--- Day changed Mon Jun 09 2008 01:19 < percent> You screwed up Ramen 01:19 < percent> ? 01:19 < kanzure> Nah. :) 01:38 < Vedestin> we don't have ramen here 01:39 < Vedestin> the brand i mean 01:42 * Vedestin heads off ot make some maggi noodles 02:04 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has quit ["Leaving."] 02:31 < ybit> there's an entire magazine dedicated to various types of ramen in japan :) 10:10 -!- nsh- [n=chatzill@wikipedia/nsh] has joined #hplusroadmap 10:21 -!- nsh [n=nsh@87-94-146-186.tampere.customers.dnainternet.fi] has quit [Read error: 104 (Connection reset by peer)] 10:21 -!- nsh [n=nsh@87-94-146-186.tampere.customers.dnainternet.fi] has joined #hplusroadmap 11:00 -!- faceface [n=chatzill@bioinformatics.org] has quit ["Bye, and thanks... probably."] 11:04 -!- nsh- [n=chatzill@wikipedia/nsh] has quit ["relevant to my interests"] 11:12 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has quit ["Client exited"] 11:12 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has joined #hplusroadmap 11:31 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has quit ["User pushed the X - because it's Xtra, baby"] 11:50 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has joined #hplusroadmap 12:05 -!- cis-action [n=cis-acti@c-24-128-50-50.hsd1.ma.comcast.net] has joined #hplusroadmap 12:05 < kanzure> Hey cis-action. 12:06 < 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 12:11 < cis-action> cool 12:11 < cis-action> I'll check it out 12:11 < cis-action> back in a sec... 12:14 -!- cis-action [n=cis-acti@c-24-128-50-50.hsd1.ma.comcast.net] has quit [] 12:25 -!- nsh- [n=nsh@87-94-146-186.tampere.customers.dnainternet.fi] has joined #hplusroadmap 12:26 -!- nsh [n=nsh@87-94-146-186.tampere.customers.dnainternet.fi] has quit [Connection timed out] 12:28 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 13:09 < 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 13:10 < 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 13:23 -!- percent [n=percent@66.158.193.28] has quit [" "] 13:30 < fenn> duhh. use a cell, fucktard 13:30 < fenn> emulsion.. gah 13:31 < fenn> how big is a typical TRN reaction vessel? i'd think the speed would be proportional to the size 13:35 < fenn> nsh-: i read permutation city. rather depressing. 13:36 < 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 13:37 < fenn> (one of the flaws.. i dunno about the whole subjectivity = reality aspect) 13:38 < 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 13:40 < 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 13:41 < 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 13:42 < fenn> nsh-: permutation city reminds me of philip dick's "VALIS" 13:44 < 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 ... 13:45 < 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 13:46 < fenn> you could select for specificity and low crosstalk? 13:47 < 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 13:48 < 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? 13:49 < fenn> selecting for a large set of 'addresses' in-vitro with minimal cross-talk 13:49 < kanzure> you don't select it in vitro 13:50 < 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 13:51 < 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' 13:52 < fenn> i dont see why you cant do it in a cell, besides the difficulty of getting dna into a cell 13:53 < 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 13:54 < 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 13:55 < 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? 13:56 < fenn> google flop :( 13:57 < kanzure> so do we *have* to compartmentalize genotype+phenotype 13:58 < fenn> ah yes, it is: http://galileo.phys.virginia.edu/classes/152.mf1i.spring02/RandomWalk.htm 14:00 < fenn> kanzure: it might work, you just have to set the 'noise' below the threshold of turning on the switch 14:01 < fenn> binding to a surface is a good idea. i thought you meant just sticking them on the same place in the genome/plasmid 14:02 < 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 14:04 < fenn> transcriptional switches have a threshold, right? 14:06 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 14:06 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 14:08 < fenn> signal to noise ratio is more or less proportional to the amount of time you spend computing the address sequences 14:08 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 14:08 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 14:11 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [Remote closed the connection] 14:11 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 14:16 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [Client Quit] 14:20 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 14:26 -!- cis-action_ [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 14:42 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [Read error: 110 (Connection timed out)] 14:44 < fenn> it would be fun to turn a blender model into DNA pepakura 14:50 < nsh-> interesting comparison, fenn (VALIS and Permutation City) 14:51 -!- nsh- is now known as nsh 15:12 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has quit [Connection timed out] 16:15 < fenn> permutation city is also quite similar to http://www.orionsarm.com/eg/r/Re-Rg.html#Reality_Intratextualization_Project 16:16 < fenn> i dont know what the upstream source of that is called though 16:19 < fenn> it might be this, but its kinda dense http://www.frc.ri.cmu.edu/~hpm/project.archive/general.articles/1987/wave.ltx 16:21 < 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 16:22 -!- Splicer [n=p@h71n3c1o261.bredband.skanova.com] has joined #hplusroadmap 16:26 -!- cis-action_ [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [] 16:42 -!- Phreedom [n=freedom@www.online.dn.ua] has quit [Read error: 104 (Connection reset by peer)] 17:02 < 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 17:19 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has joined #hplusroadmap 17:46 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has joined #hplusroadmap 17:50 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has quit [Client Quit] 18:29 -!- cis-action [n=cis-acti@c-98-216-106-110.hsd1.ma.comcast.net] has quit [] 18:35 -!- cis-action [n=cis-acti@c-66-31-201-16.hsd1.ma.comcast.net] has joined #hplusroadmap 19:25 -!- shogunx [n=shogunx@rrcs-24-73-158-97.se.biz.rr.com] has quit [Remote closed the connection] 19:52 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has joined #hplusroadmap 19:52 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has quit [Read error: 104 (Connection reset by peer)] 19:54 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has joined #hplusroadmap 20:08 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has joined #hplusroadmap 20:11 < 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 20:12 < 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 20:13 < kanzure> :-/ 20:13 < Vedestin> i guess fenn is afk? 20:13 < kanzure> fenn is always afk :) 20:14 < 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* 20:28 < 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 21:54 -!- pupnik [n=pupnik@unaffiliated/pupnik] has joined #hplusroadmap 21:54 < 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. 21:55 < 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 21:56 < 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 21:57 < fenn> its like stumbling upon an abandoned factory in mint condition 21:57 < kanzure> otherwise it's just starting from scratch 21:57 -!- cis-action [n=cis-acti@c-66-31-201-16.hsd1.ma.comcast.net] has quit [] 21:57 < 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. 21:58 < 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 21:59 < 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 22:00 < 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 22:01 < 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 22:02 < kanzure> to make it a realtime "during selection" feedback thingy :-/ 22:02 < pupnik> i don't know if it's standard now 22:02 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has quit ["User pushed the X - because it's Xtra, baby"] 22:02 < 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 22:03 < 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 22:04 * 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 22:05 < 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 22:06 < 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 22:07 < 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? 22:08 < 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 22:09 < 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 22:10 < 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 22:11 < 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 22:12 < kanzure> we solve practical problems 22:12 < pupnik> well consider my words as a favor to the newbie 22:13 < 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 22:14 < 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. 22:16 < procto> hehe good one 22:24 -!- parodyoflanguage [i=pseudony@mmds-216-19-34-118.twm.az.commspeed.net] has quit [Read error: 110 (Connection timed out)] 22:24 -!- parodyoflanguage [i=pseudony@mmds-216-19-34-118.twm.az.commspeed.net] has joined #hplusroadmap 22:30 < kanzure> fenn: back? 22:30 < fenn> yo 22:31 < pupnik> i was just going to sleep 22:31 < pupnik> but wanted to say one more thing 22:32 < 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 22:33 < pupnik> ok now really sleeping 22:40 < 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 22:41 * kanzure gets a link 22:42 < 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? 22:43 < procto> ehehe 22:43 < procto> that part totally perplexed me 22:43 < procto> I don't get it 22:44 < 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* :> 22:45 < 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? 22:46 < 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 22:47 < 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 22:48 < 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 22:49 < 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 22:51 < 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 22:52 < 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? 22:53 < 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 22:54 < 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 22:55 < 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 22:56 < 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 22:57 < 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 22:58 < 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. 22:59 < 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 23:00 < 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 23:01 < 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 23:02 < 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 23:03 < 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? 23:04 < 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 23:05 < 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 ? 23:06 < 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 23:07 < 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 23:08 < 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) 23:09 < 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 23:10 < 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) 23:11 < 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 23:12 < procto> well, it's a very contentious word. like "mind" or "conciousness". 23:16 < 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* 23:17 < 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*) 23:18 < 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. 23:19 * kanzure likes the Howto re: cyborgs; http://web.archive.org/web/20020409125125/www.tzekit.com/aw/cyborg101/main.html 23:20 < 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 23:21 < 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. 23:22 < 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! 23:25 < 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' 23:26 < 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 23:27 < 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 23:28 < 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? 23:29 < 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 23:30 < 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 23:31 < 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 23:32 < 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 23:33 < 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 23:34 < 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 23:35 < 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 23:36 < 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? 23:38 < 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 23:39 < 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 23:41 < 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" 23:42 < fenn> or by finagling stupid patent laws 23:50 -!- 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 23:51 -!- Irssi: Join to #hplusroadmap was synced in 34 secs 23:51 < fenn> wah. 23:56 < 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 23:57 < kanzure> so, they popped up with their own kernels and operating systems etc. 23:58 < kanzure> buh? http://www.cc.gatech.edu/~pesti/roadmap/ 23:59 < fenn> just aggregations of other futurists' predictions