--- Log opened Thu Mar 15 00:00:52 2012
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05:23 < 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
05:31 < rdb> what value?  negative 0.001*omega*sqrt(-1) ohm?
05:34 < 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
05:36 < 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
05:37 < strangewarp> Those are the ultra-tiny ones?
05:37 < strangewarp> (still sort of a noob here, just not a blatant one anymore)
05:38 < 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
05:39 < 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
05:40 < strangewarp> and the memory of skimming over it made my brain go "gleep?"
05:41 < 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
05:42 < strangewarp> those, even. derp
05:43 < 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
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05:46 < rdb> how's life?
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08:19 < chris_99> http://www.bbc.co.uk/iplayer/episode/b01dlglq/Horizon_20112012_Out_of_Control/
08:19 < chris_99> on the brain
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09:03 < thylane> http://www.sciencedaily.com/releases/2012/03/120314142843.htm
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10:21 < 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?
10:22 < Mokbortolan_> from what I read, what little carbon is found in cremains is in the form of carbonates
10:25 < thylane> Mokbortolan_  Did you read my link yet?
10:25 < Mokbortolan_> yes
10:26 < Mokbortolan_> but it didn't really go into specifics
10:26 < Mokbortolan_> ohw ait, wrong room :p
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10:27 < 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
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10:36 < thylane> I was over thinking the article, until I realized they siad human children can do ratcheting
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11:27 < kanzure> there is a pleasing number of results for the search "against antibiotic resistance"
11:27 < kanzure> i think that means anti-antiantibiotics
11:28 < kanzure> shouldn't it just be "against biotics"
11:28 < archels> anti-evolution in bacteria?
11:29 < kanzure> for example there's the "swedish strategic programme against antibiotic resistance"
11:30 < archels> a bacteria evolves a mutation that makes it immune to a certain antibiotic or class thereof
11:30 < kanzure> sure
11:31 < archels> What strategies are there to prevent this?
11:31 < archels> I mean, you can't really *prevent* it, can you?
11:39 < kanzure> man the soviet union knew how to pick good names
11:39 < kanzure> "Department of the Mobilisation of Scientific Forces"
11:40 < archels> pubmed for those keywords: Results: 1 to 20 of 19763
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11:40 < archels> Got a paper suggestion for me, kanzure?
11:40 < kanzure> are you looking for antibiotic resistance evidence?
11:41 < archels> No, I just want to know about the mechanisms, or directions of research that go towards preventing antibiotic resistance.
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11:42 < archels> A one-sentence summary might also do. ;)
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12:03 < thylane> http://www.youtube.com/user/SingularitySummits
12:03 < thylane> http://www.youtube.com/user/SingularitySummits
12:07 < Mariu> thanks thylane
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12:18 < kanzure> hrm a panda3d developer
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12:19 < 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
12:20 < 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
12:21 < 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/
12:23 < 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."
12:24 < 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
12:25 < 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
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12:26 < 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
12:27 < roksprok> hah i don't think its worth bugging you if its available elsewhere
12:27 < kanzure> on the contrary
12:28 < 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
12:29 < 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
12:30 < kanzure> also.. /random is written poorly. i keep pinging the poor embed.ly servers for the same info over and over again
12:31 < 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 :|
12:32 < 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
12:33 < 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
12:34 < 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)
12:35 < 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
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12:35 < 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
12:37 < 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
12:39 < roksprok> i think its good as is, but i am just using it like your directory of papers
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12:40 < 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
12:41 < Steel2> which vids
12:41 < roksprok> diyhpl.us:9001
12:41 < kanzure> i don't really care if he knows
12:42 < 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
12:46 < roksprok> i've often thought that wikis generally lacked vids
12:46 < roksprok> of relevant talks
12:51 < roksprok> kanzure do you work out of your apartment? or the austin hackerspace? or someplace else
12:52 < roksprok> if you don't mind me asking
13:08 < kanzure> roksprok: i work wherever
13:09 < 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
13:11 < 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
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13:12 < 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?
13:13 < 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
13:14 < 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
13:15 < 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
13:16 < kanzure> where are you?
13:16 < lichen> portland, oregon
13:17 < kanzure> okay
13:18 < 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
13:19 < thylane> I think its because they are so  entrenched in  statistical medicine
13:19 < kanzure> complaining about it will not help her
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13:49 < kanzure> visual transistor-level simulation of 6502 http://visual6502.org/
13:52 < kanzure> http://visual6502.org/JSSim/index.html
13:54 < ThomasEgi> that page is pretty awesome
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14:10 < kanzure> sciencehackday chicago http://sciencehackday.pbworks.com/chicagoideas
14:12 < roksprok> kanzure do you know jack lloyd at triple ring?
14:12 < kanzure> not yet
14:13 < 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
14:14 < 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)
14:15 < 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?
14:16 < kanzure> did he do some venture backed stuff?
14:17 < 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"
14:18 < 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
14:19 < 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
14:20 < 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
14:21 < roksprok> ha well 498 to go
14:22 < kanzure> it is exceedingly unlikely that your first pitch will land you money
14:38 < lichen> just scored an interview with intel o.o
14:38 < lichen> not my dream job but its something?
14:44 < kanzure> http://news.cnet.com/8301-30252_3-57397557-246/hacker-collective-focuses-on-biotech-audio-slideshow/
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15:17 < Vicarious> aww..
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15:24 < kanzure> Vicarious: ?
15:25 < Vicarious> hi kanzure
15:28 < Vicarious> tomororw there's a meetup planned, regarding BIY biohacking and stuff
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15:29 < Vicarious> but I'm unable to attend it, I have to work until 16:30, meeting starts 18:00
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15:31 < roksprok> what city vicarious?
15:33 < kanzure> probably copenhagen
15:33 < kanzure> oops wait he's in the netherlands somewhere
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15:34 < roksprok> thats far
15:37 < Juul> copenhagen, netherlands, it's basically the same thing
15:37 < Vicarious> roksprok: the meetup takes place in the hague, the netherlands
15:38 < 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
15:39 < Juul> yeah, well i'm already impressed that you even try to keep track of everyone
15:41 < kanzure> WHO ARE YOU PEOPLE
15:41 < kanzure> WHY DO I KNOW YOU
15:41 < kanzure> thanks
15:42 < 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
15:43 < kanzure> the hague, ok
15:43 < Vicarious> according to http://www.meetup.com/Dutch-DIY-Bio/events/52332122/
15:53 < kanzure> bbl
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16:11 < ThomasEgi> http://chzmemebase.files.wordpress.com/2012/03/koma-comic-strip-comixed-its-effective.jpg
16:11 < ThomasEgi> proven to work
16:12 < Juul> Vicarious, nice. Will you document?
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16:17 < Vicarious> Juul: I won't be attending, there's not much for me to document
16:18 < Juul> Vicarious, ah yes. you said that. sorry
16:18 < Vicarious> np
16:20 < Vicarious> I was wondering if I'm the only one who has a magnet implant, among the dutch DIY biohackers
16:23 < Vicarious> hey Steel2, don't you know it's rude to message people without asking for their permission first?
16:24 < Vicarious> I don't know you
16:25 < 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
16:26  * 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
16:27 < Steel2> as that's not something I've ever run into before
16:27 < katsmeow-afk> this is a newer channel
16:29 < Vicarious> usually when irc clients message me without asking for permission, and I don't know them personally.. they're spammers :/
16:30 < 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
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16:34 < Vicarious> Steel2: anyway, I closed the private message window already, what did you want to ask?
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16:35 < Steel2> I wrote out an idea for an experimental protocol for people with magnetic implants
16:36 < Vicarious> ok
16:37 < Steel2> I was wondering if you were interested.
16:38 < 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
16:39 < 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.
16:40 < 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
16:41 < 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
16:43 < katsmeow-afk> "as your advisor, i advise you to do this before i rip your head off"
16:44 < Vicarious> throwie = magnet + LED + battery, wrapped in tape
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17:56 < 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
17:57 < 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/
17:58 < Urchin> A-Lusion: no, it's like thinking all the thoughts of a year in 30 seconds
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17:58 < Urchin> you'd end up being ancient very quickly
17:58 < A-Lusion> mentally though yeah?
17:59 < 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'
18:00 < 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
18:01 < kanzure> A-Lusion: i don't think a subjective year would pass in 30 deconds
18:01 < kanzure> *seconds
18:02 < 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
18:03 < 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
18:04 < 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
18:05 < 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
18:06 < A-Lusion> I wanna know more about kurzweils vitamin diet lol
18:06 < lichen> yeah
18:07 < 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
18:08 < lichen> sometimes some nootropics but i havent for a while
18:09 < 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
18:10 < 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
18:11 < 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..
18:12 < 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
18:13 < 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
18:14 < 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
18:15 < 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
18:17 < A-Lusion> I see what you mean, exercising for the sake of exercising is sort of a  unfavorable yeah?
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18:20 < Urchin> yes
18:20 < Urchin> it does not work out in the long term
18:22 < jrayhawk> The performance-equals-health mentality is problematic, and complete disregard for stimulus/response curves in excersize is really really problematic
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18:25 < 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
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18:28 < Urchin> I've last read it about 6 years ago
18:29 < 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)
18:30 < 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
18:31 < Urchin> and used by Orion's Arm
18:31 < Urchin> pitty they stopped using creative commons
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18:32 < kanzure> orion's arm is ok if you want worldbuilding
18:33 < 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.
18:34 < 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?
18:35 < 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
18:36 < A-Lusion> Lol do you keep a list?
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18:36 < 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
18:37 < 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
18:39  * 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
18:40 < 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)
18:41 < Urchin> *asteroid belt
18:42 < 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
18:43 < 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
18:44 < 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
18:45 < 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
18:46 < 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
18:47 < Urchin> essentially you would be making a lab provider separate from the researchers
18:47 < Urchin> lab for hire
18:47 < Urchin> interesting notion
18:48 < 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
18:49 < 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
18:50 < 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
18:51 < 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
18:52 < 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
18:53 < 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
18:54 < 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
18:55 < 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
18:56 < 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
18:57 < 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?
18:58 < 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
18:59 < kanzure> well, depending on which insects
18:59 < Mariu> Ladybirds
19:00 < 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.
19:01 < 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
19:02 < kanzure> roksprok: i'm pretty sure the "general leftish direction" stuff was just "electrode sitting on the head"
19:03 < 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?
19:04 < 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?
19:05 < 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
19:06 < 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
19:07 < 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 :(
19:09 < 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
19:10 < kanzure> roksprok: what money?
19:10 < roksprok> money to buy a spikerbox?
19:11 < 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
19:12 < 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
19:13 < 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
19:14 < 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
19:15 < 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
19:16 < lichen> yeah
19:16 -!- delinquentme [~asdfasdf@c-67-171-66-113.hsd1.pa.comcast.net] has quit [Ping timeout: 246 seconds]
19:16 < 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....
19:17 < 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)
19:18 < 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
19:19 < 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
19:20 < 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
19:21 < 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
19:22 < lichen> not the time to sit around researching brands and sites
19:23 < 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..
19:24 < 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"?
19:25 < 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
19:26 < 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.
19:27 < 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
19:28 < 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
19:29 < 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:
19:30 < 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."
19:31 < 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
19:32 < kanzure> your scrapers?
19:32  * katsmeow-afk nods
19:32 < kanzure> can you show it to me
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19:32 < 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
19:33 < 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
19:34 < 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
19:35 < 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
19:36 < 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
19:37 < 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
19:38 < 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
19:39 < 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
19:40 < 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
19:41 < lichen> lack of publicity or lack of features and usability?
19:41 < kanzure> everyone knows about it
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19:41 < 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
19:42 < 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
19:43 < 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?
19:44 < 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
19:45 < 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
19:46 < 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
19:47 < 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
19:48 < 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
19:49 < 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 :)
19:50 < Juul> lichen, ah :-)
19:51 < 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 -!- d3nd3 [~dende@cpc10-croy17-2-0-cust245.croy.cable.virginmedia.com] has quit [Quit: Leaving.]
19:51 < 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
19:52 < 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
19:53 < 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"
19:54 < 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
19:55 < 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
19:56 < kanzure> otherwise you will screw up a step and forget if you just pipetted or not
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19:56 < kanzure> yashgaroth: why a few mil?
19:57 < 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
19:58 < 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
19:59 < 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
20:00 < 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
20:01 < 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
20:02 < lichen> all those grad students gotta work somewhere
20:04 < 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
20:05 < 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
20:06 < lichen> thats because you are on drugs
20:06 < lichen> caffeine is pretty strong provided youre not addicted to it
20:08 < Juul> yes. this is why I don't use caffeine on a regular basis
20:09 < 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
20:14 < 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
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20:15 < lichen> fucking misogynists
20:15 < lichen> makes me afraid to enter the software industry
20:15 < lichen> since its rather notorious for that
20:45 < roksprok> anyone have suggestions for a free website mockup tool?
20:47 < Juul> lichen, yeah it's pretty bad
20:49 -!- nsh_ [~nsh@cpc21-broo7-2-0-cust83.14-2.cable.virginmedia.com] has joined ##hplusroadmap
20:49 < kanzure> for some reason my grandmother is in town
20:50 < 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)
20:51 < 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
20:52 < nsh_> ah
20:52 < Juul> i like pen and paper
20:52 < Juul> or whiteboards and cameraphones
20:52 -!- augur [~augur@129.2.129.35] has quit [Remote host closed the connection]
20:54 -!- Mariu [Jimmy98@89.41.57.33] has quit [Ping timeout: 265 seconds]
20:57 < nsh_> also, what's a Gottendammerung literalist?
20:58 < 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
20:59 < 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
21:00 < 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
21:01 < strangewarp> np
21:02 < Juul> hmm
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21:03 < 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??
21:04 < 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
21:05 < 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
21:06 < kanzure> i tried to do xml but i don't think it works
21:06 < kanzure> http://diyhpl.us/~bryan/irc/pcr.xml
21:07 < kanzure> those <step>s are just english :/
21:07 < kanzure> but the other metadata is useful
21:08 < 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
21:09 < 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."
21:10 < Juul> wasn't this exact thinking what lead us to COBOL ?
21:11 < 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
21:12 < 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
21:13 < 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.
21:14 < 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?
21:15 < 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
21:16 < 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
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21:16 < kanzure> what incentives are there for digitization other than automation?
21:16 < Juul> https://www.thinkgeek.com/tshirts-apparel/unisex/frustrations/374d/
21:17 < 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
21:18 < 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
21:19 < 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
21:20 < 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
21:21 < 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
21:22 < 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
21:23 < yashgaroth> gimme
21:23 < kanzure> um
21:23 < yashgaroth> *please
21:24 < kanzure> i am trying to figure out wtf i have
21:24 < roksprok> do people use protocol online?
21:25 < kanzure> yes
21:25 < kanzure> kanzure@pikachu:/mnt/externia/backups/davinci/home/bryan/cache/protocol-online/www.protocol-online.org/
21:26 < 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
21:27 < kanzure> and from when i was using.. perl.. to do scraping. yikes
21:28 < 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/
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21:28 < kanzure> Juul: hey some of that path was legit
21:29 < Juul> :)
21:30 < 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)
21:31 < 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
21:32 < kanzure> here's all their outgoing links http://diyhpl.us/~bryan/irc/protocol-online/links_cgi.txt
21:33 < kanzure> it will be a while for the 150+ MB file to upload (capped upload speed)
21:35 < 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
21:36 < 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_> :)
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21:39 < 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
21:40 < 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.
21:41 < roksprok> http://lab.methodmint.com/methods/1437/
21:41 < roksprok> that has tags and lets people edit and discuss it
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21:42 < kanzure> yeah looks ok to me
21:43 < kanzure> so yeah, like that
21:44 < 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
21:45 < 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^
21:46 < kanzure> roksprok: here's one with just steps http://lab.methodmint.com/methods/1458/
21:47 < kanzure> only 19 users?
21:47 < Juul> looks like someone is using stackexchange software or a knockoff
21:47 < kanzure> yeh
21:48 < 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
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21:50 < 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
21:51 < 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.
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22:04 < Mokbortolan> can anybody tell me why we use TLDs?
22:05 < 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
22:06 < 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
22:07 < 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
22:08  * Mokbortolan starts mining namecoin.
22:09 < nsh_> Juul: what's the title of the article?
22:09 < nsh_> (approximately)
22:10 < 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
22:14 < kanzure> what was his phantom company?
22:14 < kanzure> dark integers corporation?
22:15 < 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> "
22:16 < nsh_> nice
22:16 < nsh_> i liked the metaphysical backdrop of the story
22:17 < nsh_> communication between platonic domains facilitated by proofing esoteric theorems at the fractal borderline therebetween
22:29 < 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
22:30 < kanzure> sounds tedious
22:30 < nsh_> but nostalgic
22:31 < nsh_> at best one can hope for a diverse diet of tedium
22:32 < 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?
22:33 < 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/
22:34 < nsh_> asian or african china?
22:34 < kanzure> africa dissolved and was annexed by china
22:35 < 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
22:36 < 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
22:37 < kanzure> http://gnusha.org/logs/2012-03-15.log
22:37 < kanzure> has some links, you might like to grab a copy or something..
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22:38 < kanzure> :|
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22:39 < kanzure> wb
22:39 < kanzure> http://gnusha.org/logs/2012-03-15.log
22:41 < wvoq> thanks
22:45 < 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
22:46 < 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?
22:47 < 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
22:48 < 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
22:49 < 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?
22:50 < 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
22:51 < 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
22:52 < 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
22:53 < 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...
22:54 < 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
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22:57 < 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?
22:59 < 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
23:00 < 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
23:01 < 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)
23:03 < kanzure> then i spent a bunch of time writing a thingiverse clone based on git repositories
23:04 < 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
23:07 < 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
23:08 < 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
23:09 < kanzure> uh and http://diyhpl.us/~bryan/papers2/microfluidics/
23:12 < wvoq> huh, neat
23:14 < 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
23:16 < yashgaroth> biological constructs = genetically modified organisms, I should hope
23:18 < 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
23:19 < kanzure> ordering plasmids is stupid
23:19 < kanzure> you should just synthesize what you want
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23:19 < kanzure> and ordering primers just so you can get the gene you want is also dumb
23:19 < kanzure> just synthesize the gene sequence :/
23:20 < kanzure> wvoq: my current project is a microfluidic dna synthesizer
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23:22 < 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
23:23 < kanzure> to get around the fact that everyone was stuck in the past
23:24 < 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
23:25 < wvoq> and the most frustrating aspect of it is that we know it's alchemy
23:25 < kanzure> it's "institutional knowledge"
23:26 < wvoq> it's lore you learned at your PI's knee
23:27 < 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
23:28 < 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/
23:29 < 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
23:30 < 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"
23:31 < 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
23:32 < 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?
23:33 < 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 -!- strangewarp [~strangewa@c-76-25-200-47.hsd1.co.comcast.net] has joined ##hplusroadmap
23:34 < 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
23:35 < 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
23:36 < 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
23:37 < 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
23:38 < 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
23:39 < 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
23:40 < 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
23:41 < 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
23:42 < 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
23:43 < 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
23:44 < 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?
23:45 < 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
23:46 < 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?
23:47 < 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
23:48 < 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
23:49 < kanzure> what other operations? incubation parameters can probably be deduced by the genome (evenutally)
23:49 < kanzure> *eventually
23:50 < 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
23:51 < 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
23:54 -!- wvoq` [~user@c-68-55-255-90.hsd1.md.comcast.net] has joined ##hplusroadmap
23:54 -!- wvoq [~user@c-68-55-255-90.hsd1.md.comcast.net] has quit [Ping timeout: 246 seconds]
23:54 < wvoq`> sorry, my neighbor's wifi keeps dropping me
23:55 < Juul> wvoq`, most neighbors will only let you borrow one cup of wifi at a time
23:56 -!- ParahSailin [~parah@unaffiliated/parahsailin] has quit [Ping timeout: 252 seconds]
23:57 < 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_
23:58 < 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
23:59  * Juul walks off to Denny's
--- Log closed Fri Mar 16 00:00:12 2012