehackday.pbworks.com/chicagoideas | 14:10 |
| roksprok | kanzure do you know jack lloyd at triple ring? | 14:12 |
| kanzure | not yet | 14:12 |
| roksprok | he seems interesting in that he's founded a bunch of tech companies but only has a bs in engineering | 14:13 |
| kanzure | degrees are worth absolutely squat.. | 14:13 |
| roksprok | i'd like to know how he convinced people to give him money tho | 14:13 |
| kanzure | there are many ways to do that | 14:14 |
| kanzure | first is to make money on your own | 14:14 |
| kanzure | second is to play the numbers game (talking with a sufficient number of people and iterating on your presentation skills) | 14:14 |
| kanzure | i don't know why i am counting these off if i claim there are many ways :) | 14:15 |
| roksprok | money on your own is pretty obvious | 14:15 |
| kanzure | are you sure people gave him money? | 14:15 |
| kanzure | did he do some venture backed stuff? | 14:16 |
| roksprok | i think so | 14:17 |
| roksprok | nellcor | 14:17 |
| kanzure | "1981: Nellcor was started by Dr. William NEw, Jack LLoyd and Jim CORenman in Hayward, California to develop and market pulse oximetry systems" | 14:17 |
| kanzure | there was a huge surge of biotech vc money in the 80s | 14:18 |
| roksprok | o did not know that | 14:18 |
| kanzure | but having someone with a phd is helpful | 14:18 |
| kanzure | what looks the best to vc groups is "yeah we're a team of 4 people with 9 PhDs collectively, making a product for a 40 billion dollar market that grows 8% annually" | 14:19 |
| roksprok | i guess i should start networking | 14:19 |
| roksprok | bummer | 14:20 |
| kanzure | yeah it's really a game of numbers when you are fundraising | 14:20 |
| kanzure | but people are friendly | 14:20 |
| kanzure | step 1) talk to 500 people | 14:20 |
| kanzure | heh | 14:20 |
| roksprok | ha well 498 to go | 14:21 |
| kanzure | it is exceedingly unlikely that your first pitch will land you money | 14:22 |
| lichen | just scored an interview with intel o.o | 14:38 |
| lichen | not my dream job but its something? | 14:38 |
| kanzure | http://news.cnet.com/8301-30252_3-57397557-246/hacker-collective-focuses-on-biotech-audio-slideshow/ | 14:44 |
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| Vicarious | aww.. | 15:17 |
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| kanzure | Vicarious: ? | 15:24 |
| Vicarious | hi kanzure | 15:25 |
| Vicarious | tomororw there's a meetup planned, regarding BIY biohacking and stuff | 15:28 |
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| Vicarious | but I'm unable to attend it, I have to work until 16:30, meeting starts 18:00 | 15:29 |
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| roksprok | what city vicarious? | 15:31 |
| kanzure | probably copenhagen | 15:33 |
| kanzure | oops wait he's in the netherlands somewhere | 15:33 |
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| roksprok | thats far | 15:34 |
| Juul | copenhagen, netherlands, it's basically the same thing | 15:37 |
| Vicarious | roksprok: the meetup takes place in the hague, the netherlands | 15:37 |
| Juul | Vicarious, is DSM a big presence in synth bio in Holland? | 15:38 |
| kanzure | Juul: bah geography | 15:38 |
| kanzure | pokeman is np-hard http://arxiv.org/pdf/1203.1895v1.pdf | 15:38 |
| Juul | kanzure, culturally they are actually extremely close, which i guess is why people mix them up | 15:38 |
| kanzure | Juul: i just keep forgetting where everyone lives | 15:38 |
| Juul | yeah, well i'm already impressed that you even try to keep track of everyone | 15:39 |
| kanzure | WHO ARE YOU PEOPLE | 15:41 |
| kanzure | WHY DO I KNOW YOU | 15:41 |
| kanzure | thanks | 15:41 |
| Vicarious | it takes 3 hours by train + 20 minutes by foot to travel from my city to the location where the meetup takes place | 15:42 |
| kanzure | and which city is this | 15:42 |
| Vicarious | kanzure: the meetup takes place in the hague, the netherlands | 15:42 |
| kanzure | the hague, ok | 15:43 |
| Vicarious | according to http://www.meetup.com/Dutch-DIY-Bio/events/52332122/ | 15:43 |
| kanzure | bbl | 15:53 |
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| ThomasEgi | http://chzmemebase.files.wordpress.com/2012/03/koma-comic-strip-comixed-its-effective.jpg | 16:11 |
| ThomasEgi | proven to work | 16:11 |
| Juul | Vicarious, nice. Will you document? | 16:12 |
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| Vicarious | Juul: I won't be attending, there's not much for me to document | 16:17 |
| Juul | Vicarious, ah yes. you said that. sorry | 16:18 |
| Vicarious | np | 16:18 |
| Vicarious | I was wondering if I'm the only one who has a magnet implant, among the dutch DIY biohackers | 16:20 |
| Vicarious | hey Steel2, don't you know it's rude to message people without asking for their permission first? | 16:23 |
| Vicarious | I don't know you | 16:24 |
| Steel2 | Uh, that's not particularly something I'd been told before in the 6-7 years I've been on irc, no. | 16:25 |
| katsmeow-afk | my appologies for not telling you when you msg'd me the other day | 16:25 |
| * katsmeow-afk has been irc'ing since 1996 | 16:26 | |
| Steel2 | yeh, I'm a young fucker | 16:26 |
| Vicarious | same here, since summer '96 | 16:26 |
| Steel2 | maybe irc protocols have changed in newer channels :P | 16:26 |
| katsmeow-afk | nope | 16:26 |
| Steel2 | but I apologize | 16:26 |
| Steel2 | as that's not something I've ever run into before | 16:27 |
| katsmeow-afk | this is a newer channel | 16:27 |
| Vicarious | usually when irc clients message me without asking for permission, and I don't know them personally.. they're spammers :/ | 16:29 |
| Steel2 | I haven't really been hit with spammers. | 16:30 |
| Steel2 | russians who think I'm someone else, yes | 16:30 |
| katsmeow-afk | Steel2, it's also possible the person you are msging is simply too busy to chat one-on-one , or they believe your question should be in open channel where there's more minds to deal with it | 16:30 |
| Vicarious | yep | 16:30 |
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| Vicarious | Steel2: anyway, I closed the private message window already, what did you want to ask? | 16:34 |
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| Steel2 | I wrote out an idea for an experimental protocol for people with magnetic implants | 16:35 |
| Vicarious | ok | 16:36 |
| Steel2 | I was wondering if you were interested. | 16:37 |
| fenn | except the brain is not a uniform conductor | 16:38 |
| Steel2 | fenn: what? | 16:38 |
| Vicarious | a while ago I read a document "A Novel Human-Machine Interface using Subdermal Magnetic Implants", it involves an electromagnet | 16:38 |
| katsmeow-afk | magnetic implants where? to do what? | 16:38 |
| Steel2 | a number of people have fingertip magnetic implants, katsmeow-afk | 16:38 |
| Steel2 | so they can feel EM fields | 16:38 |
| Vicarious | do you have one, Steel2 ? | 16:39 |
| katsmeow-afk | i heard of that a couple yrs ago, yeas, seems silly | 16:39 |
| Steel2 | Vicarious: It's not practical for job reasons. | 16:39 |
| Vicarious | me neither.. mine isn't in the fingertip, it's under the skin in the back of my hand | 16:40 |
| katsmeow-afk | is it practical in any case? | 16:40 |
| Steel2 | do you want another sense? if yes, you can make it practical | 16:40 |
| Vicarious | yes, I can attach a throwie to the magnet :P | 16:40 |
| Steel2 | for instance, some people are hooking up ultrasonic rangers to finger tip implants | 16:40 |
| Steel2 | and they can 'feel' how far away walls are | 16:40 |
| katsmeow-afk | i'd be interested in RF fields, but my poorly designed neural system wouldn't pick up magnet vibrations that fast | 16:41 |
| Steel2 | anyway, I gotta go rewrite a bunch of this paper before my advisor rips my head off. | 16:41 |
| Steel2 | bbl. | 16:41 |
| Vicarious | hf | 16:41 |
| katsmeow-afk | "as your advisor, i advise you to do this before i rip your head off" | 16:43 |
| Vicarious | throwie = magnet + LED + battery, wrapped in tape | 16:44 |
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| A-Lusion | "For example, if the speed of thought could be increased a million-fold, a subjective year would pass in 30 physical seconds." | 17:56 |
| A-Lusion | Does anyone have any insight into this? | 17:56 |
| yashgaroth | seems pretty self-explanatory | 17:56 |
| A-Lusion | I guess so. | 17:57 |
| Urchin | I'm pretty sure that's what would happen, all else remaining the same | 17:57 |
| Urchin | I wouldn't count on more than 4 orders of magnitude increase, though | 17:57 |
| A-Lusion | Sorta like how Time is an illusion or how if one were to be under the influence of LSD 5 minutes could seem like an hour? | 17:57 |
| kanzure | A-Lusion: perception of time is a weird thing, for sure | 17:57 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/time-perception/ | 17:57 |
| Urchin | A-Lusion: no, it's like thinking all the thoughts of a year in 30 seconds | 17:58 |
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| Urchin | you'd end up being ancient very quickly | 17:58 |
| A-Lusion | mentally though yeah? | 17:58 |
| yashgaroth | I'd think the main problem would be going insane from boredom | 17:59 |
| Urchin | kind of like the 'Old One' in Vinge's 'A Fire Upon the Deep' | 17:59 |
| Urchin | note that the old one is a 10 year old | 18:00 |
| kanzure | A-Lusion: there was a paper discussed in here the other day about a patient with some brain trauma that caused him to not perceive time accurately for short durations | 18:00 |
| kanzure | yashgaroth: boredom is bullshit | 18:00 |
| kanzure | A-Lusion: i don't think a subjective year would pass in 30 deconds | 18:01 |
| kanzure | *seconds | 18:01 |
| A-Lusion | This idea of why time appears to speed up with age is depressing | 18:02 |
| kanzure | i don't think anyone has measured whether or not people accurately perceive a year or not | 18:02 |
| kanzure | A-Lusion: yeah there might be some chemical intervention that you can do there | 18:02 |
| yashgaroth | it appears to speed up because your memory gets worse | 18:02 |
| kanzure | yashgaroth: can you prove that | 18:03 |
| yashgaroth | you and your 'proof', pah | 18:03 |
| A-Lusion | lol | 18:03 |
| A-Lusion | I hope I don't become bitter with age | 18:03 |
| A-Lusion | Nor do I want to perceive the coming singularity as a race against time towards salvation of my own spirit | 18:04 |
| A-Lusion | I'd get deluded | 18:04 |
| lichen | its somewhat frightening to think that there's a chance our generation could just miss the breakeven point | 18:05 |
| lichen | which im sure explains a lot of the temporary strategies used by older transhumanists | 18:05 |
| lichen | intense vitamin regemins and such | 18:05 |
| yashgaroth | starving themselves to near-death | 18:05 |
| A-Lusion | I wanna know more about kurzweils vitamin diet lol | 18:06 |
| lichen | yeah | 18:06 |
| A-Lusion | He pops em like nothing. I'm only taking mostly essential things; multivitamin, fish oil, flaxseed oil, ginko, B's, ... n thats it i think | 18:07 |
| lichen | i take a multi vitamin and choline | 18:07 |
| lichen | sometimes some nootropics but i havent for a while | 18:08 |
| lichen | might be smart to use fish oil as well | 18:09 |
| Urchin | at least one singularity already happened | 18:09 |
| A-Lusion | So how abiding is research on long term effects for nootropics at the moment? | 18:09 |
| Urchin | back in 1930s | 18:09 |
| A-Lusion | Seems legit for a couple like pira and choline | 18:10 |
| kanzure | A-Lusion: spirit? what the hell is that | 18:10 |
| A-Lusion | good question | 18:10 |
| kanzure | A-Lusion: kurzweil's regiment is not exactly recommended | 18:10 |
| A-Lusion | Yeah well he's also much older than I. I've not heard of anyone else as exuberant about vitamins and supplements as he is | 18:11 |
| A-Lusion | Probably pretty costly too.. | 18:11 |
| lichen | ^ | 18:12 |
| lichen | big reason why i dont take a lot of vitamins | 18:12 |
| Urchin | I take some suplements | 18:12 |
| Urchin | mostly omega-3 | 18:12 |
| Urchin | though I take other stuff as needed | 18:13 |
| A-Lusion | I think a more effective and natural diet as well as exercise would accord better than making up for it with vitamins n supplements anyhow | 18:13 |
| A-Lusion | I'm in the process of loading up my mp3 with audiobooks for daily jogs just so I can make it a sorta mind and body crunch | 18:14 |
| Urchin | excercise has proven to be not so great as it's cracked up to be | 18:15 |
| A-Lusion | lol | 18:15 |
| Urchin | a lot better is a lifestyle that nudges you into some physical activity a lot | 18:15 |
| A-Lusion | I see what you mean, exercising for the sake of exercising is sort of a unfavorable yeah? | 18:17 |
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| Urchin | yes | 18:20 |
| Urchin | it does not work out in the long term | 18:20 |
| jrayhawk | The performance-equals-health mentality is problematic, and complete disregard for stimulus/response curves in excersize is really really problematic | 18:22 |
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| A-Lusion | hmm looks like I have the book (A Fire upon the Deep) | 18:25 |
| A-Lusion | :D | 18:25 |
| yashgaroth | it's good, I just read it a couple months ago in fact | 18:25 |
| yashgaroth | it's no deepness in the sky, but still | 18:25 |
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| Urchin | I've last read it about 6 years ago | 18:28 |
| strangewarp | A-Lusion: Have fun. Lovely story. Definite classic among classics | 18:29 |
| thylane | http://www.reddit.com/r/singularity/ | 18:29 |
| Urchin | it's one of the early treatments of singularity, actually (fire) | 18:29 |
| A-Lusion | I think fiction is more relative and honest than non fiction, especially in an era where ideas are just a matter of time and commitment | 18:30 |
| strangewarp | It does something clever so it can have a steady-state worldbuilding, even though there is crazy singularity stuff. Love the setting. [trying not to spoil anything] | 18:30 |
| Urchin | yes, it was a trick | 18:30 |
| Urchin | Lem's trick is also noteworthy | 18:30 |
| Urchin | and used by Orion's Arm | 18:31 |
| Urchin | pitty they stopped using creative commons | 18:31 |
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| kanzure | orion's arm is ok if you want worldbuilding | 18:32 |
| strangewarp | There is a sequel too, The Children of The Sky, and several more books planned in the series. CotS is good. I'm hoping Vinge wraps it all up with something crazy. | 18:33 |
| Urchin | I haven't read that one yet | 18:34 |
| Urchin | I've mostly read military sf for the last couple of years | 18:34 |
| A-Lusion | Is there an invention or some kind of gadget that you've found out in a science fiction novel that captured your imagination or gave a sorta incentive to make happen? | 18:34 |
| strangewarp | It's good, maybe a bit awkward in one or two places, but it's a middle book of a series so eh | 18:34 |
| Urchin | and I've also been a bit out of touch with transhumanism | 18:34 |
| A-Lusion | Or something that you DID make happen? | 18:34 |
| kanzure | A-Lusion: are you just asking what projects we work on in here? | 18:35 |
| A-Lusion | smaller more personal projects | 18:35 |
| Urchin | I've been thinking of making an eyetap for myself for a while now | 18:35 |
| Urchin | but never got around to it | 18:35 |
| A-Lusion | What's that? | 18:35 |
| kanzure | A-Lusion: ok do you want like a list? or what.. | 18:35 |
| thylane | http://www.reddit.com/r/singularity/ | 18:35 |
| strangewarp | I saw an unfilled niche in music-performance software in my imagination, and then I filled the niche with a modest but flexible script | 18:35 |
| strangewarp | bam | 18:35 |
| kanzure | thylane: stop repeating links :P | 18:35 |
| Urchin | http://en.wikipedia.org/wiki/Eyetap | 18:35 |
| A-Lusion | Lol do you keep a list? | 18:36 |
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| kanzure | A-Lusion: not of people's projects in here, but i could type one out real quick | 18:36 |
| kanzure | it would not be exhaustive | 18:36 |
| thylane | sorry thought I posted somethign else earlier | 18:36 |
| strangewarp | Dat reddit | 18:37 |
| A-Lusion | Ooh these things are already coming into existence ;D | 18:37 |
| Urchin | tunneling microscopy is interesting | 18:37 |
| strangewarp | "Should we re-engineer our species to save the planet?" Com on, think big. The answer is no. Instead: re-engineer the species AND the planet. :P | 18:37 |
| * Urchin is in favor of just leaving | 18:39 | |
| Urchin | earth's crust is resource poor if you really think about it | 18:39 |
| A-Lusion | ..ehh | 18:39 |
| Urchin | with O'Neill's old estimates it should be possible to make equivilent living space of 10000 Earth's surfaces from the material in the asteroid field alone (that's 1970s technology) | 18:40 |
| Urchin | *asteroid belt | 18:41 |
| A-Lusion | I'd be more concerned about the transition to a type 1 civilization. The rumor that the earth is getting crowded is absolutely false. Once a person can become completely self sufficient on any point on the planet | 18:42 |
| Urchin | I really should get some sleep | 18:42 |
| Vicarious | gn | 18:42 |
| A-Lusion | Then we can focus more on outter terrestrial travel | 18:42 |
| Urchin | a person can not be self-sufficient on any point of the planet right now | 18:42 |
| Urchin | I've looked into the logistics of it | 18:42 |
| A-Lusion | Yeah | 18:43 |
| A-Lusion | Exactly. | 18:43 |
| Urchin | I think it's better to simply leave for an environment where travel is easier | 18:43 |
| thylane | I can't imagine a singularity without some massive world war. My reasoning is that corporations will not be brought "quietly" out of their current models of exchange. | 18:43 |
| A-Lusion | Nah Earth is a great "tutorial" level | 18:43 |
| A-Lusion | If we can barely make it past that | 18:44 |
| Mariu | hey, Urchin ... you asked me what kind of bots I'm using on Undernet | 18:44 |
| Mariu | that would be: EnergyMech 2.9.3 | 18:44 |
| Mariu | I received some technical details about them | 18:44 |
| roksprok | so while we are on the subject of kind of out there stuff | 18:45 |
| Urchin | old school | 18:45 |
| roksprok | what does everyone think about this? | 18:45 |
| Urchin | written in C | 18:45 |
| Urchin | interesting | 18:45 |
| roksprok | http://pastebin.com/s7yUDJyF | 18:45 |
| Mariu | Maybe it will happen like in Deus Ex | 18:45 |
| roksprok | ^ idea of combining for-profit/non-profits | 18:45 |
| Mariu | Singularity witb start with the rise of Helios | 18:45 |
| Mariu | merging with a human being | 18:46 |
| strangewarp | lame | 18:46 |
| Mariu | =p | 18:46 |
| roksprok | steel2 i already told you this stuff | 18:46 |
| strangewarp | needs more dragons | 18:46 |
| Mariu | Helios is an AI | 18:46 |
| Mariu | by the way | 18:46 |
| Urchin | essentially you would be making a lab provider separate from the researchers | 18:47 |
| Urchin | lab for hire | 18:47 |
| Urchin | interesting notion | 18:47 |
| kanzure | roksprok: are you talking about an incubator? | 18:48 |
| roksprok | i thought people applied to incubators? | 18:48 |
| roksprok | this would more have its own research programs | 18:48 |
| kanzure | roksprok: i don't think grants are a good plan for a non-profit | 18:48 |
| kanzure | i mean, if you want to write lots of grant applications and hope-and-pray you get money.. that's cool i guess | 18:49 |
| roksprok | well it would be better than donations, right? | 18:49 |
| kanzure | donations are also lame unless you're getting >$100k donations | 18:49 |
| kanzure | well.. >$10k donations i guess | 18:49 |
| roksprok | i mean this would be to bootstrap it, once stuff started happening it would be funded with equity in its for-profit offshoots | 18:50 |
| roksprok | another source of funding is patent licensing | 18:50 |
| kanzure | i don't think patents are a good idea | 18:50 |
| Urchin | neither do I | 18:50 |
| kanzure | but yes you can sometimes make money on licensing | 18:50 |
| kanzure | in general people who want patents are against open source hardware | 18:51 |
| kanzure | although there are some people who want to do open hardware licenses on top of patents (which is sorta neat) | 18:51 |
| kanzure | anyway! i don't understand what your goal is | 18:51 |
| kanzure | is your goal to make money? | 18:51 |
| lichen | this is reminding me of that bit in accelerando | 18:51 |
| roksprok | no the goal is to be like the cure is now | 18:51 |
| kanzure | why | 18:51 |
| roksprok | except get stuff done | 18:51 |
| lichen | with self-replicating corporations switching ip with each other | 18:51 |
| kanzure | roksprok: thecureisnow is not something to model after :P | 18:52 |
| kanzure | roksprok: ok. so your goal is research? drug development? | 18:52 |
| lichen | you can always patent and then give the patents away for free | 18:52 |
| lichen | just to stop others from locking down the tech later | 18:52 |
| roksprok | well a way to fund directed research into the technologies we want to see come about | 18:52 |
| kanzure | ok... why don't you just work on those technologies instead | 18:53 |
| kanzure | i mean it sounds like you're going a really long round-about way | 18:53 |
| roksprok | money? | 18:53 |
| lichen | being able to live off of your work is nice | 18:53 |
| roksprok | and to get people to work on stuff with me? | 18:53 |
| kanzure | roksprok: "make an org to make orgs that may or may not go on to make the technology that you're wishing for" | 18:53 |
| kanzure | how about you just work on the tech instead :x | 18:53 |
| roksprok | because it costs money | 18:54 |
| roksprok | and i don't have money | 18:54 |
| kanzure | not as much money as you think | 18:54 |
| kanzure | most of the costs come from things like patents | 18:54 |
| lichen | and multi-thousand dollar technical and scientific equipment | 18:54 |
| kanzure | that's mostly overpriced stuff anyway | 18:54 |
| kanzure | if you're lean you can build something better or buy much cheaper | 18:55 |
| kanzure | like, just hire one guy to build your lab equipment.. you pay his salary (<$200k) instead of buying >$300k equipment | 18:55 |
| kanzure | (or you can just do it yourself of course) | 18:55 |
| roksprok | again, this costs money | 18:55 |
| Mariu | make a loan | 18:55 |
| Mariu | hire a manager, I don't know | 18:56 |
| kanzure | roksprok: is there any way i could convince you against grants? | 18:56 |
| kanzure | like if you want to write grant applications for me, that's great | 18:56 |
| kanzure | but iirc you're not a grant writer | 18:56 |
| lichen | heh | 18:56 |
| roksprok | actually you pretty much already have, i mean i agree they are about the worst source of funding | 18:56 |
| kanzure | ok.. pretend funding isn't a problem | 18:57 |
| kanzure | now work out an idea :) | 18:57 |
| roksprok | so should i just get a job to fund the stuff i want to do until i can get prototypes and convince people to work with me? | 18:57 |
| roksprok | ideas are one thing i am not short of | 18:57 |
| kanzure | what are you prototyping? | 18:57 |
| roksprok | a few things.... | 18:58 |
| lichen | pick one and finish it? | 18:58 |
| roksprok | wristband that stores your pulse | 18:58 |
| roksprok | remote control insects | 18:58 |
| kanzure | these things are pretty cheap to do | 18:58 |
| kanzure | well, depending on which insects | 18:59 |
| Mariu | Ladybirds | 18:59 |
| roksprok | ok, so i should get a job and work on this in my spare time? | 19:00 |
| jrayhawk | I thought we had remote control cockroaches already? | 19:00 |
| lichen | i think thats pretty much always a good idea unless youre loaded | 19:00 |
| roksprok | jrayhawk: they suck | 19:00 |
| roksprok | this is state of the art | 19:00 |
| kanzure | jrayhawk: yep.. and beetles and stuff. but i don't know if anyone has done it DIY yet. | 19:00 |
| roksprok | http://www.youtube.com/watch?v=zCK-mNqhx44 | 19:01 |
| kanzure | roksprok: you should always take care of your own financials first, always | 19:01 |
| roksprok | it is not remote control if you can just get it to 'move in a general leftish direction' | 19:01 |
| kanzure | but if you can coast for a while, maybe you should try to do a venture with a cofounder/investment | 19:01 |
| jrayhawk | huh, neat | 19:01 |
| kanzure | roksprok: i'm pretty sure the "general leftish direction" stuff was just "electrode sitting on the head" | 19:02 |
| kanzure | right? | 19:03 |
| roksprok | if its the one i'm thinking of they were stimulating the antennae | 19:03 |
| kanzure | ick | 19:03 |
| kanzure | that's cool but not sufficient | 19:03 |
| roksprok | which is basically slapping it in the face | 19:03 |
| kanzure | have you tried the electrode arrays? | 19:03 |
| roksprok | not successfully | 19:04 |
| roksprok | i was trying to get a recording from my nematodes | 19:04 |
| roksprok | but couldn't, so i'm back to the drawing board | 19:04 |
| kanzure | have you debugged it? | 19:04 |
| roksprok | no, it was way too simple to actually work | 19:05 |
| roksprok | so i'm reading up more on what filters i need | 19:05 |
| Mariu | http://farm1.staticflickr.com/113/314431413_e81bd1c829.jpg | 19:05 |
| yashgaroth | wait was that a pun | 19:05 |
| kanzure | nematode recording is a diyable thing.. maybe you should post up your setup to the diybio group | 19:06 |
| kanzure | or in here | 19:06 |
| kanzure | and we can help you debug things | 19:06 |
| kanzure | the backyardbrains people have been doing pretty good work with cockroaches | 19:06 |
| roksprok | i agree....i may just order one of their spikerboxes | 19:07 |
| kanzure | tim will have some ideas about a nematode setup | 19:07 |
| kanzure | i haven't done one :( | 19:07 |
| roksprok | actually i think that is what i will do, now that i think about it | 19:09 |
| roksprok | that way i at least have something to compare it too | 19:09 |
| roksprok | and the money will go to good people | 19:09 |
| kanzure | http://www.wormbook.org/chapters/www_intromethodsneurophys/intromethodsneurophys.html | 19:09 |
| kanzure | Neurophysiological methods in C. elegans: an introduction | 19:09 |
| kanzure | roksprok: what money? | 19:10 |
| roksprok | money to buy a spikerbox? | 19:10 |
| roksprok | i am not completely broke, i have a few grand, its just that that will last me for a few months of food/rent | 19:11 |
| roksprok | not leaving much to spend on projects | 19:11 |
| kanzure | how did you previously get money? | 19:11 |
| roksprok | my parents | 19:11 |
| roksprok | and i had a job a while ago | 19:12 |
| kanzure | and where are you? | 19:12 |
| roksprok | cincinnati, oh | 19:12 |
| kanzure | and do you do any software stuff | 19:12 |
| roksprok | i also have a place in chicago, il i can live in | 19:12 |
| roksprok | i am ok with access and just got through learn python the hard way | 19:13 |
| roksprok | so no | 19:13 |
| kanzure | lichen: you and roksprok should work on a project for ~20 days and then get overpaid at some job | 19:13 |
| kanzure | python is good enough :P | 19:13 |
| lichen | im in oregon | 19:13 |
| kanzure | doesn't matter | 19:13 |
| lichen | for software stuff yeah it doesnt matter | 19:13 |
| kanzure | the process works like this: | 19:13 |
| roksprok | lichen do you know python? | 19:13 |
| lichen | i can pick it up easily enough, but im mostly focused in c/c++ | 19:13 |
| kanzure | i suspect lichen would not have trouble with python since lichen knows asm/c | 19:13 |
| lichen | mhmm | 19:14 |
| roksprok | ok lichen is way beyond me then | 19:14 |
| kanzure | (1) pick some transhumanist-related project that you guys like | 19:14 |
| kanzure | (2) figure out some really great idea that would involve software | 19:14 |
| lichen | ive got a huge long term project in mind for myself | 19:14 |
| kanzure | (3) make the simplest, dumbest version (you'll hate this) | 19:14 |
| lichen | but if there's something smaller id be up for hearing it | 19:14 |
| kanzure | (4) code it in 20 days, slap it on a resume | 19:14 |
| lichen | easy enough to set up a github profile | 19:14 |
| kanzure | then you'd immediately qualify for those weird "minimum $50k/year" jobs that keep hiring for python people | 19:14 |
| lichen | and start working with other people | 19:14 |
| lichen | mhmm | 19:15 |
| kanzure | so, one of the projects i was working on with klafka was a nootropic price engine | 19:15 |
| kanzure | http://drugstack.com/ | 19:15 |
| kanzure | it scrapes nootropics data and the idea is to do price comparison shopping | 19:15 |
| lichen | neat | 19:15 |
| kanzure | but i never implemented the user-interfacing-search part o it | 19:15 |
| kanzure | *of it | 19:15 |
| lichen | nice customer quote, lol | 19:15 |
| kanzure | but it's just an example; you can see how that might be something that can be thrown together in 20 days | 19:15 |
| lichen | yeah | 19:16 |
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| kanzure | roksprok: would that be interesting to you? | 19:16 |
| kanzure | not that particular proj | 19:16 |
| roksprok | ok.....stupid ideas off the top of my head.... | 19:16 |
| kanzure | one site i've been wanting is a lab protocol beautifucation site | 19:17 |
| kanzure | *beautification | 19:17 |
| kanzure | because lab protocol docs look like ass.. i know they don't *need* to look good, but dam. | 19:17 |
| kanzure | *damn | 19:17 |
| roksprok | like putting them in standard format? | 19:17 |
| katsmeow-afk | irc spell checer! | 19:17 |
| katsmeow-afk | *checker | 19:17 |
| kanzure | in fact, just any generic lab protocol site.. to compete against protocol-online.org (which sucks) | 19:17 |
| kanzure | roksprok: sorta.. i would love it if there *could* be a standard format, but that's a challenging problem | 19:18 |
| kanzure | the "small" problems in lab protocols are aggregation, versioning, display, formatting.. representation is a huge unsolved problem | 19:18 |
| lichen | even better if you can make it community edited | 19:18 |
| kanzure | well, what you cuold also do to make money | 19:18 |
| kanzure | is set up one-click ordering of the reagents in the protocol | 19:19 |
| kanzure | instead of tracking things down on 10 or 20 sites | 19:19 |
| kanzure | because fuck that | 19:19 |
| katsmeow-afk | yeas, but once you have something set up, 50 people look at it, say it isn't needed, and you delete years of work | 19:20 |
| kanzure | i actually want that for electronics too- a more general "setup a bill of materials, and let people do one-click-ordering" - and have products from digikey, mouser, sparkfun, etc. | 19:20 |
| kanzure | katsmeow-afk: yeh so a wiki is obviously not the best format | 19:20 |
| katsmeow-afk | did that, i mined Mouser AND Digikey | 19:20 |
| kanzure | it would probably be more like "Fork this project" | 19:20 |
| kanzure | katsmeow-afk: ya but did you have one-click credit card ordering | 19:20 |
| katsmeow-afk | i scraped every product price datasheets | 19:20 |
| katsmeow-afk | nope, noone saw any point in it | 19:21 |
| kanzure | what i want is something like bit.ly/cockroach-control-kit and type in my card, and get an entire backyards brain kit | 19:21 |
| lichen | make it as easy as possible for average joe to get into science | 19:21 |
| kanzure | what does "get into" mean | 19:21 |
| lichen | without needing to spend weeks researching whats the cheapest and what works | 19:21 |
| kanzure | oh you mean for kits | 19:21 |
| kanzure | ok yeah | 19:21 |
| lichen | somebody with an interest but not the time | 19:21 |
| thylane | http://i.imgur.com/e4jIu.jpg | 19:21 |
| lichen | not the time to sit around researching brands and sites | 19:22 |
| roksprok | kanzure, why wouldn't you just go to backyard brains and order the kit? | 19:23 |
| kanzure | thylane: is that supposed to be funny? or informational? | 19:23 |
| kanzure | roksprok: bad example :) | 19:23 |
| thylane | kanzure I thought it was funny. | 19:23 |
| roksprok | would instructables be a better example | 19:23 |
| thylane | kanzure why are you always so gruff? | 19:23 |
| roksprok | ' | 19:23 |
| kanzure | roksprok: there's lots of electronics projects that don't have selling kits yet | 19:23 |
| roksprok | like order the parts for this instructable? | 19:23 |
| kanzure | thylane: i was honestly wondering. i know now that you found it funny | 19:23 |
| kanzure | roksprok: right.. | 19:23 |
| kanzure | roksprok: and people would be incentivized to use this service, because the person who "writes the kit" gets a % commission or something (who knows) | 19:24 |
| katsmeow-afk | ok, so i wasted my time gathing the data from Mouser, Digikey, Newark, and 100 oems of electronics products | 19:24 |
| roksprok | could it just be built with stuff like open protocols and instructables? | 19:24 |
| kanzure | katsmeow-afk: could i have the data? | 19:24 |
| kanzure | roksprok: what is "open protocols"? | 19:24 |
| kanzure | roksprok: instructables does not always list product IDs | 19:25 |
| katsmeow-afk | it's useless, why could i be bothered to send it to you? | 19:25 |
| kanzure | katsmeow-afk: because i'll have to write the scrapers myself eventually | 19:25 |
| katsmeow-afk | or employ me | 19:25 |
| roksprok | wasn't there some community protocol thing? | 19:25 |
| kanzure | katsmeow-afk: i think it's cheaper for me to just write the scrapers | 19:25 |
| katsmeow-afk | k, have fun | 19:25 |
| kanzure | roksprok: no openprotocols.net was just someone making a pitch, apparently | 19:25 |
| roksprok | well like the protocols online site then | 19:25 |
| kanzure | it's old and busted | 19:25 |
| kanzure | that dataset needs to be scraped and liberated | 19:26 |
| kanzure | actually, i think i have a copy on my server.. one sec | 19:26 |
| roksprok | maybe have it so you find a protocol/thing you like, type in oursite.com/whatever-is-after-the-domain-name | 19:26 |
| kanzure | damn. i do not have a copy online. i'd have to upload it. | 19:26 |
| roksprok | and you get reviews, order-stuff-now, and discussion about it | 19:27 |
| roksprok | and if it was an instructable that didn't have part numbers there would be some 'warning: no part numbers were given, these are our best guesses' | 19:27 |
| kanzure | protocol-online.org is surely not the best that our civilization can come up with | 19:27 |
| kanzure | i'm sorry, are you talking about scraping things from instructables.com? | 19:28 |
| roksprok | yes | 19:28 |
| kanzure | the people (eric meltzer, etc.) behind openprotocols.net were trying to make a social network around protocols | 19:28 |
| roksprok | as opposed to having an empty site | 19:28 |
| kanzure | i didn't really understand what their strategy was | 19:28 |
| lichen | apparently they never included a designer on their team | 19:29 |
| kanzure | http://news.ycombinator.com/item?id=2191105 | 19:29 |
| lichen | wait no, thinking of that other site you mentioned | 19:29 |
| kanzure | also, the diybio group commented on their openprotocols.net project http://groups.google.com/group/diybio/browse_thread/thread/19df187ef1014735 | 19:29 |
| kanzure | apparently they did not have a programmer among themselves :rolleyes: | 19:29 |
| lichen | fuuuuck | 19:30 |
| lichen | how do you get into tech and not have an overabundance of programmers | 19:30 |
| kanzure | if you are a programmer, why would you want to give 50% of your venture to someone who hasn't bothered to learn to code? | 19:30 |
| lichen | haha, true | 19:30 |
| kanzure | "The API for Biocoder feels all wrong for numerous reasons; on top of that, nobody is going to learn a new API, library or programming language just to write down a protocol, unless they are being paid, or there's some really compelling reason to do so (which, there isn't)." | 19:30 |
| katsmeow-afk | i just demo'd that to you, i did work as a programmer, i amd my work are worthless | 19:30 |
| kanzure | "Without something changing here, you just end up with a giant corpus of protocols like we presently have, without metadata and basically useless unless you already know what you want or need, or have the time to manually check and double check everything in each protocol you might be using." | 19:30 |
| kanzure | katsmeow-afk: i had to write off your work because you are unwilling to share it or use it or show it | 19:31 |
| kanzure | so basically i will pretend like it does not exist. | 19:31 |
| katsmeow-afk | you had already said it was worthless | 19:31 |
| kanzure | your scrapers? | 19:32 |
| * katsmeow-afk nods | 19:32 | |
| kanzure | can you show it to me | 19:32 |
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| kanzure | lichen: you might be interested in jonathan's work on parsing english-written protocols | 19:32 |
| kanzure | lichen: http://88proof.com/synthetic_biology/blog/archives/290 | 19:32 |
| kanzure | Juul: i am trying to hook lichen+roksprok up on some 20-day-web-project idea | 19:32 |
| lichen | interesting | 19:33 |
| katsmeow-afk | i need to ask why i would bother to show you, vs deleting it | 19:33 |
| kanzure | katsmeow-afk: well, if you wanted to save me the time of writing those scrapers in the future | 19:33 |
| katsmeow-afk | near as i can tell, i wasted my time gathering it, and don't want to waste any more time on it | 19:33 |
| kanzure | Juul: so far i've suggested a lab protocol site to modernize protocol-online.org | 19:33 |
| Juul | kanzure, i approve this project | 19:33 |
| katsmeow-afk | kanzure, anyone can write a scraper, i am willing to use them and provide the data in exchange for some renumeration | 19:34 |
| kanzure | katsmeow-afk: it would be faster for me to write it than continue to argue with you about it :( | 19:34 |
| katsmeow-afk | *remuneration | 19:34 |
| katsmeow-afk | ok | 19:34 |
| katsmeow-afk | i can delete it all | 19:35 |
| kanzure | that's a horrible negotiation tactic | 19:35 |
| lichen | im not even sure what the argument here is | 19:35 |
| katsmeow-afk | i wasn't negotiating | 19:35 |
| kanzure | lichen: katsmeow has a scraper for digikey+mouser | 19:36 |
| kanzure | and she doesn't want to share | 19:36 |
| lichen | so? | 19:36 |
| katsmeow-afk | because it isn't worth it, you said so | 19:36 |
| roksprok | ok....i am going to think about this for tonight and do some napkin-sketches of the site that i will show tomorrow.... | 19:36 |
| kanzure | lichen: yeah.. so there's no problem :) | 19:36 |
| lichen | heh | 19:36 |
| * Juul breaks out into a rendition of the Free Software Song | 19:36 | |
| Juul | come on now and, share the soooftware | 19:36 |
| kanzure | Juul: what would you want on a modernized protocol site | 19:36 |
| Juul | you'll be free hackers, you'll be free | 19:36 |
| kanzure | protocol-online.org is just old as shit | 19:37 |
| kanzure | and, let's not worry about it making money | 19:37 |
| katsmeow-afk | Juul, i had already given it to others, my point is he said it was worthless, so it's not worth me sending it to anyone else | 19:37 |
| roksprok | would you be interested in this lichen? i'm just going to be upfront in saying i am a noob and will be very slow, but i am willing to put in the work | 19:37 |
| lichen | depends on the idea | 19:37 |
| lichen | im also getting kind of a full plate as it were | 19:37 |
| kanzure | ah i thought you were looking for ideas lichen | 19:37 |
| lichen | job hunting and possibly doing freelance work for somebody (which seems to be falling through) | 19:38 |
| lichen | ive got ideas of my own | 19:38 |
| lichen | but if working with roksprok | 19:38 |
| kanzure | always assume reelancing work will fall through uless you are holding the check in your hand | 19:38 |
| lichen | im saying whether i help or not depends on how feasible it really is | 19:38 |
| lichen | exactly kanzure | 19:38 |
| kanzure | well i think the most basic thing would be: | 19:38 |
| roksprok | ok, well there are coders galore in here, i think i will still do some branstorming and mockups if only to motivate myself to learn to code well enough to get it built | 19:38 |
| kanzure | ask me for my scraped version of protocol-online.org | 19:38 |
| kanzure | i'll upload it tonight when i find it | 19:39 |
| kanzure | then: figure out what to do with this data on a site | 19:39 |
| lichen | just trying to pretty up what they have? | 19:39 |
| kanzure | "just displaying it" might be sufficient yes | 19:39 |
| kanzure | yeah i mean.. protocol-online.org is *crap* | 19:39 |
| kanzure | but then there's all sorts of features that you can imagine, like uh.. tagging | 19:39 |
| roksprok | they already display it don't they? | 19:40 |
| lichen | its readable and usable in a very 1994 way | 19:40 |
| kanzure | tagging, aggregating, one-click kits, etc. | 19:40 |
| kanzure | roksprok: they actually link over to a pdf most of the time | 19:40 |
| lichen | but not a very 2012 way | 19:40 |
| kanzure | ike a cached copy | 19:40 |
| kanzure | *like | 19:40 |
| kanzure | and it's definitely not mobile friendly | 19:40 |
| kanzure | and i don't know /anyone/ who has ever contributed a protocol to that site | 19:40 |
| lichen | lack of publicity or lack of features and usability? | 19:41 |
| kanzure | everyone knows about it | 19:41 |
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| Juul | hm, I guess I'd like some DIY-friendliness, and more collaboration, where people can add variations of parts of a protocol or the whole, and suitable (cheap) replacements for instruments and materials. Information about the policies of companies selling materials on dealing with private groups / individuals. List of labs and DIY people willing to help you out when it comes to getting specific strains / materials. | 19:41 |
| kanzure | Juul: how about "example graphs" and example data | 19:41 |
| roksprok | so a general format/font/display style? | 19:41 |
| kanzure | roksprok: well, having the same representation for everything would be fantastic | 19:41 |
| roksprok | is that what you mean by displaying it | 19:41 |
| Juul | kanzure, that would rock | 19:41 |
| kanzure | yeah | 19:41 |
| kanzure | Juul: and how about one-click ordering of the reagents | 19:41 |
| Juul | haha | 19:42 |
| kanzure | c'mon gotta dream big | 19:42 |
| Juul | cat walks on keyboard --> FBI watchlist :P | 19:42 |
| kanzure | i would also like to do comparative pricing on reagents.. but that's not protocol-oriented necessarily | 19:42 |
| roksprok | does protocols online scrape stuff or is it all submitted? | 19:43 |
| Juul | one of us needs to do a sparkfun for diybio | 19:43 |
| Juul | i don't really think the market is there yet | 19:43 |
| Juul | but still | 19:43 |
| kanzure | Juul: i don't think the market is diybio necessarily | 19:43 |
| Juul | oh? what then? | 19:43 |
| roksprok | does anyone work in an academic lab? how do you all find protocols anyway? | 19:44 |
| kanzure | hm? i just mean diybio is not the main buyers of reagents | 19:44 |
| Juul | ah yes | 19:44 |
| Juul | this is true | 19:44 |
| kanzure | roksprok: you are usually given the protocols as a hand-me-down | 19:44 |
| kanzure | or you read them in a protocol chronology.. like springer protocols | 19:44 |
| Juul | usually the first one though | 19:44 |
| roksprok | is this system really in need of improvement for researchers? | 19:45 |
| Juul | or you go talk to someone who has actually done it before | 19:45 |
| kanzure | "ah yeah man just trust me. 10X PE here" | 19:45 |
| Juul | if no-one in your lab has the expertise | 19:45 |
| roksprok | like if you are ordering thousands of dollars of reagants you probably have a pretty good science-social-network | 19:45 |
| Juul | it's like a combination of cooking recipes and superstition | 19:45 |
| yashgaroth | ^ | 19:45 |
| kanzure | you will not be implementing the ordering stuff in 20 days | 19:45 |
| kanzure | (1) yes it is needed | 19:45 |
| kanzure | (2) even if it wasn't... the idea is to make a site in 20 days to put on your resume | 19:46 |
| kanzure | and this idea just so happens to be something that interests you | 19:46 |
| roksprok | will that really get me a coding job? | 19:47 |
| katsmeow-afk | no | 19:47 |
| kanzure | haha katsmeow is just angry | 19:47 |
| lichen | being smart, adaptable and experienced | 19:47 |
| lichen | will get you a coding job | 19:47 |
| lichen | step one is actually knowing how to code | 19:47 |
| kanzure | if you're willing to move, and have a shiny project like this on your portfolio using python/django, yes you can get hired | 19:47 |
| Juul | (or rails, don't forget the rails!) | 19:48 |
| kanzure | he knows python | 19:48 |
| Juul | oh | 19:48 |
| kanzure | yeh i wouldn't suggest django if he knew ruby | 19:48 |
| lichen | i should probably teach myself ruby and python and java | 19:48 |
| lichen | just havent had a good enough reason to yet | 19:48 |
| Juul | lichen, what do you know now? | 19:48 |
| roksprok | is there not a glut of ruby on rails people? | 19:48 |
| lichen | c/c++/asm | 19:48 |
| kanzure | roksprok: SF is unable to hire fast enough | 19:49 |
| kanzure | they are so hurting for any rails people | 19:49 |
| Juul | i agree with kanzure | 19:49 |
| kanzure | as long as you are reasonably not an idiot | 19:49 |
| kanzure | which.. by what i know of you.. you are not a total idiot | 19:49 |
| kanzure | but i haven't seen your code yet :) | 19:49 |
| Juul | lichen, ah :-) | 19:50 |
| lichen | ive very little experience in web development (other than crap html/css in college) | 19:51 |
| lichen | mostly just in desktop application development | 19:51 |
| Juul | honestly, web dev takes a long time to learn | 19:51 |
| lichen | but i should probably learn web dev languages to be more flexible | 19:51 |
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| Juul | especially if you want to be decent at both back-end and front-end | 19:51 |
| lichen | yeah | 19:51 |
| lichen | there's a lot to it | 19:51 |
| Juul | ayup | 19:52 |
| kanzure | lots of us in here can help you with those parts | 19:52 |
| kanzure | Juul: you know, it would be cool if there's an algorithmic way you could make the protocol site remove superstition from protocols | 19:52 |
| kanzure | Juul: i'm sure many common protocols are not 100% optimized | 19:52 |
| roksprok | ok, well i suppose i will get started then, but if anyone knows anyone in chicago who needs a cheap lab tech i would like to have a job | 19:53 |
| lichen | superstition in protocols? lol | 19:53 |
| lichen | step 4: pray that the lab works | 19:53 |
| kanzure | lichen: yeah, "this is the protocol. you do not vary from the protocol." is very common | 19:53 |
| kanzure | no you have no idea | 19:53 |
| Juul | kanzure, haha yeah it would be. i think people find something that works for them and then stop optimizing. why waste time fixing something that works (especially when the compile-time is so slow) | 19:53 |
| kanzure | it is very difficult to debug protocols | 19:53 |
| lichen | oh | 19:53 |
| kanzure | you spend *years* debugging sometimes | 19:53 |
| kanzure | like.. "oh you mean i accidentally breathed into the microtube that first time? FUCK" | 19:53 |
| yashgaroth | roksprok: like bio lab tech? there's no biotech in chicago | 19:54 |
| kanzure | or "you mean the pipettte tip was not supposed to hit the side of the tube? FUCK" | 19:54 |
| kanzure | roksprok: btw, there's the chicago open science group that has recently started | 19:54 |
| roksprok | yashgaroth: honestly any lab tech | 19:54 |
| kanzure | they don't have a lab space yet but they meet regularly | 19:54 |
| kanzure | ben hyink and a few others | 19:54 |
| yashgaroth | my company lost probably a million dollars because one protocol got miswrote and no one noticed for months | 19:54 |
| roksprok | they are getting lab space in ps1 | 19:54 |
| kanzure | yashgaroth: tell it like a story | 19:54 |
| kanzure | when i was in sf recently someone pitched me on their company.. they were selling software for checklists | 19:55 |
| kanzure | so for any company that has a checklist or process.. the idea is to just let employees check shit off | 19:55 |
| yashgaroth | um someone wrote 10x instead of 1x and the rest is history | 19:55 |
| kanzure | very simple concept and laughable.. but checking things off matters on the lab bench | 19:55 |
| kanzure | otherwise you will screw up a step and forget if you just pipetted or not | 19:56 |
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| kanzure | yashgaroth: why a few mil? | 19:56 |
| kanzure | roksprok: ok just making sure you know them.. | 19:57 |
| yashgaroth | because all the panning relied on the boiled casein being made correctly, idk the details, it happened in the mol bio department, not our superior biochem department | 19:57 |
| yashgaroth | a mil in time, not physical buffer-making costs | 19:57 |
| roksprok | thanks kanz, i was actually emailing a tiny bit with them but stopped after my uni account got cut off | 19:57 |
| roksprok | ben is a organizational machine | 19:57 |
| roksprok | pretty impressive actualy | 19:57 |
| yashgaroth | our place costs 30k a day to run, and it's only two dozen people | 19:58 |
| Juul | maybe i've asked this before, but does anyone know if there are any efforts to make vegan casein? | 19:58 |
| Juul | it might be a fun little diybio project if not | 19:58 |
| yashgaroth | easier than vegan FBS | 19:58 |
| kanzure | yashgaroth: so $1k/person-day | 19:59 |
| kanzure | or are you talking about material cost | 19:59 |
| yashgaroth | yep, although that includes our hugely useful VPs | 19:59 |
| yashgaroth | that's for everything; labspace, salaries, reagents | 19:59 |
| kanzure | all hail upper management | 19:59 |
| yashgaroth | though tbh I use more than $1k in reagents per day, even on a slow day | 20:00 |
| Juul | i want vegan gouda | 20:00 |
| kanzure | high throughput? | 20:00 |
| yashgaroth | medium-throughput, everything just costs a lot when it's all single-use | 20:00 |
| yashgaroth | we don't re-use pipette tips, unlike some unnamed academic labs | 20:00 |
| Juul | single-use lab assistants | 20:00 |
| Juul | those are expensive | 20:01 |
| yashgaroth | disposal for lab assistants is what gets you | 20:01 |
| yashgaroth | can't shove more than 3 into a biohazard bin, I've tried | 20:01 |
| lichen | meh, thats what coffee shops are for | 20:01 |
| lichen | all those grad students gotta work somewhere | 20:02 |
| Juul | damn | 20:04 |
| Juul | i had coffee today | 20:04 |
| Juul | i never have coffee | 20:04 |
| Juul | i feel like i'm on drugs | 20:04 |
| A-Lusion | > drinking coffee right now :D | 20:04 |
| roksprok | where do you work yash? | 20:04 |
| yashgaroth | startup in san diego | 20:04 |
| Juul | yashgaroth, i've heard conflicting stories about whether or not SD has a hackerspace | 20:05 |
| Juul | can you enlighten? | 20:05 |
| yashgaroth | it doth not, that I know of | 20:05 |
| yashgaroth | maybe for electrical stuff, but who cares about that | 20:05 |
| lichen | thats because you are on drugs | 20:06 |
| lichen | caffeine is pretty strong provided youre not addicted to it | 20:06 |
| Juul | yes. this is why I don't use caffeine on a regular basis | 20:08 |
| Juul | so i can have an effect when i need it | 20:09 |
| Juul | but i definitely overdid it today | 20:09 |
| A-Lusion | pshh | 20:09 |
| strangewarp | Yuck, one of my other venues is infested with a crazy survivalist/Gottendammerung literalist, who shames women for enjoying sex, and drives down levels of conversation and then complains that the venue is dying | 20:14 |
| lichen | the fuck? | 20:14 |
| A-Lusion | lol | 20:14 |
| A-Lusion | what a list of woes | 20:14 |
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| lichen | fucking misogynists | 20:15 |
| lichen | makes me afraid to enter the software industry | 20:15 |
| lichen | since its rather notorious for that | 20:15 |
| roksprok | anyone have suggestions for a free website mockup tool? | 20:45 |
| Juul | lichen, yeah it's pretty bad | 20:47 |
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| kanzure | for some reason my grandmother is in town | 20:49 |
| kanzure | and she somehow got a glimpse of my screen | 20:50 |
| kanzure | "what's a fucking misogynist?" | 20:50 |
| nsh_ | lol | 20:50 |
| nsh_ | what did she see? | 20:50 |
| kanzure | nsh_: just some backlog in here (see the logs) | 20:50 |
| kanzure | roksprok: depends on what you want to mock up.. most people just use html/css to do rapid prototyping, but some people use mockingbird or balismiq or whatever | 20:51 |
| kanzure | win 4 | 20:51 |
| kanzure | oops.. ignore that | 20:51 |
| nsh_ | ah | 20:52 |
| Juul | i like pen and paper | 20:52 |
| Juul | or whiteboards and cameraphones | 20:52 |
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| nsh_ | also, what's a Gottendammerung literalist? | 20:57 |
| nsh_ | ( strangewarp ) | 20:58 |
| strangewarp | Sorry, exotic term. | 20:58 |
| kanzure | Juul: or.. just steal this part and move on, and replace it when you need to | 20:58 |
| strangewarp | Person who believes that Gottendammerung, the twilight of the icons; AKA the cosmology where everything is inevitably worse than things were in the past, is literally true. | 20:59 |
| kanzure | someone was asking about automated protocols on diybio a few minutes ago.. | 20:59 |
| kanzure | https://groups.google.com/forum/?fromgroups#!topic/diybio/Zlyv0fYKsbs | 20:59 |
| Juul | kanzure, hm yeah I guess. I often find it difficult to do that with HTML/CSS though | 20:59 |
| kanzure | er i mean | 20:59 |
| kanzure | https://groups.google.com/group/diybio/browse_thread/thread/665cafd1f60ab1bb | 20:59 |
| kanzure | Juul: copying other people's work? very easy to do | 20:59 |
| kanzure | esp. with css.. just redo the styles on your page with whatever you want to change it to later | 21:00 |
| kanzure | in the mean time you have something that looks ok | 21:00 |
| nsh_ | strangewarp: heh thanks | 21:00 |
| strangewarp | np | 21:01 |
| Juul | hmm | 21:02 |
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| roksprok | y don't you like biocoder kanzure? | 21:03 |
| kanzure | roksprok: have you seen the api :( | 21:03 |
| nsh_ | i think "the Gottendammerung gradient" is a good term for something i've experienced from time to time in altered states of consciousness | 21:03 |
| kanzure | they provide a C++ SDK that you write in | 21:03 |
| kanzure | they make fluid transfer the same thing as calling a function?? | 21:03 |
| kanzure | a fluid transfer operation should not be written out as move_liquid_to_vile_with_number(5) | 21:04 |
| kanzure | that's just wrong on so many levels :( | 21:04 |
| katsmeow-afk | vial | 21:04 |
| kanzure | it's a vile vial >:( | 21:04 |
| katsmeow-afk | o | 21:04 |
| kanzure | hee | 21:04 |
| nsh_ | fluid transfer is a method of the lab assistant instance | 21:04 |
| kanzure | nope not in biocoder | 21:05 |
| kanzure | it's a global namespace method | 21:05 |
| kanzure | bleh | 21:05 |
| nsh_ | pfft# | 21:05 |
| roksprok | do you want something with an api for protocols? or would merely typing it out be ok | 21:05 |
| kanzure | a representation format for protocols is very important to me | 21:05 |
| kanzure | i tried to do xml but i don't think it works | 21:06 |
| kanzure | http://diyhpl.us/~bryan/irc/pcr.xml | 21:06 |
| kanzure | those <step>s are just english :/ | 21:07 |
| kanzure | but the other metadata is useful | 21:07 |
| kanzure | i don't know how a good way to break down step-based planning into a representation format that is (A) easy to read/write for humans and (B) easy to parse | 21:08 |
| kanzure | this is why jonathan cline just resorted to parsing english-based protocols (but i don't think the mapping is guaranteed.. i dunno) | 21:08 |
| kanzure | http://88proof.com/synthetic_biology/blog/archives/290 | 21:08 |
| kanzure | "Wait a minute! Isn’t that what robots are for? Unfortunately, programming a bioscience robot to do a task might take half a day or a full day (or more, if it hasn’t been calibrated recently, or needs some equipment moved around). " | 21:09 |
| kanzure | " If this task has to be performed 100 or 10,000 times then it is a good idea to use a robot. If it only has to be done twice or 10 times, it may be more trouble than it’s worth. Is there a middle ground here?" | 21:09 |
| kanzure | "If regular English-language biology protocols could be fed directly into a machine, and the machine could learn what to do on it’s own, wouldn’t that be great? What if these biology protocols could be downloaded from the web, from a site like protocol-online.org ? " | 21:09 |
| kanzure | " It’s possible! (Within the limited range of tasks that are required in a biology lab, and the limited range of language expected in a biology protocol.)" | 21:09 |
| kanzure | "The point of this prototype project is this: there are thousands of biology protocols in existence, and biologists won’t quickly transition to learning enough engineering to write automated language themselves (and it is also more effort than should be necessary to use a “easy-to-use GUI” for training a robot)." | 21:09 |
| strangewarp | It's possible! (within limits) | 21:09 |
| strangewarp | I love it :p | 21:09 |
| kanzure | "The computer itself should be used to bridge the language gap. Microfluidics automation platforms (Lab on Chip) may be able to carry out the bulk of busy work without excessive “training” required." | 21:09 |
| kanzure | "It's possible! For varying definitions of possible." | 21:09 |
| Juul | wasn't this exact thinking what lead us to COBOL ? | 21:10 |
| strangewarp | Oh christ, don't mention COBOL around my mom, it gives her flashbacks | 21:11 |
| kanzure | i am not sure if english-based parsing is the best we can do... i would prefer some way where we can clearly write out, in a parsable way, exactly what is supposed to happen. protocols are currently not that.. | 21:11 |
| Juul | one of my friends had to learn it last year | 21:11 |
| Juul | _last_ _year_ | 21:11 |
| katsmeow-afk | i could have sworn there was a chemistry translator to take written instructions and apply some 500 scripts to it, and churn out equations and such | 21:11 |
| kanzure | it might be possible to parse english-based protocols *initially* and then do clean-up in whatever better format | 21:11 |
| kanzure | katsmeow-afk: sure.. but equations isn't necessarily the same thing as "Run this bunsen burner on this particular glassware for 40 hours at 2 mL/hr" | 21:12 |
| Juul | yes, but there is the danger of running into the Commodore 128 problem | 21:12 |
| katsmeow-afk | kanzure, right, it displayed a little "add heat for 2 hrs here" in the equation | 21:13 |
| katsmeow-afk | the Commodore 128 problem? | 21:13 |
| Juul | The Commodore 128 had a switch to make it run in Commodore 64 mode, which meant it became a Commodore 64. Almost no-one invested the extra effort to make Commodore 128 programs, since they could just make Commodore 64 programs and everyone would be able to run them. | 21:13 |
| katsmeow-afk | shame, that | 21:14 |
| kanzure | well nobody has an incentive to write lab protocols in a computational format | 21:14 |
| Juul | kanzure, they do but they don't know that they do! | 21:14 |
| kanzure | what is the incentive? | 21:14 |
| Juul | if they already had all of their protocols in a machine-readable standard format, then going from "one person manually running the protocol" to "robot running it for you" would nearly be reduced to loading the chemicals in the machine | 21:15 |
| kanzure | they don't have robots either ;) they have students | 21:15 |
| Juul | hah | 21:15 |
| Juul | well, maybe they biofab had a unique problem there | 21:15 |
| kanzure | i agree that going from protocols to a microfluidic circuit would be fantastic | 21:15 |
| kanzure | and i also agree it's possible | 21:15 |
| Juul | "Go away, or I will replace you with a very small microfluidics device." ? | 21:16 |
| kanzure | but let's- for a moment- assume that protocols (for some reason) need to be digitized first before that happens | 21:16 |
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| kanzure | what incentives are there for digitization other than automation? | 21:16 |
| Juul | https://www.thinkgeek.com/tshirts-apparel/unisex/frustrations/374d/ | 21:16 |
| nsh_ | kanzure: digitisation of protocols allows for efficient archival, categorisation and analysis | 21:17 |
| kanzure | Juul: i messed up and accidentally replaced /myself/ with a small shell script | 21:17 |
| Juul | kanzure, management, and easier ordering. e.g. "we need to run this experiment 96 times" and the app tells you exactly how much of each reagent you will need | 21:17 |
| nsh_ | new protocols could be inferred from existing ones automatically | 21:17 |
| kanzure | Juul: 96 times just means multiplication | 21:17 |
| Juul | yes | 21:18 |
| kanzure | i do think that data analysis is an interesting idea | 21:18 |
| kanzure | like store graphs and charts that people have collected | 21:18 |
| kanzure | each protocol should come with debugging steps and software to analyze results | 21:18 |
| Juul | kanzure, damn, you made the mistake of implementing a shell-script-implementing shell script | 21:18 |
| Juul | never do that | 21:18 |
| nsh_ | they could also be comparatively assessed | 21:18 |
| nsh_ | and "evolved" | 21:18 |
| kanzure | so you could imagine some standard protocol debugging library that runs through "typical debugging steps necessary for when you are pipetting" | 21:18 |
| nsh_ | on the basis of metrics applied formally | 21:18 |
| kanzure | nsh_: that's a neat concept, but not something that would incite this to happen :P | 21:19 |
| nsh_ | :) | 21:19 |
| nsh_ | why encourage people to do with neat concepts when you have a large stick with nails poking out | 21:19 |
| nsh_ | *do things with | 21:19 |
| kanzure | huh? | 21:20 |
| kanzure | i mean, let's say you type up 200 protocols for me | 21:20 |
| Juul | kanzure, hm yes, that would be useful mostly for people without a lot of experience though wouldn't it | 21:20 |
| kanzure | what are you going to do now? | 21:20 |
| Juul | we need to target the wet-lab guys who are entrenched in their ways | 21:20 |
| Juul | somehow | 21:20 |
| kanzure | i don't understand what this provides them | 21:20 |
| kanzure | (until you get the microfluidics automation; i don't think this helps other types of automation) | 21:20 |
| * nsh_ shrugs | 21:20 | |
| nsh_ | automation is just one benefit. standardisation and interoperability are others | 21:21 |
| kanzure | standardization of protocols? | 21:21 |
| nsh_ | standardisation of the execution of protocols | 21:21 |
| Juul | i'm not sure we're quite ready for standardization of protocols | 21:21 |
| kanzure | some protocols are meant to be versioned differently | 21:22 |
| * nsh_ nods | 21:22 | |
| kanzure | ok i have found my 169 MB copy of protocol-online | 21:22 |
| yashgaroth | gimme | 21:23 |
| kanzure | um | 21:23 |
| yashgaroth | *please | 21:23 |
| kanzure | i am trying to figure out wtf i have | 21:24 |
| roksprok | do people use protocol online? | 21:24 |
| kanzure | yes | 21:25 |
| kanzure | kanzure@pikachu:/mnt/externia/backups/davinci/home/bryan/cache/protocol-online/www.protocol-online.org/ | 21:25 |
| kanzure | protocol-cache.zip prot.zip all_view_cache_links.txt cat-all.sh files.sh full-library.txt library-of-protocols.txt links_cgi.txt linkex.pl links.txt list-of-files parsed.txt yet-another2.txt yet-another-library-of-protocols.txt | 21:26 |
| kanzure | oh god this was from before i took care of my filenames | 21:26 |
| kanzure | and from when i was using.. perl.. to do scraping. yikes | 21:27 |
| Juul | /this/is/the/directory/that/never/ends/yes/it/goes/on/and/on/again/some/people/started/a/bash/script/without/rtfm/and/it/continues/mkdir-ing/forever/just/because/ | 21:28 |
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| kanzure | Juul: hey some of that path was legit | 21:28 |
| Juul | :) | 21:29 |
| kanzure | ok so first i'll upload this 2.3 MB zip file.. looks like it has some weird perl and just basic index html files (not the actual content) | 21:30 |
| kanzure | http://diyhpl.us/~bryan/irc/protocol-online/prot | 21:31 |
| kanzure | this does not look particularly useful | 21:31 |
| kanzure | zip file is in parent | 21:31 |
| kanzure | here's all their outgoing links http://diyhpl.us/~bryan/irc/protocol-online/links_cgi.txt | 21:32 |
| kanzure | it will be a while for the 150+ MB file to upload (capped upload speed) | 21:33 |
| nsh_ | that list would be more useful if you resolved the urls | 21:35 |
| yashgaroth | that includes the scraped outgoing link files? | 21:35 |
| kanzure | the uploading file has the .docs and .pds and shit | 21:35 |
| kanzure | *.pdfs | 21:35 |
| kanzure | nsh_: yeah i was pretty stupid | 21:35 |
| kanzure | one of the file is a mapping table with titles and urls but i think i'll just redo this scrape real quick | 21:36 |
| nsh_ | :) | 21:36 |
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| roksprok | um so i seem to have forgotten what you want from this site is it just something where we have a standard format (such as this http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=945) and have every protocol obey that format? | 21:39 |
| strangewarp | Needs more countries. Need a country density of 2 per person minimum. Also, countries are people, and each has two of itself, and so on | 21:39 |
| kanzure | roksprok: yep that's the basic idea | 21:40 |
| kanzure | but also things like, a list of equipment, and being able to say, "this is the endo f the list" or | 21:40 |
| kanzure | or being able to add tags to protocols.. i don't know. simple things. | 21:40 |
| roksprok | http://lab.methodmint.com/methods/1437/ | 21:41 |
| roksprok | that has tags and lets people edit and discuss it | 21:41 |
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| kanzure | yeah looks ok to me | 21:42 |
| kanzure | so yeah, like that | 21:43 |
| kanzure | oh geeze | 21:44 |
| kanzure | http://lab.methodmint.com/methods/1376/ | 21:44 |
| roksprok | k cool so something like that to start and then find a way to convert all the protocols to it | 21:44 |
| kanzure | walls of text | 21:44 |
| roksprok | why break it into steps | 21:44 |
| roksprok | if each step is a pararaph | 21:44 |
| roksprok | paragraph | 21:44 |
| kanzure | the paragraph format is not optimal | 21:45 |
| kanzure | it's supposed to be steps :/ | 21:45 |
| kanzure | if there's if/then statements, it should be code | 21:45 |
| kanzure | Juul: what do you think of that site^ | 21:45 |
| kanzure | roksprok: here's one with just steps http://lab.methodmint.com/methods/1458/ | 21:46 |
| kanzure | only 19 users? | 21:47 |
| Juul | looks like someone is using stackexchange software or a knockoff | 21:47 |
| kanzure | yeh | 21:47 |
| kanzure | except.. with a twitter bootstrap layotu | 21:48 |
| kanzure | *layout | 21:48 |
| kanzure | ok my upload is done | 21:48 |
| kanzure | i'm not sure if making it social is the right answer? | 21:48 |
| kanzure | i guess it helps | 21:48 |
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| kanzure | raw files: http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/ | 21:50 |
| kanzure | zip is: http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache.zip | 21:50 |
| kanzure | hmm.. i definitely think graphs, charts, analysis, software, and debugging would be the way to go on a protocol site. Q&A is necessary too though. | 21:51 |
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| Mokbortolan | can anybody tell me why we use TLDs? | 22:04 |
| Juul | Mokbortolan, i'm not sure what you're asking? the historical reasons DNS was implemented the way it was, or the reasons we stick with that system or something else entirely? | 22:05 |
| kanzure | we use ip addresses | 22:05 |
| Juul | did i mention that my failure to remember to turn off IP over DNS on the lbl.gov network has resulted in a scientific article being published? | 22:06 |
| Juul | impressive sysadmins are impressive | 22:06 |
| Juul | well, i guess it's technically still out for review | 22:07 |
| Mokbortolan | the RFC said it was intended to split up administration of DNS | 22:07 |
| * Mokbortolan starts mining namecoin. | 22:08 | |
| nsh_ | Juul: what's the title of the article? | 22:09 |
| nsh_ | (approximately) | 22:09 |
| nsh_ | there was an cute bit in a Greg Egan novel(a) where some hackers hijack the computational capacity of the global name resolution service to create a virtual supercomputer | 22:10 |
| nsh_ | required a little suspension of disbelief | 22:10 |
| kanzure | what was his phantom company? | 22:14 |
| kanzure | dark integers corporation? | 22:14 |
| kanzure | http://www.asimovs.com/_issue_0805/DarkINtegers.shtml | 22:15 |
| kanzure | although i recall prefering the first half and not this second one | 22:15 |
| Juul | "On Bounding Surreptitious Communication Over DNS | 22:15 |
| Juul | " | 22:15 |
| nsh_ | nice | 22:16 |
| nsh_ | i liked the metaphysical backdrop of the story | 22:16 |
| nsh_ | communication between platonic domains facilitated by proofing esoteric theorems at the fractal borderline therebetween | 22:17 |
| kanzure | nsh_: what's up? | 22:29 |
| kanzure | hi wvoq | 22:29 |
| nsh_ | i found some old bookmarks and i'm seeing which ones are still live | 22:29 |
| kanzure | sounds tedious | 22:30 |
| nsh_ | but nostalgic | 22:30 |
| nsh_ | at best one can hope for a diverse diet of tedium | 22:31 |
| kanzure | the USDA in a surprising flash of clarity judged that tedium is awful | 22:32 |
| nsh_ | so its production is no longer being supported by federal subsidies? | 22:32 |
| kanzure | all of it is being mined in china | 22:33 |
| nsh_ | considering entering a competition to program NASA robots: http://gigaom.com/2012/03/06/space-hackathon-coders-set-to-compete-on-nasadarpa-project/ | 22:33 |
| nsh_ | asian or african china? | 22:34 |
| kanzure | africa dissolved and was annexed by china | 22:34 |
| wvoq | hey zanzure | 22:35 |
| wvoq | thanks for your reply on diy-bio | 22:35 |
| wvoq | this is pat | 22:35 |
| wvoq | *k | 22:35 |
| kanzure | oh hi | 22:35 |
| kanzure | welcome to the real internet | 22:35 |
| wvoq | exactly | 22:35 |
| wvoq | sorry about the repost-- I had tried poking through the archives before posting | 22:35 |
| kanzure | no reposting is ok :P | 22:36 |
| wvoq | but without much success | 22:36 |
| kanzure | but i figured you probably did not see those | 22:36 |
| Juul | no reposting, is ok | 22:36 |
| Juul | no, reposting is ok | 22:36 |
| Juul | hmmm | 22:36 |
| kanzure | no, reposting is ok | 22:36 |
| kanzure | fuck commas | 22:36 |
| kanzure | wvoq: we were just discussing this old data set i had | 22:36 |
| kanzure | a scrape of protocol-online.org | 22:36 |
| kanzure | http://gnusha.org/logs/2012-03-15.log | 22:37 |
| kanzure | has some links, you might like to grab a copy or something.. | 22:37 |
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| kanzure | :| | 22:38 |
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| kanzure | wb | 22:39 |
| kanzure | http://gnusha.org/logs/2012-03-15.log | 22:39 |
| wvoq | thanks | 22:41 |
| wvoq | yeah, I have roughly 4 or 5 years to make an appreciable dent in a hard problem | 22:45 |
| wvoq | I'm beginning to wonder whether this is it | 22:45 |
| kanzure | why only four or five.. what? | 22:45 |
| wvoq | well, to take a Ph.D.-sized bite out of it | 22:45 |
| kanzure | do you have an advisor | 22:46 |
| wvoq | sure | 22:46 |
| wvoq | we've kicked it back and forth a bit, but I don't think I've managed to convince him that it's simultaneously doable and worthwhile | 22:46 |
| kanzure | protocol representation? | 22:46 |
| wvoq | (the Scylla and Charybdis of dissertation properties) | 22:47 |
| wvoq | protocol representation, generation and debugging | 22:47 |
| kanzure | i think debugging is where it's at btw | 22:47 |
| kanzure | "OOPS i prayed to the wrong cardinal direction" can really blow up your experiments | 22:48 |
| wvoq | the golden standard would literally be "grad student mode" | 22:48 |
| wvoq | hopped on the wrong foot, &c. | 22:48 |
| kanzure | is this science or black magic | 22:48 |
| * nsh_ muses | 22:48 | |
| kanzure | "Why gel streaks are the bane of my existence, chapter 1" | 22:48 |
| wvoq | i.e. where you could take dictation, more or less, and generate instructions at, or better than, a teaching protocol | 22:48 |
| nsh_ | why isn't every execution of a protocol logged somewhere with a correlation to the experiment's result? | 22:49 |
| kanzure | wvoq: i've been working on a library to automatically generate microfluidic circuits | 22:49 |
| wvoq | we will look back on this age as one of dark barbarism | 22:49 |
| kanzure | i would really like to take a lab protocol and then spit out a circuit diagram | 22:49 |
| nsh_ | you can outsource the autopsy to people who have more interest in the perfection of the protocol, if you're just worried about getting the right result | 22:49 |
| wvoq | totally | 22:49 |
| kanzure | even if it's a one-time use thing | 22:49 |
| wvoq | is there code up anywhere yet? | 22:49 |
| kanzure | wvoq: soort of | 22:50 |
| kanzure | there's a general framework that is broader | 22:50 |
| kanzure | http://gnusha.org/skdb/ | 22:50 |
| kanzure | but the actual microfluidics code keeps getting rewritten because i can't figure out how i like it best :/ | 22:50 |
| wvoq | previous remark should read: at, or better than, /the level of/ a teaching protocol | 22:50 |
| kanzure | what i want are things like: svg output, laser cutter control, mask generation, parts w/ interfaces that connect | 22:51 |
| kanzure | and ideally some way to mathematically define each part so that you can plug it into your flow simulations | 22:51 |
| kanzure | although- certain elements like heaters (for pcr; either heater blocks, lasers or other methods) require non-svg-output-related design features, but w/e | 22:52 |
| nsh_ | why do heaters need to be output in non-vector form? | 22:53 |
| nsh_ | oh, nm | 22:53 |
| kanzure | your laser cutter can only cut | 22:53 |
| nsh_ | give it time... | 22:53 |
| nsh_ | it's only a pup | 22:54 |
| kanzure | arguably it wouldn't be a laser cutter then | 22:54 |
| wvoq | "By 'hardware' we mean not just designs for circuit boards, but also biological constructs" | 22:54 |
| nsh_ | name is grandfathered in | 22:54 |
| wvoq | sudo apt-get install sv40? | 22:54 |
| kanzure | wvoq: sudo apt-get install adderall | 22:54 |
| kanzure | oh, hm | 22:54 |
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| kanzure | nsh_: you can already outsource the labor of course.. (scienceexchange is new to the scene, yadda yadda) | 22:57 |
| wvoq | this looks interesting. Is it properly released yet? | 22:57 |
| kanzure | it's a bunch of code that doesn't work | 22:59 |
| wvoq | we've all been there | 22:59 |
| wvoq | I am there most of the time, actually | 22:59 |
| kanzure | we need more manpower able to think of architecturally-sound designs | 22:59 |
| kanzure | also one of the barriers was that there were too many proprietary CAD formats | 22:59 |
| kanzure | and the open source formats are never parametric and rarely surface-based (all just meshes) | 23:00 |
| kanzure | i mean.. meshes like object code | 23:00 |
| kanzure | so anyway.. i started to write code for CAD under lolcad.git on http://diyhpl.us/cgit/ | 23:00 |
| kanzure | but that's like a phd thesis of work right there | 23:00 |
| kanzure | lately i've been trying out f-rep-based CAD instead of NURBS-based CAD; i need to write a visualizer to confirm that it's working (just boolean trees w/ inequalities to define your geometry) | 23:01 |
| kanzure | then i spent a bunch of time writing a thingiverse clone based on git repositories | 23:03 |
| wvoq | yeah, I recall rms saying once that getting CAD right will be like the end of history for free software | 23:04 |
| katsmeow-afk | re: reading english description of chemistry procedures and making etc etc : http://duckduckgo.com/?q=OPSIN+Daniel+Lowe+IUPAC | 23:04 |
| kanzure | OpenCASCADE is just terribly written | 23:04 |
| kanzure | plus their licensing is screwed up | 23:04 |
| kanzure | BRLCAD is great but they don't do NURBS or any sort of modern CAD | 23:04 |
| wvoq | chemistry procedures, or IUPAC names? | 23:07 |
| katsmeow-afk | read the top 1/4 of http://blogs.ch.cam.ac.uk/pmr/2011/11/25/the-scandal-of-publisher-forbidden-textmining-the-vision-denied/ | 23:07 |
| kanzure | for procedures... i like http://diyhpl.us/~bryan/papers2/Route%20designer%20-%20a%20retrosynthetic%20analysis%20tool%20utilizing%20automated%20retrosynthetic%20rule%20generation.pdf | 23:07 |
| kanzure | wvoq: btw.. http://diyhpl.us/~bryan/papers2/ | 23:08 |
| wvoq | oh yeah, I remember reading that | 23:08 |
| kanzure | see /bio /DNA /polymerase /longevity /stem-cells /gene-therapy /nanotech | 23:08 |
| kanzure | uh and http://diyhpl.us/~bryan/papers2/microfluidics/ | 23:09 |
| wvoq | huh, neat | 23:12 |
| wvoq | so when you mention biological constructs you primarily mean microfluidics chip + reagents + robot? | 23:14 |
| ParahSailin | that two photon resin nanopatterning recent pr hit was pretty cool-looking | 23:14 |
| yashgaroth | biological constructs = genetically modified organisms, I should hope | 23:16 |
| wvoq | I mean, as far as kanzure is concerned with downloading them | 23:18 |
| kanzure | making reagents, media, culturing, dna synthesis | 23:18 |
| wvoq | consider: the current state of the art for obtaining a given plasmid is asking nicely and having someone mail it to you | 23:18 |
| kanzure | ordering plasmids is stupid | 23:19 |
| kanzure | you should just synthesize what you want | 23:19 |
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| kanzure | and ordering primers just so you can get the gene you want is also dumb | 23:19 |
| kanzure | just synthesize the gene sequence :/ | 23:19 |
| kanzure | wvoq: my current project is a microfluidic dna synthesizer | 23:20 |
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| wvoq | I mean, the stupid thing is that it's still marginally easier/cheaper to do it the old-fashioned way. Or it's impossible to synthesize because the donating lab never actually did the sequencing | 23:22 |
| kanzure | the old-fashioned way is a hack on top of a hack | 23:22 |
| kanzure | to get around the fact that everyone was stuck in the past | 23:23 |
| wvoq | no, I don't disagree at all | 23:24 |
| wvoq | honestly, a lot of current biological practice is just barely this side of alchemy | 23:24 |
| wvoq | and the most frustrating aspect of it is that we know it's alchemy | 23:25 |
| kanzure | it's "institutional knowledge" | 23:25 |
| wvoq | it's lore you learned at your PI's knee | 23:26 |
| wvoq | so, Hilary Mason ran an interesting experiment a while ago | 23:27 |
| wvoq | by optimizing chocolate chip cookies | 23:27 |
| kanzure | sounds good so far | 23:27 |
| wvoq | mining the web for like 150 recipes and effectively just averaging them | 23:28 |
| wvoq | http://www.foodandtechconnect.com/site/2011/09/22/hilary-mason-on-hacking-the-food-system-the-story-of-the-ultimate-cookie/ | 23:28 |
| kanzure | the ultimate cookie? or.. the average cookie | 23:29 |
| wvoq | and so the natural thing to do is to try this with every, say, GFP transformation on online-protocols | 23:29 |
| katsmeow-afk | fwiw, Tiggr has several gigabytes of recipies | 23:29 |
| wvoq | turns out they're the same thin | 23:29 |
| wvoq | g | 23:29 |
| kanzure | katsmeow-afk: yeah but you won't give us the data | 23:29 |
| kanzure | wvoq: yeah, it's all recipes | 23:29 |
| wvoq | which makes sense: the optimal ratio of sugar to flour probably isn't exactly 1:1 or 2:1 | 23:29 |
| kanzure | there was this great 1985 book called "Computational Cooking" by some guy from the food automation industry | 23:29 |
| kanzure | (yes there's a food automation industry) | 23:30 |
| katsmeow-afk | kanzure, i'd like to feel useful, you'd rather mine it all yourself, making me useless | 23:30 |
| kanzure | katsmeow-afk: you won't give us the daaata | 23:30 |
| wvoq | but if recipes proliferate roughly according to their fitness, you should expect the mean to reflect the best ratio | 23:30 |
| kanzure | katsmeow-afk: it's like saying, "OK i have a cure to cancer. Nope, you can't have it, because then you'll have it and I will feel useless" | 23:30 |
| ParahSailin | i didnt have a postdoc or a pi to learn the lore from | 23:31 |
| katsmeow-afk | not what i said | 23:31 |
| kanzure | wvoq: that's an interesting idea | 23:31 |
| wvoq | the obvious problem is that protocols are not "linear" in the sense that cookie recipes mostly are | 23:31 |
| wvoq | so when you make your model and do the regression, you end up needing the very knowledge you're running the regression in order to learn | 23:32 |
| kanzure | there's probably some fancier regression models that can do that | 23:32 |
| wvoq | parasailin: so where did you learn your lore? | 23:32 |
| wvoq | I think your model needs to know all of chemistry | 23:33 |
| kanzure | ok there's some databases you can steal for that | 23:33 |
| kanzure | at least reaction mechanisms | 23:33 |
| kanzure | for organic chemistry. heh' | 23:33 |
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| wvoq | that's why I'm beginning to suspect that automatic protocol generation is going to be more than a weekend hack | 23:34 |
| kanzure | oh no i don't think you should generate the protocols themselves | 23:34 |
| wvoq | all of the efforts I've seen represent the protocol only as deeply as the monkey performing it needs to know | 23:35 |
| wvoq | right, that's the holy grail | 23:35 |
| kanzure | hrmm no i see protocols more like nuggets of random-ass knowledge | 23:36 |
| wvoq | well, in a sense they are | 23:36 |
| kanzure | like cacl2 transformation | 23:36 |
| kanzure | there's this "knowledge" bit and these variables people figured out | 23:36 |
| wvoq | sure, and at the bleeding edge there are protocols where the only thing the authors can claim is that it works | 23:36 |
| kanzure | and then the protocol is english text describing how to setup the scenario | 23:36 |
| kanzure | and what needs to happen in the scenario | 23:37 |
| kanzure | so theoretically a represetnation format would just be the main nugget- "run your liquid at 50C in this machine for 10 min and ramp down to 30C followig this curve" | 23:37 |
| kanzure | *following | 23:37 |
| kanzure | er.. yeah i am really bad at this | 23:38 |
| Juul | somewhere in this building I think some electronics just went *poof* | 23:38 |
| Juul | i can vaguely smell the distinct smell of burning plastic | 23:38 |
| kanzure | are you stealing lab equipment from LBL again | 23:38 |
| kanzure | ah | 23:38 |
| Juul | yet i've now been all around the lab and i can't locate the smell | 23:38 |
| Juul | it might be from one of the other labs downstairs | 23:38 |
| Juul | or some of the electronics in the ceiling | 23:39 |
| kanzure | best to ignore it and pretend everything is ok | 23:39 |
| Juul | yeah | 23:39 |
| kanzure | OR steal all the pipette tips while nobody is looking | 23:39 |
| wvoq | kanzure: but in many cases the theory is well-understood | 23:39 |
| kanzure | wvoq: my main complaint is that biocoder is insufficient | 23:39 |
| Juul | maybe i'm imagining it | 23:39 |
| kanzure | this is not OK http://research.microsoft.com/en-us/um/india/projects/biocoder/documentation/source_code.html | 23:40 |
| kanzure | Fluid medium = new_fluid("rich medium (LB, YT, or Terrific medium)containing appropriate antibiotic", vol(2, ML)); | 23:40 |
| kanzure | Fluid sol1 = new_fluid("Alkaline Lysis Solution I","50 mM Glucose,25 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0)"); | 23:40 |
| kanzure | gah | 23:40 |
| kanzure | next_step(); | 23:40 |
| kanzure | measure_fluid(sol2, vol(200, UL), microfuge_tube); | 23:40 |
| kanzure | invert(microfuge_tube, 5); | 23:40 |
| kanzure | comment("Do not vortex!"); | 23:40 |
| kanzure | store(microfuge_tube, ON_ICE); | 23:40 |
| kanzure | this is not good api design | 23:40 |
| wvoq | so, on one hand, there's the fact that no one will ever read or write this without a gun to their head | 23:41 |
| kanzure | yes | 23:41 |
| kanzure | there's very little benefit to the author :x | 23:41 |
| wvoq | in the short term, at least | 23:41 |
| * kanzure nods | 23:41 | |
| wvoq | on the other, if you had asked anyone in practically any industrial field, such as they were, 100 years ago | 23:42 |
| wvoq | whether they could foresee the practices of designing sewers or bridges with machines | 23:42 |
| wvoq | they would have laughed you out of the room | 23:43 |
| wvoq | 100 years ago, writing a technical memo that got turned into a civil works project by a large team of trained engineers was good enough | 23:43 |
| wvoq | the very conceit of CAD was preposterous | 23:44 |
| wvoq | why spend an hour dicking around with a mouse and a monitor when you could just use a T-square and some splines? | 23:44 |
| wvoq | the point about it being a pain to write is well-taken | 23:45 |
| wvoq | but there are a limited number of replies, AFAICT: | 23:45 |
| kanzure | many protocols describe things that are basically accidents | 23:45 |
| wvoq | true | 23:45 |
| kanzure | or coincidences | 23:46 |
| kanzure | although.. for the basic operations of a biology lab there are usually solid state options | 23:46 |
| kanzure | for instance, transformation can be done with lasers and electroporation | 23:46 |
| wvoq | in general, like for arbitrary mammalian cells? | 23:46 |
| kanzure | i think if you want the most generally applicable solution you can use a plasmid-coated AFM tip | 23:47 |
| kanzure | or do single-cell-needle-injection | 23:47 |
| kanzure | single cell transfection using afm: | 23:48 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/Single%20cell%20transfection%20using%20plasmid%20decorated%20AFM%20probes%20-%2030%20percent%20efficiency.pdf | 23:48 |
| wvoq | ok, cool | 23:48 |
| kanzure | single-plasmid pcr: | 23:48 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/Recovery%20and%20amplification%20of%20plasmid%20DNA%20with%20AFM%20and%20PCR%20-%20single-plasmid%20PCR.pdf | 23:48 |
| kanzure | what other operations? incubation parameters can probably be deduced by the genome (evenutally) | 23:49 |
| kanzure | *eventually | 23:49 |
| kanzure | sequencing has gone solid state (nanopores, afm sequencing, stm sequencing..) | 23:50 |
| wvoq | are you saying that reading the e. coli genome will tell you to incubate at 37 degrees? | 23:50 |
| kanzure | synthesis will be (controlled polymerases) | 23:50 |
| kanzure | wvoq: i hope so heh | 23:50 |
| kanzure | i'm generally suggesting that there are options for moving towards protocols that are mechanical steps and less.. hopping on one foot for hours at a time | 23:51 |
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| wvoq` | sorry, my neighbor's wifi keeps dropping me | 23:54 |
| Juul | wvoq`, most neighbors will only let you borrow one cup of wifi at a time | 23:55 |
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| wvoq` | it's cool, they downloaded my car last week, so we're even | 23:57 |
| wvoq` | though I guess downloading cars is actually serious business here | 23:57 |
| Juul | *gasp* they _wouldn't_ | 23:57 |
| Juul | this phantom smell is getting to me | 23:58 |
| Juul | and i'm hungry | 23:58 |
| Juul | grrr | 23:58 |
| Juul | i'm going to stoop | 23:58 |
| Juul | so low | 23:58 |
| kanzure | i need to sleep | 23:58 |
| kanzure | good night | 23:58 |
| Juul | night | 23:58 |
| wvoq` | night | 23:58 |
| * Juul walks off to Denny's | 23:59 | |
| --- Log closed Fri Mar 16 00:00:12 2012 | ||
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