| --- Day changed Mon Jun 09 2008 | ||
| percent | You screwed up Ramen | 01:19 |
|---|---|---|
| percent | ? | 01:19 |
| kanzure | Nah. :) | 01:19 |
| Vedestin | we don't have ramen here | 01:38 |
| Vedestin | the brand i mean | 01:39 |
| * Vedestin heads off ot make some maggi noodles | 01:42 | |
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| ybit | there's an entire magazine dedicated to various types of ramen in japan :) | 02:31 |
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| kanzure | Hey cis-action. | 12:05 |
| cis-action | hey kanzure | 12:06 |
| kanzure | I threw up the youtube video. | 12:06 |
| cis-action | awesome | 12:06 |
| cis-action | url? | 12:06 |
| kanzure | http://www.youtube.com/watch?v=ZXKbzbeipmI | 12:06 |
| cis-action | cool | 12:11 |
| cis-action | I'll check it out | 12:11 |
| cis-action | back in a sec... | 12:11 |
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| kanzure | fenn: so it turns out that Andy wants some 'compartmentalization', he mentions emulsions | 13:09 |
| kanzure | but I'm skeptical since you'd need to do communication between the emulsions and so on | 13:09 |
| kanzure | not fun stuff, and I don't see the point of it | 13:09 |
| kanzure | I mentioned the ability to do physical address space stuff with the switches, even in gene regulatory networks, and while he gets that, he also wants, for some reason, some way to physically compartmentalize these circuits | 13:10 |
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| fenn | duhh. use a cell, fucktard | 13:30 |
| fenn | emulsion.. gah | 13:30 |
| fenn | how big is a typical TRN reaction vessel? i'd think the speed would be proportional to the size | 13:31 |
| fenn | nsh-: i read permutation city. rather depressing. | 13:35 |
| fenn | who'd want to live in a clockwork universe? | 13:36 |
| fenn | the flaw in his logic is that determining whether you really are in a deterministic simulation is computationally intractable | 13:36 |
| fenn | (one of the flaws.. i dunno about the whole subjectivity = reality aspect) | 13:37 |
| kanzure | cells suck for this sort of thing, :-/ | 13:38 |
| kanzure | possible vessels: vesicles, emulsions, nanobeads stuffs, not much else? | 13:38 |
| kanzure | http://heybryan.org/mediawiki/index.php/2008-06-09 see my notes on cell-free translation systems | 13:38 |
| fenn | why are cells bad? | 13:40 |
| kanzure | can't grow many of them apparently | 13:40 |
| kanzure | also, the protein functionality that you want to evolve doesn't necessarily agree with the cell | 13:40 |
| kanzure | now, I'm not sure if the goal is proteins | 13:40 |
| kanzure | so that's rather odd | 13:40 |
| fenn | TRN's dont use proteins though | 13:40 |
| kanzure | it seems that they want to "link genotype and phenotype" information | 13:40 |
| kanzure | TRNs = ? | 13:40 |
| fenn | transcriptional regulatory network == transcriptional switch | 13:40 |
| fenn | but more analog | 13:41 |
| fenn | cant make an oscillator out of switches | 13:41 |
| kanzure | buh? | 13:41 |
| kanzure | what is the substrate? | 13:41 |
| kanzure | wait | 13:41 |
| fenn | DNA/RNA i guess.. you're the expert | 13:41 |
| kanzure | yeah | 13:41 |
| kanzure | the vessel is usually a giant test tube | 13:41 |
| fenn | nsh-: permutation city reminds me of philip dick's "VALIS" | 13:42 |
| fenn | so, ellington likes the direct write idea? | 13:44 |
| kanzure | haven't told him | 13:44 |
| fenn | why does he want compartmentalization? | 13:44 |
| kanzure | no clue | 13:44 |
| kanzure | because it would only make sense with direct write or something | 13:44 |
| kanzure | there's nothing 'evolvable' about transcriptional switches floating around in a tube | 13:44 |
| kanzure | even if you compartmentalize it ... | 13:44 |
| fenn | sure there is, you can do selections like for aptamers | 13:45 |
| fenn | RNA-life stuff | 13:45 |
| fenn | nowhere near as convenient as with cells of course | 13:45 |
| kanzure | what would you select for? | 13:45 |
| kanzure | you already know the transcriptional switches that you inserted into the system | 13:45 |
| fenn | you could select for specificity and low crosstalk? | 13:46 |
| fenn | i dont have a scheme for how to do it off the top of my head | 13:47 |
| kanzure | why ? you could just run calculations to get that specificty and low crosstalk anyway | 13:47 |
| kanzure | http://heybryan.org/winfree.html | 13:47 |
| kanzure | search for cross-talk or something on there and you'll find some notes on that | 13:47 |
| fenn | we've talked about this before and didnt come up with a way to make it work in-vitro | 13:48 |
| kanzure | make what work in vitro? | 13:48 |
| fenn | selecting for a large set of 'addresses' in-vitro with minimal cross-talk | 13:49 |
| kanzure | you don't select it in vitro | 13:49 |
| kanzure | you generate a list of sequences that match the specifications | 13:50 |
| kanzure | and then you do some GAs and so on to help on that point | 13:50 |
| fenn | i know, the idea was to reduce computation by doing it in vitro | 13:50 |
| fenn | in parallel | 13:50 |
| fenn | zillions of molecules | 13:50 |
| kanzure | yeah, but you needed something like 4^n or something which sucked immensely | 13:50 |
| kanzure | right | 13:50 |
| kanzure | hrm | 13:50 |
| kanzure | so what was wrong with the simulation idea? | 13:50 |
| kanzure | I think it was simply that it's hard to scale, that's all | 13:50 |
| fenn | it only works for small numbers of combinations | 13:51 |
| fenn | that's probably why he wants compartmentalization, because there's a limit to how big the system can be before you get into intractable 'emergenticity' | 13:51 |
| fenn | i dont see why you cant do it in a cell, besides the difficulty of getting dna into a cell | 13:52 |
| kanzure | I think that's the problem | 13:53 |
| kanzure | also, communication between compartments | 13:53 |
| kanzure | I don't like the compartments idea because it involves messy membranes | 13:53 |
| fenn | communication between compartments is the problem with the solution to the other problem | 13:54 |
| kanzure | huh? | 13:54 |
| fenn | it's just a side effect | 13:54 |
| kanzure | why not just do localization | 13:54 |
| kanzure | bind the switches to a surface | 13:54 |
| kanzure | and have them grouped together ? | 13:55 |
| fenn | because brownian motion is random | 13:55 |
| fenn | i think you get a gaussian probability distribution? | 13:55 |
| fenn | google flop :( | 13:56 |
| kanzure | so do we *have* to compartmentalize genotype+phenotype | 13:57 |
| fenn | ah yes, it is: http://galileo.phys.virginia.edu/classes/152.mf1i.spring02/RandomWalk.htm | 13:58 |
| fenn | kanzure: it might work, you just have to set the 'noise' below the threshold of turning on the switch | 14:00 |
| fenn | binding to a surface is a good idea. i thought you meant just sticking them on the same place in the genome/plasmid | 14:01 |
| fenn | in mesh wifi networks, you can hear the other wifi routers on your channel, but if they're far enough away you can just treat them as noise | 14:02 |
| fenn | transcriptional switches have a threshold, right? | 14:04 |
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| fenn | signal to noise ratio is more or less proportional to the amount of time you spend computing the address sequences | 14:08 |
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| fenn | it would be fun to turn a blender model into DNA pepakura | 14:44 |
| nsh- | interesting comparison, fenn (VALIS and Permutation City) | 14:50 |
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| fenn | permutation city is also quite similar to http://www.orionsarm.com/eg/r/Re-Rg.html#Reality_Intratextualization_Project | 16:15 |
| fenn | i dont know what the upstream source of that is called though | 16:16 |
| fenn | it might be this, but its kinda dense http://www.frc.ri.cmu.edu/~hpm/project.archive/general.articles/1987/wave.ltx | 16:19 |
| fenn | he Fourier transform is | 16:21 |
| fenn | but one of an infinite class of ``orthogonal transforms'' that have | 16:21 |
| fenn | the same basic properties. Each of these is capable of taking a | 16:21 |
| fenn | description of a volume, and operating over it to produce a different | 16:21 |
| fenn | description with the same information, but with each original point | 16:21 |
| fenn | spread to every location in the result. This leads to the possibility | 16:21 |
| fenn | of an infinity of universes, each a different combination of the same | 16:21 |
| fenn | underlying stuff | 16:21 |
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| fenn | fun with sed: cat hplusroadmap.log | sed 's/^.*>//g' | sed 's/\W/ /g' | sed 's/ /\n/g' | sort | uniq -c | sort -nr | 17:02 |
| fenn | http://fennetic.net/pub/irc/histo3 | 17:02 |
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| kanzure | fenn: I've become very skeptical of the entire scenario that these guys are proposing | 20:11 |
| kanzure | First, they want to do amorphosu computing | 20:11 |
| kanzure | but that, for some reason, involves physically binding the switches | 20:11 |
| kanzure | which seems like a violation of the idea of amorphous computing in the first place | 20:11 |
| kanzure | secondly, they supposedly want to get it to manufacture something eventually, not just sit there passing bits and so on | 20:11 |
| kanzure | but they also don't have a way to measure anything based off of the switches, right now they want to measure inhibitors but that doesn't tell you anything since inhibitors don't degrade quickly enough and it degrades | 20:12 |
| kanzure | *and it builds up. | 20:12 |
| kanzure | So basically one of the lab members wants to outdo Drexler and actually do what Drexler's been saying he wants to do for the past 40 years or whatever | 20:12 |
| kanzure | :-/ | 20:13 |
| Vedestin | i guess fenn is afk? | 20:13 |
| kanzure | fenn is always afk :) | 20:13 |
| kanzure | there might be a way to make it all work with the writozyme idea, plus compartmentalized translation (to make up proteins), but I don't really like the idea of using proteins | 20:14 |
| kanzure | so while the bioreactor idea still might be plausible, the idea of amorphous computation, even amorphous fabrication, doesn't seem to be going anywhere, but I'm not quite sure *why* | 20:14 |
| kanzure | it's probably because all of the input/output stuff is totally whack | 20:28 |
| kanzure | the only reason you'd want it is if you are going to evolve programs to do something interesting within either an artificial cell or something that you are later going to characterize and 'decode' into a program | 20:28 |
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| pupnik | hi, my dad founded the institute of human genetics at the university of minnesota | 21:54 |
| pupnik | hope we can have some discussions | 21:54 |
| procto | hi pupnik | 21:54 |
| Vedestin | with your dad? | 21:54 |
| kanzure | Hello pupnik. | 21:54 |
| procto | that's a snappy introduction :> | 21:54 |
| kanzure | Indeed it is. | 21:54 |
| kanzure | pupnik: Do you know about the projects from this channel? | 21:55 |
| procto | he doesn't :> | 21:55 |
| kanzure | procto: You know him? | 21:55 |
| pupnik | i'm not active in anything, very alcoholic | 21:55 |
| pupnik | but enjoy chatting | 21:55 |
| kanzure | but do you understand what this channel is about, to some extent? :) | 21:56 |
| kanzure | you've found the right place for this sort of discussion, of course | 21:56 |
| pupnik | procto invited me | 21:56 |
| kanzure | some of the subprojects in here include personal genomics | 21:56 |
| kanzure | ah, okay | 21:56 |
| kanzure | so procto gave you a bit of an explanation I bet | 21:56 |
| fenn | kanzure: re: failure of amorphous computing: the lure of bio-nano is that it's a fantastically easy shortcut | 21:56 |
| kanzure | fenn: it is a good shortcut, *if* you maintain the manufacturing aspects or something, or at least the evolvability | 21:56 |
| fenn | its like stumbling upon an abandoned factory in mint condition | 21:57 |
| kanzure | otherwise it's just starting from scratch | 21:57 |
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| kanzure | the computation itself doesn't seem all that exciting since there are a limited number of possible hooks | 21:57 |
| pupnik | anybody active in genetics/cell biology? | 21:57 |
| kanzure | pupnik: Yes. | 21:57 |
| kanzure | I'm in a lab. | 21:57 |
| Vedestin | really? whose lab? | 21:58 |
| pupnik | shit load of stuff to learn man | 21:58 |
| kanzure | Vedestin: http://ellingtonlab.org/ | 21:58 |
| kanzure | sure | 21:58 |
| fenn | kanzure: the computation is just too slow (if you can even call it computation) | 21:58 |
| Vedestin | oh, i didn't know you'd talked to ellington | 21:58 |
| kanzure | Vedestin: evolutionary engineering, acceleration of evolutionary processes, synthetic biology, DNA synthesis, all sorts of good stuff | 21:58 |
| kanzure | fenn: well, it's not going to compete with silicon; the point is the manufacturing I thought. And if you can't use protein engineering, then what the hell are you doing? | 21:58 |
| Vedestin | last i heard of this, i asked why you wanted to be at austin | 21:58 |
| Vedestin | and you said you were interested in that guys work | 21:59 |
| kanzure | I'm starting to think the idea of the writozyme is the only thing that makes any of this legitimate | 21:59 |
| kanzure | I am interested in that guys work :) | 21:59 |
| kanzure | guy's | 21:59 |
| procto | I could have given pupnik a bit more of an intro than he got :> I was very minimal | 21:59 |
| Vedestin | but it's your work too now? | 21:59 |
| kanzure | Vedestin: Damn right. :) | 21:59 |
| fenn | pupnik: its mostly poor terminology giving a facade of understanding.. we really dont know much of anything (as a scientific community) | 21:59 |
| pupnik | i'm published in 3 papers | 21:59 |
| pupnik | but i don't know shit | 21:59 |
| kanzure | nobody knows much shit anyway | 21:59 |
| kanzure | so that's good | 21:59 |
| kanzure | so, pupnik, are you familiar with open source software | 21:59 |
| pupnik | well that's my hobby | 22:00 |
| pupnik | nokia just invited me to linuxtag full-fare paid :) | 22:00 |
| kanzure | fenn: the writozyme is the only thing that makes any of this legitimate, since that's synthesis and could possibly used to, ah, okay | 22:00 |
| kanzure | fenn: so here's my idea to make any of this legitimate | 22:00 |
| kanzure | fenn: the idea is to embed logic within the selection experiments itself | 22:00 |
| fenn | kanzure: well, even with sucky biotech techniques you can do some neat things (DNA origami) | 22:00 |
| kanzure | fenn: so that you have aptamers feedbacking into the switches or something like that | 22:00 |
| kanzure | so that you "unfold" programs or whatever as the selection is going a certain way | 22:00 |
| kanzure | pupnik: ok, so we want to do open source for 'everything else' | 22:00 |
| pupnik | i have a nice trick if any of you are doing electrophoresis | 22:00 |
| fenn | kanzure: like, the switch is on when the aptamer's got something? | 22:01 |
| kanzure | pupnik: http://heybryan.org/exp.html is a proposal of ours | 22:01 |
| kanzure | fenn: yes, maybe something about inhibition or something | 22:01 |
| fenn | pupnik: dont slip in the bs :) | 22:01 |
| kanzure | yeah no kidding | 22:01 |
| pupnik | no it's a nice trick | 22:01 |
| kanzure | there's lots of bs in terminologies | 22:01 |
| kanzure | in exp.html | 22:01 |
| kanzure | fenn: and that works especially well if you can rewrite the aptamers in real time or something | 22:01 |
| kanzure | to make it a realtime "during selection" feedback thingy :-/ | 22:02 |
| pupnik | i don't know if it's standard now | 22:02 |
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| fenn | kanzure: the aptamer selection process would have to be rewritten from the ground up most likely | 22:02 |
| kanzure | fenn: the ruthemund work is basically the same thing with 'self-assembling DNA' except that's just a DNA implementation and it just makes maps or something, instead of trying to explore a nucleic acid possibility space | 22:02 |
| kanzure | fenn: it's just an example; I'm sure it could work with RNA sequencing and having portions of RNA molecules detect something | 22:02 |
| kanzure | I mean, what the hell else is this going to be useful for | 22:03 |
| kanzure | writozymes to make biological things for humans, at best | 22:03 |
| procto | I think pupnik is just establishing cred :> | 22:03 |
| fenn | like, it has to grab onto your molecule AND change conformation | 22:03 |
| kanzure | or making new hacks to lifeforms | 22:03 |
| fenn | terraforming | 22:03 |
| kanzure | hrm? | 22:03 |
| fenn | (if anyone cares about terraforming anymore) | 22:03 |
| pupnik | procto: it was new back when we did it. maybe it's standard now? i don't know | 22:03 |
| procto | right | 22:03 |
| procto | i understand | 22:03 |
| fenn | kanzure: i think with easy enough access to DNA synthesis, the protein folding problem will become obvious | 22:03 |
| * procto has only just started really getting into bio stuff | 22:04 | |
| procto | i've been doing neuro for quite a while | 22:04 |
| kanzure | fenn: has DNA synthesis been our barrier to protein folding characterization ? | 22:04 |
| fenn | not the 'how does this sequence fold' problem - but 'how to make this structure' starting from scratch | 22:04 |
| procto | but totally fresh to molecular bio | 22:04 |
| kanzure | procto: neuro is awesome :) | 22:04 |
| kanzure | http://heybryan.org/recursion.html | 22:04 |
| procto | I had an amazing neuro class in highschool | 22:04 |
| kanzure | http://heybryan.org/mediawiki/index.php/Henry_Markram | 22:04 |
| procto | the teacher was amazing | 22:04 |
| pupnik | hey if you are interested in consciousness, rodney cotterill's 'enchanted looms' is heavy! better than minskian crap imo | 22:04 |
| kanzure | http://heybryan.org/mediawiki/index.php/Computational_neuroscience | 22:04 |
| kanzure | http://heybryan.org/mediawiki/index.php/Neurofarm | 22:04 |
| fenn | kanzure: also atom-level imaging.. that's why i'm interested in high-res NMR | 22:05 |
| fenn | or MRI if you prefer | 22:05 |
| pupnik | fuck. high-density channel | 22:05 |
| kanzure | pupnik: I don't know what the hell consciousness is. | 22:05 |
| kanzure | pupnik: hell yeah :) | 22:05 |
| procto | it was better than what some friends got in my univesrity over 2 years, and we have a very good neuro program (at BRandeis University) | 22:05 |
| procto | basically, spent a year cutting up brains | 22:05 |
| kanzure | fenn: ok, so with DNA synthesis then we can try to do protein folding I guess | 22:05 |
| kanzure | fenn: but that's not quite solid state and I'm not sure if that's worth our time | 22:05 |
| procto | and getting 100/200 on tests (which was just aove the average) | 22:06 |
| kanzure | at best the writozyme is useful for the bioreactor/kit/thing that can help us interface with our own biologies | 22:06 |
| kanzure | anything else -- like ecological terraforming and so on -- seems 'meh' in comparison | 22:06 |
| kanzure | not sure | 22:06 |
| fenn | kanzure: there's gotta be a middle ground between drexler and biology | 22:06 |
| kanzure | maybe I'm just depressed tonight :) | 22:06 |
| kanzure | fenn: ah | 22:06 |
| kanzure | good point, I need to reconsider | 22:06 |
| fenn | i think that's what gershenfeld is trying to do | 22:06 |
| kanzure | okay, and to some extent what we're trying too | 22:06 |
| fenn | with GIK | 22:06 |
| kanzure | GIK? | 22:06 |
| fenn | press fit construction system | 22:06 |
| fenn | "great invention kit" | 22:07 |
| fenn | its those puzzle shape pieces | 22:07 |
| procto | pupnik: very high. I remarked on it just a couple of days ago | 22:07 |
| procto | pupnik: it's quite delightful that way | 22:07 |
| kanzure | so, Zack, one of the guys that hangs around the lab, has a proposal for a synthetic amorphous computing setup. your DNA molecule is connected via tethers to molecules at the end that diffuse messengers between each other. So you just write the sequence to make new programs in a certain order. Not sure if I care that much about this. | 22:07 |
| kanzure | fenn: uh? so just "build a house from a box of (large?) puzzle pieces' ? | 22:07 |
| pupnik | i will have to mostly lurk | 22:07 |
| procto | pupnik: it's sorta like how I am on phreadom, but it's not just me:> | 22:07 |
| kanzure | phreadom? | 22:07 |
| fenn | kanzure: GIK comes in many length scales | 22:08 |
| kanzure | fenn: is it lego for construction? | 22:08 |
| fenn | from 1m to 100micron? something like that | 22:08 |
| * kanzure is missing the analogy | 22:08 | |
| fenn | its like lego but 2d | 22:08 |
| kanzure | neat | 22:08 |
| pupnik | i'll shoot down any bullshit i detect for fun and ?profit? though | 22:08 |
| fenn | it evolved out of their playing with laser cutters | 22:08 |
| procto | kanzure: another channel, probably not your scene | 22:08 |
| fenn | vote for ron paul? bleagh | 22:09 |
| fenn | he's a politician, right? | 22:09 |
| pupnik | lets leave politics out of it | 22:09 |
| fenn | its in the topic | 22:09 |
| kanzure | wtf | 22:09 |
| kanzure | why is Ron Paul in the topic | 22:10 |
| fenn | er, in #phreadom | 22:10 |
| kanzure | oh | 22:10 |
| * kanzure sighs | 22:10 | |
| procto | hence, my caveat :> | 22:10 |
| pupnik | it's easy. you're in favor of force and fraud or not | 22:10 |
| kanzure | what the fuck? | 22:10 |
| pupnik | force | 22:10 |
| pupnik | fraud | 22:10 |
| fenn | i wish irssi didnt color pupnik and procto the same | 22:11 |
| procto | fenn: sorry | 22:11 |
| fenn | brb. new kernel. play nice :) | 22:11 |
| pupnik | just consider that voluntary associations are preferable to forcible ones | 22:11 |
| pupnik | and let that color your politics | 22:11 |
| kanzure | politics is totally bunk around here | 22:11 |
| pupnik | and we can be friends | 22:11 |
| kanzure | we're technologists | 22:11 |
| kanzure | we solve practical problems | 22:12 |
| pupnik | well consider my words as a favor to the newbie | 22:12 |
| pupnik | i have to fly to vienna in 3 hours and i'm pretty trashed | 22:13 |
| kanzure | http://www.youtube.com/watch?v=rNM4eFsX68Y | 22:13 |
| pupnik | hope to talk later | 22:13 |
| kanzure | oh, don't watch that one | 22:13 |
| procto | too late! | 22:14 |
| kanzure | here we go | 22:14 |
| kanzure | http://www.youtube.com/watch?v=i68cEsALWt0&feature=related | 22:14 |
| kanzure | That's the relevant one. | 22:14 |
| procto | hehe good one | 22:16 |
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| kanzure | fenn: back? | 22:30 |
| fenn | yo | 22:30 |
| pupnik | i was just going to sleep | 22:31 |
| pupnik | but wanted to say one more thing | 22:31 |
| pupnik | having 'invented' transhumanism | 22:32 |
| fenn | nobody invented transhumanism | 22:32 |
| pupnik | the point of the universe is to increase the depth of the self reflection | 22:32 |
| pupnik | make the flower prettier, the fractal deeper | 22:32 |
| pupnik | before the heat death | 22:32 |
| pupnik | ok now really sleeping | 22:33 |
| kanzure | before the heat death? | 22:40 |
| kanzure | *cough* Masque of the Heat Death *cough* | 22:40 |
| kanzure | fenn: cis-factor just sent a nasty email out | 22:40 |
| kanzure | very territorial people | 22:40 |
| * kanzure gets a link | 22:41 | |
| kanzure | http://groups.google.com/group/diybio/browse_frm/thread/330a449671e6b22d | 22:42 |
| kanzure | ' | 22:42 |
| kanzure | * p.s. bryan bishop: we want to produce a high-quality, highly-granular | 22:42 |
| kanzure | collection of links, not a gigantic disorganized grab-bag' | 22:42 |
| kanzure | by that they mean | 22:42 |
| kanzure | "go add links to del.ico.us' | 22:42 |
| kanzure | which is a terrible, terrible strategy | 22:42 |
| kanzure | argh | 22:42 |
| kanzure | have programmers lost their mind? | 22:42 |
| procto | ehehe | 22:43 |
| procto | that part totally perplexed me | 22:43 |
| procto | I don't get it | 22:43 |
| kanzure | procto: They're complaining about the biohacking toolkit project. | 22:44 |
| kanzure | without actually making a good suggestion | 22:44 |
| procto | oh, I got *that* :> | 22:44 |
| kanzure | Good news. | 22:45 |
| kanzure | The mailing list has surpassed 150 subscribers. | 22:45 |
| procto | I'm still a bit unsure about the way that works, but I'm not sure their delicious links plan is any better, or even as good | 22:45 |
| procto | kanzure: which list? hplusroadmap? | 22:45 |
| procto | I should join that | 22:46 |
| kanzure | procto: yep | 22:46 |
| kanzure | probably :) | 22:46 |
| procto | which page has the signup i'm looking for? | 22:46 |
| kanzure | http://heybryan.org/cgi-bin/mailman/listinfo/hplusroadmap | 22:46 |
| procto | thanks | 22:46 |
| * kanzure wrote a script last night to automatically 'friend' people on twitter; has been getting a lot of new contacts through that method, oddly enough | 22:46 | |
| kanzure | I took a list of 70 people on a biohack tweet list thing, and then automatically recursed through that | 22:47 |
| kanzure | took a few hacks with wget, but nothing too terrible | 22:47 |
| kanzure | maybe I'll organize the scripts and throw them up on my site later | 22:47 |
| kanzure | okay, so the delicious method isn't that good either because the database is totally cutoff from us | 22:48 |
| kanzure | so it's just like adding links in a very useless spot | 22:48 |
| kanzure | the links need to be added to files or a local database solution | 22:48 |
| kanzure | it's not too hard to then dump those links into delicious if the delicious developers are interested or something | 22:49 |
| kanzure | but this information is something that you need to have locally, not on the web | 22:49 |
| kanzure | I wonder if I should start holding nightly lectures or something | 22:51 |
| kanzure | or maybe just announce to the mailing list that we are still in here | 22:51 |
| kanzure | :-/ | 22:51 |
| procto | kanzure: actually, since my main background is in linguistics | 22:51 |
| fenn | are there no open source (or at least friendly to data exchange) social bookmarking tools? | 22:51 |
| procto | i can devise some fun semantic ontology | 22:51 |
| procto | for organization | 22:51 |
| procto | for things like biohack | 22:52 |
| procto | I'll give it several thinks | 22:52 |
| fenn | procto: we dont need terms that aren't self explanatory | 22:52 |
| kanzure | fenn: Noah, who I met through David (as in, David-who-was-mentioned-in-IEEE-Spectrum, aka Gershenfeld's David), was mentioning to me last night a silly php+mysql+apache setup that is trying to do the social bookmarking stuff on the clientside via lightweight httpdaemons. | 22:52 |
| kanzure | semantic ontologies suck | 22:52 |
| procto | fenn: hich terms? | 22:52 |
| kanzure | the point isn't so much the semantic ontology | 22:53 |
| kanzure | but rather the idea of the people behind it | 22:53 |
| kanzure | and those people that are doing some daily things to keep everything moving | 22:53 |
| fenn | the point is clarity of communication | 22:53 |
| kanzure | any static ontology is going to suck immensely :) | 22:53 |
| kanzure | and anything that requires constant rehashing is going to suck immensely too | 22:53 |
| procto | certainly | 22:53 |
| kanzure | I'd like to route around this problem somehow | 22:53 |
| procto | the idea is to merely construct the seed in the right way | 22:53 |
| kanzure | in many ways the seeds are already there | 22:54 |
| kanzure | i.e., git+ikiwiki+wiki in general+skdb+databases+filesystems+files+folders etc. etc. | 22:54 |
| kanzure | oh, I guess if epitron was in here (or maybe nsh) one of them would complain about the metaphors for computing | 22:54 |
| fenn | kanzure: actually the la?mp bookmark tool doesnt sound so bad | 22:54 |
| kanzure | oh, Enki-2 would too | 22:54 |
| kanzure | fenn: it doesn't do anything yet, so it's basically just a lamp installation | 22:54 |
| procto | just to clarify, I was replying to your post on diybio | 22:54 |
| kanzure | with some crappy php libraries that supposedly do some xml parsing maybe | 22:54 |
| kanzure | let me go look it up | 22:55 |
| kanzure | procto: yeah :) | 22:55 |
| kanzure | procto: oh, I see what you mean | 22:55 |
| kanzure | but still | 22:55 |
| fenn | doesnt do anything? how hard could it be to keep track of URL's? | 22:55 |
| fenn | and some words. sheesh | 22:55 |
| kanzure | fenn: it's more focused on the social networking aspects at the moment | 22:55 |
| kanzure | however, adding a module for links and whatever | 22:55 |
| kanzure | is sounding like a five minute job | 22:55 |
| kanzure | php is kinda like that | 22:55 |
| kanzure | easy in, easy out | 22:55 |
| fenn | i just want tagged bookmarks ferchrissakes | 22:56 |
| kanzure | http://noserub.com/ | 22:56 |
| kanzure | I want tagged bookmarks in anything BUT a browser | 22:56 |
| fenn | and tagged tags? | 22:56 |
| kanzure | i.e., tagged file system | 22:56 |
| kanzure | hrm | 22:56 |
| kanzure | I wonder if that's marketable | 22:56 |
| kanzure | I'm sure somebody would be willing to pay somebody to do a tagged file system | 22:56 |
| kanzure | on the grounds of stuff like 'efficiency' | 22:56 |
| kanzure | and 'web2.0 voodoo magic' | 22:56 |
| fenn | heh | 22:56 |
| kanzure | procto: So, I'm thinking about your offer. | 22:57 |
| kanzure | procto: I'm wondering how to make it functionally useful. | 22:57 |
| kanzure | Not just a static ontology. | 22:57 |
| procto | well, I don't have anything good yet | 22:57 |
| kanzure | Maybe we can run some server daemons to currlate (aggregate?) things like protocols from different website.s | 22:57 |
| procto | i'll think about it and let you know if I've got something good | 22:57 |
| procto | to use a metaphor | 22:58 |
| kanzure | And then these could be processed in an inbox by some people that want to help out, and they would then go "push" it to other people that might be interested in packaging it up | 22:58 |
| procto | you need a seed for a crystal | 22:58 |
| kanzure | into packets to be included into the project and so on | 22:58 |
| kanzure | no crystals | 22:58 |
| procto | it doesn't need to be static, since it is itsel a graph | 22:58 |
| kanzure | fenn: alternative to noserub is http://gmpg.org/xfn | 22:58 |
| procto | rather, it will set "guidelines" as to how to grow the system | 22:58 |
| kanzure | fenn: seems more like soc-net stuff | 22:58 |
| kanzure | procto: I see. | 22:58 |
| kanzure | debian doesn't have any of that really | 22:59 |
| fenn | "How are you guys making money off Noserub? A: We don't. Open source, dude." its too bad that open source == starving programmers | 22:59 |
| kanzure | just general ways to manage the packages | 22:59 |
| kanzure | fenn: in vitro meat tanks => we can probably set up an operation where we feed programmers and then let them do their things | 22:59 |
| fenn | its not just about food | 22:59 |
| kanzure | housing = tents | 22:59 |
| kanzure | social contact = those guys may become best friends rather quickly | 23:00 |
| kanzure | each serious/hardcore programmer I've ever met, in person, has become a good friend or contact or something like that :) | 23:00 |
| kanzure | but social stuff doesn't really matter | 23:00 |
| kanzure | that'll be taken careof in whatever ways | 23:00 |
| fenn | kanzure: "debian doesn't have any of that really" wtf? the debian guidelines are the most important part | 23:01 |
| kanzure | erm, lemme go back to chekc | 23:01 |
| kanzure | but I seem to remember there being a single directory where they list all of the packages | 23:02 |
| kanzure | and the dependencies are determined more on a per-project basis | 23:02 |
| fenn | http://www.debian.org/social_contract is what i've been trying to get you to look at many times | 23:02 |
| fenn | just because all the files are dumped in one directory doesn't mean there's no structure or policy | 23:02 |
| kanzure | that seems to be about licensing | 23:03 |
| kanzure | there's policy in terms of what they each do, but not so much in terms of "this file must go under file 3332A-51J97. Otherwise you suck." | 23:03 |
| fenn | there is, it's somewhere else.. *googles* | 23:03 |
| kanzure | oh? | 23:03 |
| fenn | http://www.debian.org/doc/debian-policy/ | 23:04 |
| kanzure | also interesting - http://www.debian.org/devel/constitution | 23:04 |
| kanzure | hrm | 23:04 |
| kanzure | we really need to make a functional, computational system behind all of this | 23:04 |
| kanzure | it would be so easy to either (1) use debian or (2) mimic/steal :) | 23:05 |
| kanzure | but we don't have the functional fablab quite yet (even if it is just for the bioreactor setup) | 23:05 |
| procto | yeah, i use debian because it has a rather good system | 23:05 |
| fenn | there are even tools (lintian etc) to check conformity with the policy | 23:05 |
| procto | it decouples its various parst very nicely | 23:05 |
| kanzure | procto: do you know about apt-get ? | 23:05 |
| fenn | heh | 23:06 |
| fenn | procto: how many wheels on a car? | 23:06 |
| procto | though in practice it is mostly about debian gnu/linux | 23:06 |
| procto | kanzure: what about it? | 23:06 |
| procto | I mean... I use it | 23:06 |
| kanzure | procto: ok, that's what we're doing in here | 23:06 |
| kanzure | except it's not just for software | 23:06 |
| kanzure | :) | 23:07 |
| procto | yes, I understood that | 23:07 |
| kanzure | oh | 23:07 |
| kanzure | fooey. | 23:07 |
| procto | and that's what my idea of logarchy is, essentially | 23:07 |
| kanzure | oh, that's right, you had your logarchy website | 23:07 |
| procto | it's just a pretty name | 23:07 |
| procto | the log stand for logos, just so it's clear | 23:07 |
| procto | and as a first step towards acheiving "open source reality" | 23:08 |
| kanzure | reality is already 'open' | 23:08 |
| procto | I thought was merging reality and virtuality | 23:08 |
| procto | of* | 23:08 |
| procto | hence the djiyo project | 23:08 |
| kanzure | but reality could be much more 'open' :) | 23:08 |
| fenn | kanzure: yes it could | 23:08 |
| procto | well, it's open in theory | 23:08 |
| kanzure | entropy maximization, etc. etc. | 23:08 |
| procto | but we don't have all the tools | 23:08 |
| kanzure | (entropy is not disorder) | 23:08 |
| procto | and some of them are restricted on pain of coercive means | 23:09 |
| fenn | you're confusing lack of limits with clarity and ease of use | 23:09 |
| kanzure | also, lots of people confused with scarcity-centricism | 23:09 |
| procto | I am? | 23:09 |
| fenn | (that last was to kanzure) | 23:09 |
| kanzure | hrm | 23:09 |
| procto | ah | 23:09 |
| kanzure | I don't understand. | 23:10 |
| fenn | reality isn't open because it requires vast amounts of effort to understand the tiniest detail | 23:10 |
| procto | I think it's very easy to hack "local" reality, but I don't like taking psychoactive drugs | 23:10 |
| fenn | you're basically reverse-engineering (reverse-hacking in the case of bio) | 23:10 |
| procto | so I have to work on the "consensus" reality | 23:11 |
| fenn | bah. subjective viewpoint will never be reality | 23:11 |
| fenn | whether it's agreed upon or not | 23:11 |
| procto | that depends on your epistemological viewpoint | 23:11 |
| fenn | stop diluting the word | 23:11 |
| procto | i'm still working on mine :> | 23:11 |
| procto | which word? reality? or epistemology? | 23:11 |
| fenn | reality | 23:11 |
| procto | well, it's a very contentious word. like "mind" or "conciousness". | 23:12 |
| fenn | procto: could you please use words like 'information' and 'matter' instead of 'virtuality' and 'reality' since we can't agree on the meaning of these basic words | 23:16 |
| procto | oh, ok | 23:16 |
| procto | :> | 23:16 |
| procto | I can accomodate that | 23:16 |
| procto | in that case | 23:16 |
| procto | I would like to overlay information on top of our current sensory input- | 23:16 |
| fenn | great :) | 23:16 |
| procto | inputs* | 23:16 |
| kanzure | "the subjective viewpoint will never be reality" <-- I think we need to understand whether we consider a brain to actually, physically be there, and whether or not the brain is thinking about things (the subjective viewpoint) (not whether or not it is 'right' or 'wrong' -- the conversion of what the hell's going on in there, mapped to the outside world, is *WEIRD*) | 23:17 |
| procto | unfortunately there aren't any cyberneticians at my university | 23:18 |
| procto | I'd like to find some around and audit their class. | 23:18 |
| procto | haven't had the time yet. | 23:18 |
| * kanzure likes the Howto re: cyborgs; http://web.archive.org/web/20020409125125/www.tzekit.com/aw/cyborg101/main.html | 23:19 | |
| kanzure | 'In my quest for the perfect perspective with which to regard school, I created what I call the paradigm of the cyborg. It is the key manner in which learners will realise success. By viewing themselves as war-machines, of sorts, and the classroom as a battlefield, the students can destroy the notion that school is boring and mundane. This frame of reference also facilitates analysis of the situation in strategic and tactical term | 23:20 |
| fenn | too bad he didnt release it under a proper copyleft license | 23:20 |
| procto | I've seen some good cybernetic work into how a system (the brain, a computer) can map an external environment to an internal representation. alas, I can only adequately understand only a fraction so far | 23:21 |
| kanzure | fenn: since when do you care about licenses? | 23:21 |
| kanzure | are you serious? | 23:21 |
| kanzure | procto: I'd like to see some references. | 23:21 |
| procto | I will look for some tomorrow. i've made a note of it. | 23:22 |
| kanzure | :) | 23:22 |
| procto | since I'm going to sleep now :> | 23:22 |
| procto | night! | 23:22 |
| fenn | kanzure: yes i'm quite serious about licenses, since they define what's legal to do or not, which affects what is perceived as 'safe' or 'responsible' | 23:25 |
| fenn | it's stupid to contribute to something that may or may not get shut down in a year because you violated some stupid copyright that nobody cares about (but the publisher) | 23:26 |
| kanzure | I would hate to just randomly tack up a GPL license on the whole skdb thing | 23:26 |
| kanzure | much more so because of the randomness | 23:27 |
| fenn | GPL is a very strong copyleft.. it's "viral" which means you have to carefully consider the effects before using it | 23:27 |
| kanzure | not because of any objections to GPL | 23:27 |
| kanzure | eh | 23:27 |
| * kanzure wishes he could ignore this | 23:27 | |
| fenn | me too | 23:27 |
| fenn | i also wish i could ignore crypto, radiation safety, bioterrorism, etc etc | 23:27 |
| fenn | but other people won't, and i can't make decisions for them | 23:28 |
| kanzure | good side effect of openvirgle or diy spacehabitats is that you're actively constructing something against bioterrorism | 23:28 |
| fenn | maybe | 23:28 |
| kanzure | how the hell are they going to contaminate you if they can't reach you? | 23:28 |
| fenn | delayed onset | 23:29 |
| kanzure | reboot/start-from-scratch | 23:29 |
| fenn | translate your code to run on optical processors | 23:29 |
| kanzure | fun times | 23:29 |
| fenn | anyway | 23:29 |
| kanzure | I mean, why GPL over MIT over BSD over public domain over etc. ? | 23:30 |
| fenn | debian is hosted by many high bandwidth mirrors and can claim the moral high ground (and have people believe it) because everything is perfectly 100% legal | 23:30 |
| kanzure | ohcrap | 23:31 |
| fenn | you understand the difference between GPL and MIT license right? | 23:31 |
| kanzure | do we need moral high ground? | 23:31 |
| fenn | yes | 23:31 |
| kanzure | not quite :) | 23:31 |
| kanzure | remember, I avoid much of this stuff | 23:31 |
| kanzure | I just want me bits | 23:31 |
| fenn | ok, public domain is like, the least amount of protection | 23:32 |
| fenn | anyone can take it and say they wrote it | 23:32 |
| fenn | put their own license terms on it, whatever | 23:32 |
| fenn | MIT license retains copyright, but you can do whatever you want with it, sell it, refuse to give away the code to any modifications you make, etc | 23:32 |
| fenn | you can't claim you wrote a program under MIT license | 23:32 |
| kanzure | huhy? | 23:33 |
| kanzure | *huh? | 23:33 |
| fenn | BSD is similar to MIT, i dunno the difference really | 23:33 |
| kanzure | you can't claim you wrote it, hm | 23:33 |
| kanzure | okay | 23:33 |
| kanzure | really if we were going to do a 'license' I'd just want something like this: | 23:33 |
| kanzure | (1) viral | 23:33 |
| fenn | GPL was created because of the fear that people would take your program, make some awesome mod, and then refuse to share the results | 23:33 |
| kanzure | (2) viral | 23:33 |
| kanzure | right | 23:33 |
| kanzure | hm, whole open/free thing would be good too | 23:34 |
| fenn | in practice, it's hard to make that watertight, which is why there's GPL2 GPL3 LGPL etc | 23:34 |
| fenn | there's been companies "hacking" the license by doing stuff like hardware checksums to prevent running modified code (tivoisation) | 23:35 |
| kanzure | I wonder if RepRap can claim it's GPLed if they are using commodity parts (i.e., nonFree) | 23:35 |
| kanzure | wait wait wait | 23:35 |
| kanzure | just print a chip with the circuit layout | 23:36 |
| fenn | reprap only claims the software is GPL | 23:36 |
| kanzure | screw new code | 23:36 |
| kanzure | if you're going to do a checksum anyway. | 23:36 |
| fenn | just print a chip? what planet are you on? | 23:36 |
| fenn | the problem with open hardware right now is that nobody's figured out how to make a viral license for forcing you to share the designs when you produce a physical object from modified copyleft designs | 23:38 |
| fenn | stallman would say it more rhetorically compatible but that's his job | 23:39 |
| fenn | basically, industrial design copyright only applies to unmodified designs, which is totally worthless to us | 23:39 |
| fenn | then you get into the whole trademark/marketing thing where big companies can just screw you out of your own creation by throwing money at it | 23:41 |
| fenn | like, "you cant use the name SKDB because we trademarked it and used it more often" | 23:41 |
| fenn | or by finagling stupid patent laws | 23:42 |
| -!- fenn [n=pz@adsl-75-60-172-87.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap | 23:50 | |
| -!- Topic for #hplusroadmap: Intro: http://www.youtube.com/watch?v=ZXKbzbeipmI http://diybio.org/ http://openwetware.org/ | diy bio toolkit: http://biohack.sf.net/ | Automated societal knowledge (put it to work): http://heybryan.org/exp.html | Channel wiki: http://heybryan.org/mediawiki/ | F/OSS perspectives on Kurzweil: http://heybryan.org/fernhout/ | 23:50 | |
| -!- Topic set by kanzure [] [Sun Jun 8 13:00:15 2008] | 23:50 | |
| [Users #hplusroadmap] | 23:50 | |
| [ fenn ] [ nsh ] [ procto] [ Splicer] [ ybit] | 23:50 | |
| [ kanzure] [ parodyoflanguage] [ pupnik] [ wrldpc ] | 23:50 | |
| -!- Irssi: #hplusroadmap: Total of 9 nicks [0 ops, 0 halfops, 0 voices, 9 normal] | 23:50 | |
| -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008 | 23:50 | |
| -!- Irssi: Join to #hplusroadmap was synced in 34 secs | 23:51 | |
| fenn | wah. | 23:51 |
| kanzure | I think the biggest thing with open hardware is nobody's figured out how to make a setup to make the hardware really | 23:56 |
| kanzure | for example, open source experienced that problem | 23:56 |
| kanzure | businesses and investors wondered what these kids were on | 23:56 |
| kanzure | because it wouldn't possibly be compatible | 23:56 |
| kanzure | so, they popped up with their own kernels and operating systems etc. | 23:57 |
| kanzure | buh? http://www.cc.gatech.edu/~pesti/roadmap/ | 23:58 |
| fenn | just aggregations of other futurists' predictions | 23:59 |
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