--- Day changed Sun Apr 06 2008 00:04 < mechie> hahaha 00:07 < kanzure> What is it? 00:21 < mechie> a black man 00:21 < mechie> in a tshirt 00:25 < kanzure> I see it. 00:26 < kanzure> also, it occurs to me that I can use molecular parallelism to crack military encryption codes 00:26 < kanzure> i.e., use selection experiments to crack codes 00:27 < epitron> do it 00:27 < epitron> :D 00:27 < epitron> there's already been a loophole discovered in DSA encryption 00:27 < kanzure> but then I wiill not only be a bioterrorist, but also an encryptoterrorist or something 00:28 < epitron> not if you work with someone rich and powerful :) 00:28 < epitron> $ ruby sha1_attack.rb 00:28 < epitron> How long do you want it to take to crack SHA1 (in days)? [default=1] 00:28 < epitron> > 50 00:28 < epitron> Cracking it in 50.0 using old_method will require 138888888888 computers 00:28 < epitron> Cracking it in 50.0 using FAST method will require 138888 computers 00:29 < epitron> that's a sha1 hash 00:29 < epitron> so, however many bits those are 00:29 < epitron> anyhow 00:30 < epitron> what i've learned in life is that people only go to jail when they have no friends who will fight to have them freed 00:30 < epitron> justice works because people help each other 00:31 < epitron> if you make enough waves, people will have to let you go 00:33 < epitron> especailly if you didn't do anything wrong :) 00:50 < kanzure> hm 00:50 < kanzure> perhaps 00:50 < kanzure> so, 138888 computers 00:50 < kanzure> let's just call it 150k computers 00:50 < kanzure> and call it 150 THz 00:50 < kanzure> this really depends on the algorithm, I guess 00:51 < kanzure> because you don't necessarily need all of the logic gates on a microprocessor 00:51 < kanzure> terahertz/gigahertz doesn't matter 01:55 -!- davidad_ [n=me@DAVIDAD.MIT.EDU] has quit ["Lost terminal"] 01:58 < epitron> are you trying to figure out how much molecule-processing it'll take? 01:59 < kanzure> yep 01:59 < kanzure> if we have enough molecules we might be able to solve it in a few seconds 01:59 < kanzure> but not if this takes a few hundred kilograms of molecules 02:09 < kanzure> Screw the mind(or heart)/brain duality BS. "I love you with all my heart" should become "I sense a spike in my dopaminageric potentiators and a secondary 5-HT2C disturbance in my orbitofrontal cortices and sympathetic subsystems. Cardio is up, neuro is up, let's roll." 02:09 < Aulere> lol 02:24 < epitron> i got a quesiton 02:24 < epitron> how does a molecule computer efficiently serach solution space 02:24 < epitron> or does it not have to do it efficiently? 02:25 < kanzure> it bumps around 02:26 < kanzure> however, 02:26 < epitron> i see 02:27 < epitron> you have parallel solution points bumping around? 02:27 < kanzure> well 02:27 < kanzure> check this out 02:27 < kanzure> http://heybryan.org/mediawiki/index.php/Ellingtonia#DNA_computation 02:28 < epitron> ok 02:28 < epitron> sec 02:28 < epitron> i'm enntagled in dental floss 02:28 < epitron> there we go 02:28 < epitron> now i am free to use BOTH hands 02:28 < kanzure> if so, we can't observe it 02:28 < epitron> not without a powerful telescope 02:29 < epitron> hahah 02:30 < epitron> ok 02:30 < epitron> but like, the information processing ability of the universe at the atomic level is staggering 02:30 < epitron> our brains store stupid amounts of information in complex lattices made of GOO 02:30 < epitron> imagine if you made it out of crystal 02:30 < kanzure> heh 02:30 < epitron> or nanotuuuubs 02:31 < epitron> (nanotübes) 02:31 < epitron> i haven't looked into nanotube computing, but ray kurzweil was talking about it 02:31 < kanzure> hrm, nanotube computing 02:31 < kanzure> screw that 02:31 < kanzure> http://heybryan.org/graphene.html 02:31 < kanzure> graphene computing :) 02:31 < kanzure> which is carbon too 02:31 < kanzure> just not necessarily in nanotube form 02:31 < epitron> have you looked at nanotube computers? 02:32 < kanzure> nope, but I do know that CNTs have semiconductor properties 02:32 < kanzure> which I plan to take advantage of 02:32 < epitron> you can transport individual electrons down a nanotube 02:32 < kanzure> :) 02:32 < kanzure> or confine them 02:32 < epitron> yep 02:32 < kanzure> with nanovalves, was it? 02:32 < epitron> and entangle them 02:32 < epitron> and do whatever else the universe permits 02:32 < kanzure> how? 02:32 < kanzure> the entanglement, I mean. 02:32 < epitron> you know.. like ... like amplitude phase coherent photon embossing 02:33 < epitron> - second like 02:33 < epitron> + light 02:33 < epitron> (i made that up) 02:33 < epitron> :D 02:33 < epitron> anyhow, yeah, i dunno much about quantum computers 02:33 < epitron> the whole field could be the result of an experimental error 02:34 < epitron> i'll look into nanotube computing perhaps 02:34 < epitron> then i will share the info 02:37 < kanzure> this is ridiculous 02:37 < kanzure> molecular computation is a tool in search of a use 02:37 < kanzure> computation is computation, you go to the substrate that lets you do it the best 02:37 < kanzure> molecules happen to not be this substrate 02:37 < epitron> you sure? 02:37 < epitron> quantum computation and nanotubes could be a powerful combination 02:37 < epitron> i'm not saying they are 02:38 < epitron> i don't know about those two fields 02:38 < kanzure> no, I mean biomolecules 02:38 < epitron> ah 02:38 < kanzure> http://heybryan.org/mediawiki/index.php/Ellingtonia is where I am at 02:38 < kanzure> even if the goal is to copy in vivo systems into in vitro systems 02:38 < kanzure> that's really retarded 02:38 < kanzure> you should just test your system in silico 02:39 < epitron> could you summarize ellingtonia in a sentence? 02:39 < kanzure> which negates the whole idea of implementing an in vitro biomolecular 'computation' or engineered in vitro system 02:39 < kanzure> hm 02:39 < epitron> nevermind 02:39 < epitron> i read the ToC 02:39 < kanzure> My attempt at satisfying the professor's challenge to find a use of biomolecular computation. 02:39 < epitron> haha 02:39 < epitron> i see 02:40 < epitron> you should mention that in 1. Challenge 02:40 < epitron> perhaps in parentheses 02:40 < kanzure> it's in there 02:40 < epitron> ok ;) 02:40 < epitron> it's interesting 02:40 < epitron> it tells where you are 02:40 < kanzure> "Find me a class of algorithms / problems where the inherent abilities of DNA or biomolecules will shine." 02:40 < epitron> you might forget down the road 02:40 < epitron> as you look back at your wiki 02:41 < epitron> sweet 02:41 < epitron> and nobody's solved that challenge? 02:41 < kanzure> right 02:41 < epitron> that's surprising 02:41 < kanzure> it's because DNA sucks at computing 02:41 < epitron> it's not really designed for that though 02:41 < epitron> it's designed for constructing things 02:41 < epitron> and then the things do the computing 02:41 < kanzure> I've found a *use* (in vitro modeling of in vivo systems) -- i.e., synthetic biology from the ground up ("What I cannot create, I do not understand") 02:42 < kanzure> but that's not what he wants me to do 02:42 < epitron> right 02:42 < epitron> but that's what it's best at :) 02:42 < epitron> building things 02:42 < kanzure> so there needs to be some equivalence 02:42 < epitron> it can do computation, but over long timescales 02:42 < kanzure> between building things 02:42 < kanzure> and computing 02:42 < kanzure> computing == building, perhaps 02:43 < epitron> well 02:43 < kanzure> so in what roles could we have biomolecules both build and compute at the same time 02:43 < epitron> you build a computer 02:43 < epitron> it's easy :) 02:43 < kanzure> uh? 02:43 < kanzure> heh, but yes 02:43 < epitron> like, the genetic computer can communicate 02:43 < kanzure> that's how I usually work 02:43 < epitron> our bodies do it by building messages 02:43 < kanzure> you just start assuming it's all easy 02:43 < kanzure> and then in the end it turns out you were right 02:43 < epitron> then the messages slowly propagate 02:43 < epitron> and you have this slow diffusion-time-scale computation going on 02:43 < epitron> fairly stable... 02:43 < epitron> somewhat perturbable 02:43 < kanzure> but that isn't where DNA shines 02:44 < kanzure> that sucks 02:44 < epitron> right, but it's requried for large-scale coordinated construction 02:44 < epitron> otherwise you can't build a computer 02:44 < kanzure> so what would it be coordinating 02:44 < kanzure> what are the 'builder units' 02:44 < epitron> large-scale structure 02:44 < epitron> all life does it 02:44 < kanzure> what are the builder units 02:44 < epitron> they use fractal algorithms to build complex structures 02:44 < epitron> algorithsm encoded in the dna 02:44 < kanzure> ah, perhaps it can be a GPL 02:44 < epitron> and computed using diffusion 02:45 < kanzure> then using diffusion of messengers this would allow growth directed programming languages to exist 02:45 < epitron> that's true 02:45 < kanzure> and then using this you have various molecules implicating the certain synthesis of particles in DNA 02:45 < epitron> or you could build something better than a brain 02:45 < epitron> hmmm 02:45 < kanzure> but this is assuming that you don't mess up the in vitro-ness when you add in the PCR and transcription molecules 02:45 < kanzure> because when you add in the drops 02:45 < kanzure> that's diffusion and you mess it all up 02:45 < kanzure> however, if it can self-correct for that error, that would be interesting 02:45 < kanzure> here's what I'm thinking 02:46 < kanzure> there can be the diffusion of nucleic acid messengers 02:46 < kanzure> and this diffusion would be based off of the location of each of the DNA molecules or whatever 02:46 < kanzure> so the ones that are in a high concentration area of those messengers would behave differently than those in the low concentration areas 02:46 < epitron> hold on 02:46 < epitron> i just realized i don't know what GPL stands for :D 02:46 < kanzure> and construction can proceed differently *because* you can have those nucleic acid messengers block transcription of certain proteins or structures 02:46 < epitron> i'm having trouble keeping up 02:46 < kanzure> GPL stands for Growth Programming Language 02:46 < epitron> i'm high and stoned 02:47 < epitron> and drunk 02:47 < kanzure> why are you high and stoned 02:47 < kanzure> and drunk 02:47 < epitron> but also high 02:47 < epitron> :D 02:47 < epitron> because i got bored 02:47 < epitron> also i was watching a show that encouraged it 02:47 < epitron> it was called THE ROOT OF ALL EVIL 02:47 < epitron> anyhow, back to growth programming languages 02:47 < kanzure> I don't know what would be transcribed though ... I guess it could be DNA self-assembly itself, but then you loose the molecules as you build the structure 02:48 < epitron> well, 02:48 < epitron> i think the problem you'd run into is that you'd need to use goo to build the computer 02:48 < epitron> like our brain does 02:48 < kanzure> uhh 02:48 < epitron> because amino acids can't bond with cool shit like neodymium 02:48 < kanzure> sure they can 02:48 < epitron> i guess they could like encase it 02:48 < kanzure> and if not 02:48 < epitron> can they? 02:48 < kanzure> we can evolve them to 02:49 < epitron> well, amino acids have a certain pliable structure 02:49 < epitron> they're easy to break apart and put back together 02:49 < epitron> it's not that strong 02:49 < epitron> neodymium is freakin heavy 02:49 < epitron> it might bash through them 02:49 < epitron> spinning at a million revolutions a femtosecond or whatever 02:57 -!- Aulere [n=dragon_d@131.229.176.252] has quit [] 03:02 < kanzure> http://glofish.com/ 04:09 < kanzure> is somebody around to do a bullshit analysis on an email I'm about to send? 04:26 < kanzure> http://heybryan.org/mediawiki/index.php/BS-analysis-requests 08:44 < fenn> explain how it will do something you cannot predict - is that possible? 08:45 < fenn> you need to explain more on part 1 09:14 < fenn> btw "I love you with all my heart" is a statement about goals, not so much about state 09:14 < fenn> at least that's how women see it 10:12 < kanzure> hm 10:13 < kanzure> something that I can't predict 10:13 < kanzure> so maybe I just need to fake it 10:20 < fenn> maybe i'm a cranky old goat, but why would unpredictable outcomes be desirable? 10:21 < fenn> that's no way to build useful systems 10:32 < kanzure> :( 10:32 < kanzure> http://www.diybio.org/ <-- Boston group, new, announcement was sent this morning 10:35 < fenn> maybe i would be excited if school hadn't beaten the soul out of me 10:37 < kanzure> that bad? 10:39 < fenn> he's right about tech culture 10:39 < fenn> how can you do anything with bio without arousing suspicion and fear? 10:40 < fenn> desktop-STM's is one thing, de-brained mice is another 10:41 < fenn> probably the only 'safe' area is plant genetics 10:42 < fenn> the hypocrisy is amazing 10:43 < fenn> we need an institutional review board to do mouse behavior experiments, but then people go and slaughter chickens and cows by the billions 10:49 < fenn> kanzure ever think about using animals as containers for your brain-pods? 10:51 < fenn> i'm reading this: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2220020 11:14 < kanzure> I don't really want to have to do deal with meat-bodies for brains 11:15 < fenn> even cute furry meat-bodies with furry flapping wings? 11:15 < fenn> you could have eyes in the back of your head 11:15 < kanzure> however, the article looks good 11:16 < fenn> scientific discussions of morality always leave a lot to be desired 11:17 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 11:18 < kanzure> the qual-chicken stuff looks interesting 11:19 < kanzure> quail* 11:19 < kanzure> but I don't know about "conferring humanity on mice" - what the hell? 11:22 < kanzure> who were you talking about when you said "he's right about tech culture" ? 11:23 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap 11:25 < fenn> diybio.org has a google group w/mailing list and a few comments 11:25 < kanzure> oh, right 11:25 < kanzure> I didn't bother to read the messages when I joined 11:27 < kanzure> So I wonder how I should handle the Ellington stuff. Should I just go email him and tell him that I don't understand emergence? That sounds rather newbish. You don't return to the professor after a few weeks with nothing to show. 11:27 < kanzure> I was thinking I'd just do a modified ring oscillator and say "here, I don't understand emergence" 11:27 < kanzure> something like: A->B->C->A is the ring oscillator, 11:27 < kanzure> so why not do something like 11:27 < kanzure> argh 11:28 < fenn> "Of course, human consciousness trapped in a mouse’s body would truly be cruel treatment" <- how is being stuck in a mouse any worse than being stuck in a monkey? 11:28 * fenn beats on his chest and throws feces 11:29 < kanzure> no feces throwing in here 11:29 < fenn> digital feces? 11:29 < kanzure> ok, fine 11:29 < kanzure> but not the wet ones 11:30 < fenn> kanzure: i dont want to say, 'told you so' but maybe you should go to ellington and say you dont understand emergence 11:30 < fenn> he probably means something else anyway 11:31 < fenn> one man's emergence is another man's magic 11:32 < kanzure> hm 11:32 < kanzure> I'm looking on Google Scholar 11:32 < kanzure> found an interesting article by Kauffman - "Escaping the Red Queen Effect" 11:32 < fenn> it would be interesting to die in a car accident and wake up in a mouse body 11:32 < kanzure> Red Queen is where you better damn hope/intend the whole is greater than the sum of the parts if you hope to go anywhere. 11:33 < kanzure> fenn: what are you suggesting? 11:33 < fenn> i thought red queen is just an evolutionary arms race 11:33 < kanzure> you know very well that we here wouldn't mind doing those experiments 11:33 < kanzure> meanwhile the institutions aren't going to implement them 11:33 < kanzure> for 'political' reasons and whatever 11:33 < kanzure> so what do you want to do? 11:33 * fenn points at diybio.org 11:33 < kanzure> fenn: nope, red queen never involved anything other than Alice 11:33 < kanzure> fenn: hm? 11:34 < fenn> my point was that anything "diy bio" is going to instantly have a negative connotation 11:34 < fenn> its only value is that you can do things you wouldnt be able to do in a university setting 11:35 < kanzure> no, 11:35 < kanzure> some of us are not in a university willing to let us do stuff 11:35 < fenn> well, what are you going to do? 11:35 < fenn> i mean, basically anything h+ is socially unacceptable 11:36 < fenn> that leaves stuff like, sewage treatment 11:36 < kanzure> what is your point 11:36 < kanzure> we don't care about social unacceptability 11:36 < kanzure> because we have bigger guns 11:36 < fenn> what is something that you would be able to do at a university but can't because you're not at a uni? 11:37 < kanzure> get access to scientific databases 11:37 < fenn> diy doesn't help there 11:37 < kanzure> right 11:38 < fenn> unless you propose building entirely new databases from amateur experimental results 11:38 < fenn> that's a bit beyond "diy" tho 11:42 < kanzure> http://www.eminerals.org/ 11:43 < kanzure> for the sciencey stuff - http://www.eminerals.org/ 11:43 < kanzure> erm 11:43 < kanzure> http://www.eminerals.org/highlights/index.html 11:46 < fenn> oo structured water 11:49 < kanzure> "the system as a whole has the property, but the components, individually, do not" 11:49 < kanzure> heh 11:49 < kanzure> how about this 11:49 < kanzure> system X has N nodes 11:49 < kanzure> N are not special 11:49 < kanzure> X is special 11:49 < kanzure> therefore, system X has done emergence 11:49 < kanzure> I am done. I just had to call it special. 11:50 < kanzure> How is this an example of emergence?? " Robots play soccer or build heaps of collected items (cf. Figure 2)." 11:51 < kanzure> another example this paper gives is 'swarm behavior' -- like birds flying around an obstacle 11:51 < kanzure> swarm behavior is just "wisdom of the crowds" stuff 11:54 < kanzure> aha 11:54 < kanzure> http://www-users.cs.york.ac.uk/~susan/bib/ss/nonstd/iceccs06.pdf <-- Engineering Emergence. quantitative. 11:54 * fenn mumbles something about non-linearity 11:55 < kanzure> nonlinear systems from discrete components? 11:59 < kanzure> "intrinsic emergence" 11:59 < kanzure> "the system itself capitalizes on the patterns that appear" 12:00 < kanzure> "novel causal powers coming into being at specific levels of ontology" 12:01 < fenn> hurr 12:01 < fenn> self-assembly maybe 12:02 < kanzure> ... ` Hordijk et al [30] talk of “dynamical systems in which the interaction of simple components with local information storage and communication gives rise to coordinated global information processing”.` 12:02 < fenn> wtf is a causal power? 12:02 < kanzure> a flying spaghetti monster, perhaps 12:02 < fenn> looks to be associated with AI 12:05 < kanzure> `O’Conner [33] (as quoted by Bedau [10]) defines emergence as: “Property P is an emergent property of . . . O iff . . . P has a direct (‘downward’) determinative influence on the pattern of behaviour involving O’s parts.” ` 12:06 < kanzure> so how would I do that without predicting P 12:08 < kanzure> ` Kaufmann [31] considers random boolean networks (RBNs), taken to be highly simplified models of gene regulatory networks (GRNs). He analyses the structure and stability of their attractor spaces, and draws an analogy between these attractors and cell types: maybe somehow cells ‘are’ the attractors of GRNs.` 12:09 < kanzure> I know Andy's wroked with Kauffman. I wonder if that's the same guy. 12:09 < kanzure> interesting, in ref 31 they spell his name differently 12:11 < fenn> well duh, the point of a GRN is to ensure the stability of a cell 12:21 < kanzure> Abbott [2] is one of the few authors who explicitly talk about emergent properties in engineering design terms: the high level emergent is the abstract design, and the lower level is the implementation of that design. Furthermore, “these abstract designs are neither derivable from nor logical consequences of their implementations”: a creative design step is necessary. 12:22 < fenn> woo 12:22 < fenn> i'm glad someone else is saying it 12:22 < kanzure> so just come up with the abstract design 12:22 < fenn> your design must exhibit a creative abstract property! 12:22 < kanzure> and then try to splice together engineering components to make it happen 12:22 * fenn gets the ruler 12:23 < kanzure> no, 12:23 < kanzure> it seems to be that it's just 'targetting' 12:23 < kanzure> i.e., you propose a system 12:23 < kanzure> and then you go find components that can make it happen 12:23 < kanzure> but the components have to be 'weird' and 'indirect' or something? 12:24 < fenn> i think emergence as commonly used means more like, throw a bunch of crap in a pot and shake it around until a television comes out 12:24 < fenn> but that doesnt happen 12:24 < fenn> it's statistically improbably 12:25 < fenn> however, if you have an infinite improbability drive, such as our friend e. coli, you can brute-force it 12:25 < kanzure> clearly we just need to replace the 'motivator' circuits in my brain with an infinite improbability drive 12:25 < kanzure> in fact, I probably already have it, it explains so much about what I am capable of doing 12:26 < fenn> yep 12:26 < fenn> creativity, not motivation 12:26 < fenn> motivation is simple neurotransmitter circuits i think 12:27 < fenn> a knowledge synthesizer! 12:27 < fenn> hidden in plain sight 12:28 < fenn> how does it feel to be limited by your own intelligence? 12:28 < fenn> i think it feels funny 12:28 < fenn> funny-haha 12:28 < kanzure> Abbott's paper - http://arxiv.org/abs/cs/0602045 12:29 < kanzure> motivation is something much different than a simple circuit 12:29 < kanzure> Have you ever gotten programmer's syndrome? 12:29 < fenn> i dont know, what's programmer's syndrome? 12:29 < kanzure> the incredible lack of motivation that programmers get when they aren't getting results 12:30 < kanzure> I had it for a few years, until I just started assuming that motivation was a matter of assumption 12:30 < kanzure> so now I just assume I am motivated 12:30 < fenn> please elaborate 12:30 < kanzure> if you go over to any programming community, especially the allegro and gamedev.net communities where there are young programmers, you see really smart guys not getting much of anything done, not because they don't want to, but because they are "tired" 12:30 < kanzure> they do not necessarily have any depression or mental disorders and so on (other than whatever helps them be a programmer) 12:32 < fenn> i'm quite familiar with it, but not the "solution" 12:32 < kanzure> gah, 67 pages 12:32 < kanzure> the solution is weird and I can't quantify it 12:32 < kanzure> I think I *argued* myself into motivation somehow 12:32 < kanzure> so now I seemingly have an infinite supply of it ;) 12:33 < fenn> hopefully by thinking about it you dont destroy your mechanism 12:33 < kanzure> right 12:33 < kanzure> "As I move, so I move the universe." - Danlo 12:39 < kanzure> http://heybryan.org/edeism.html not related 12:40 < fenn> the edeist stuff is painfully immature sci-fi 12:45 < kanzure> immature? 12:45 < fenn> the idea is good, but the implementation is not very subtle 12:45 < kanzure> oh 12:45 < kanzure> the implementation is subtle in the story, though 12:45 < kanzure> http://en.wikipedia.org/wiki/Neverness 12:46 < kanzure> I was just taking some lines from the book. 12:46 < fenn> also the intrinsic impossibility of writing about something more intelligent than yourself 12:46 < kanzure> you can write _about_ it, but nobody says you have any idea what you're talking about 12:46 < kanzure> let me go fetch some lines 12:47 < fenn> you cant predict what it would do, therefore you cant write about it 12:47 < kanzure> Instantly the trillions of branches of the tree narrowed to one. So, it 12:47 < kanzure> was a finite tree after all. I was saved! I made another mapping to the 12:47 < kanzure> point-exit near a blue giant star. I fell out into realspace, into the 12:47 < kanzure> swarm of the ten thousand moonbrains of the Solid State Entity. 12:47 < kanzure> We talked for a while about the origins of such immense and fathomless 12:47 < kanzure> beings as the Silicon God and the Solid State Entity, and other things 12:47 < kanzure> that pilots talk about. Soli told us of his journey to the core; he 12:47 < kanzure> spoke of dense clusters of hot new stars and of a great ringworld that 12:47 < kanzure> some god or other had assembled around Betti Luz. Lionel argued that the 12:47 < kanzure> great and often insane mainbrains (he did not like to use the word 12:47 < kanzure> "gods") roaming the galaxy must be organized according to different 12:48 < kanzure> principles than were our own miniscule minds, for how else could their 12:48 < kanzure> brains separate lobes-some of which were the size of 12:48 < kanzure> moons-intercommunicate with others across light-years of space? It was 12:48 < kanzure> an old argument. 12:48 < kanzure> It was one of the many bitter arguments dividing the 12:48 < kanzure> pilots and professionals of our Order. Lionel, and many esc'hatologists, 12:48 < kanzure> programmers, and mechanics as well, believed the mainbrains had mastered 12:48 < kanzure> nearly instantaneous tachyonic information flow. He held that we should 12:48 < kanzure> seek contact with these beings, even though such contact was very 12:48 < kanzure> dangerous and might someday force the Order to change in ways repugnant 12:48 < kanzure> to older and more old-fashioned pilots such as Soli. "Who can understand 12:48 < kanzure> a brain encompassing a thousand cubic lightyears of space?" Soli asked. 12:49 < kanzure> So there's ways to work with it, I guess. 12:49 < fenn> they're talking about Ede? 12:50 < fenn> at what point does Nick Ede become the Solid State Entity? 12:50 < kanzure> Edge is another god 12:50 < kanzure> *Ede 12:52 < fenn> btw i think the logic in tat passage is flawed.. they must be organized differently because of the latency between parts, but then goes on to say that they have zero-latency communications? 12:54 < kanzure> eh, yes, Zindell stumbles on a few points like that 12:55 < kanzure> personally, I don't go for the tachyon explanation 12:55 < kanzure> I much rather prefer the latency ideas 12:55 < kanzure> if you have giant moonbrains then let them be separated, who cares if your thought takes a thousand years if it's the equivalent of a million years of other measely humans thinking? 12:55 < kanzure> plus you get to have at least human-level thoughts on the local scale of each moonbrain 13:05 < kanzure> btw, I run a megascale engineering mailing list for discussions like these 13:05 < kanzure> last I posted, I was submitting schematics and plans for assembling the Death Star. 13:15 < fenn> a sphere isnt really a good shape for high-energy stuff 13:16 < fenn> hint: dont draw inspiration from science-fantasy :) 13:25 < kanzure> heat-dissipation 13:25 < kanzure> I'm pretty sure there's been lots of calculations on this 13:26 < kanzure> esp. Anders Sandbergs - Physics of Intelligent Superobjects, 1999 13:26 < kanzure> Anders Sandberg, woops 13:36 < fenn> planets are round because they have wimpy compressive strength 13:37 < fenn> you could also make your massive object spin and use tensile strength 13:37 < fenn> or gravitational tidal forces (in orbit around a neutron star or something) 13:37 < kanzure> the best way to do heat dissipation is to maximize surface area 13:38 < fenn> well, "best" is subjective 13:38 < kanzure> most 13:38 < fenn> i might say the "best" way to do heat dissipation is to use a heat pump to raise the temperature and thus radiance 13:39 < fenn> you could have a 'colloidal suspension' of asteroids but they would just bounce IR back and forth between each other 13:40 < fenn> high surface area, but poor heat emitter 13:41 < fenn> with reversable computing, heat dissipation might not be important at all 13:41 < kanzure> hm 13:41 < fenn> reversible* 13:43 < fenn> i note that biology is quite stingy with irreversible operations 13:43 < fenn> most enzymes function in a state of equilibrium 13:44 < fenn> there's no direction, except there's more of the input type of molecule than the output 15:19 < kanzure> EUREKA 15:19 < kanzure> fenn: 15:19 < kanzure> how about liquidwars in vitro 15:19 < fenn> what's liquidwars? 15:19 < kanzure> http://sushiknights.org/alejo/liquidwars.jpg 15:19 < kanzure> it's a game for debian 15:19 < kanzure> you're a liquid and you try to take over the other liquid into your color 15:19 < kanzure> the switches would be bound to the surface of the plate 15:19 < kanzure> and then you have them all trying to convert their neighbors, sort of 15:20 < kanzure> and the 'colors' get to have their own strategies attached to them 15:20 < kanzure> if you give it an interesting configuration state, you don't necessarily know the result 15:20 < fenn> hmm is it like 'go' but less discrete? 15:20 < kanzure> not sure 15:20 < fenn> you try to surround the other liquid? 15:21 < kanzure> http://en.wikipedia.org/wiki/Go_(board_game) 15:21 < kanzure> you convert the other color-liquid into your own color 15:21 < kanzure> on the computer, you use the arrow keys to move your liquid in aggregate to weak points of the enemy 15:21 < kanzure> so you have a 'head' that you are strategically guiding 15:21 < kanzure> obviously in the in vitro instance, you'd have to program it ahead of time 15:22 < fenn> check out go 15:22 < kanzure> http://en.wikipedia.org/wiki/Go_(board_game) 15:22 < kanzure> I'm reading. 15:22 < kanzure> hm, I seem to remember it 15:22 < kanzure> it's sort of close 15:31 < fenn> phun is like my "smirf" idea: http://www.phun.at/ 15:31 < fenn> except it's not an mmo (yet) 15:33 < fenn> needs more fluid dynamics from the looks of it 15:38 < fenn> i've been playing xmoto a lot, it's basically phun, but you're a guy on a dirtbike 15:48 < kanzure> xmoto? 15:49 < fenn> http://wiki.xmoto.tuxfamily.org/index.php?title=Screenshots 15:49 < kanzure> fenn: are you on my mailing list? I just did a linkdump on DIY BIO 15:50 < kanzure> also sent it to the http://diybio.org/ group 15:50 < kanzure> xmoto looks ok 15:50 < fenn> it looks like hell but it's fun 15:50 < kanzure> I've been needing some more brain cell killing ames 15:50 < kanzure> because i've just been playing kbounce 15:50 < kanzure> and frankly this sucks 15:56 < kanzure> how do I play 15:57 < fenn> uh. up is accel, down is brake, right flip forward, left flip backwards 15:57 < fenn> start on the 'desert training' level 15:57 < fenn> should be under 'nicest levels' 15:58 < fenn> green hill zone act 1 is cool too 16:03 < kanzure> whether or not I get hit by the slope thing seems to be a function of whether or not the game hates me 16:03 < kanzure> on the first level. 16:08 < kanzure> and when I go upside down the wheel does not spin properly 16:08 < kanzure> it spins as if it was upside down 16:08 < kanzure> instead of in the direction that it is facing 16:08 < kanzure> as in, not in the direction that the person is facing 16:10 < fenn> on 001 by denis? 16:10 < kanzure> yes 16:10 < fenn> that level's stupid 16:10 < fenn> the wheel is rubbing on the top because ODE only uses the two wheels in the physics simulation 16:11 < fenn> so the ground is passing through the bike 16:11 < kanzure> yeah 16:11 < kanzure> what about #2 16:11 < kanzure> there's invisible walls? 16:11 < fenn> yes 16:11 < fenn> also stupid, there are a lot of stupid levels because anyone can post new levels 16:12 < fenn> hence why i suggested 'nicest levels' 16:19 < kanzure> I still like Icy Tower and Mario Arena. if I had a windows machien. 16:19 < kanzure> or Alex the Allegator 16:44 < kanzure> http://heybryan.org/mediawiki/index.php/Lab_equipment full list of a biotech lab 16:44 < kanzure> now I just need to fill it in with links 16:49 < kanzure> What's up with Phil Ken Sebben? 17:13 < fenn> theres a lot of stuff on that list, what's the goal? 17:31 < kanzure> the idea was to get a list of lab equipment so that we can say "here's what an amateur lab would likely need for some common expeirments' 17:31 < kanzure> *experiments 17:31 < kanzure> I was hoping to link over to (even transient) ebay auctions, websites to purchase used equipment, guides to building similar equipment, or mention how the tech is used 17:31 < kanzure> or sometimes it's not tech -- "pipette: the most advanced piece of technology in the modern lab, the conventional pipette can pipette over 500 microliters of liquid per minute" 17:31 < kanzure> :-p 17:40 < fenn> er.. pipette is all about repeatability and accuracy 17:41 < kanzure> I was joking, but yes 17:41 < fenn> i have phun running here.. now i think my computer's slow 17:41 < fenn> water sloshing 17:42 < kanzure> I have lost all concentration. I need to go. 18:28 < kanzure> http://heybryan.org/mediawiki/index.php/In_vitro_liquidwars 19:08 -!- Aulere [n=dragon_d@131.229.176.252] has joined #hplusroadmap 19:09 < kanzure> http://www.ustream.tv/channel/immortality-update <-- Anybody want to join? 19:09 < kanzure> it's the Immortality Institute board meeting. 19:09 < kanzure> http://imminst.org/ 19:11 -!- Aulere [n=dragon_d@131.229.176.252] has quit [Client Quit] 19:11 -!- Aulere [n=dragon_d@131.229.176.252] has joined #hplusroadmap 19:14 < kanzure> Hey Aulere. 19:15 < Aulere> hey 19:15 < kanzure> http://www.ustream.tv/channel/immortality-update <-- Immortality Institute board meeting 19:15 < Aulere> cool 19:18 < kanzure> There's not much biology stuff on youtube. I think I could put on better nightly news via webcam than the crappy stuff out there. 19:33 < fenn> that's the most blippy staticky digital radio i've ever heard 19:36 < Aulere> yeah 19:36 < Aulere> I'm having streaming trouble too. 19:40 < kanzure> Meh. I lost interest and went over to http://jove.com/ for a bit. 19:40 < kanzure> I emailed them and suggested them my widget-donation system 19:40 < kanzure> http://heybryan.org/projects/openpay/widget.php?projectID=1 19:40 < kanzure> (is an example of the implementation) 19:42 < kanzure> Hm. That's weird. The colors on the whiteboard ... they have become '3D'. 19:42 < fenn> argh since when did web browsers play movies 19:43 < kanzure> about the same time that they did animated GIFs, I'd guess 19:45 < kanzure> okay, screw it - I'm going into overdrive mode again -- 40 papers are pulled up on my screen, I'll do a rapid read of them all. 19:46 < kanzure> Principles of cell-free genetic circuit assembly - Noireaux, I think this is protein-protein computing 19:46 < kanzure> dangerously slow 19:46 < kanzure> SP6 RNA polymerase 19:46 < kanzure> eGFP 19:46 < kanzure> firefly luciferase 19:47 < kanzure> need a list of plasmid types 19:47 < kanzure> Picogreen kit? 19:48 < kanzure> three-stage transcriptional cascade, but no gain independent of the instruments used since there's no energy source really 19:49 < kanzure> heh, so they had to do book-keeping of a different sort in vitro 19:49 < kanzure> most papers focus on the stability of protein synthesis when doing in vitro transcription 19:49 < kanzure> but if you're doing protein-GRN logic stuff, then you have to focus on the available resources that are inserted and the various calculations for diffusion and use 19:49 < kanzure> kind of obvious 19:50 < kanzure> http://neb.com/ 19:51 < kanzure> 1967 - Arthur Winfree - phase oscillators equation/modeling 19:51 < kanzure> Kuramoto universality of phase oscillator models 19:52 < kanzure> Steve Strogatz - 1990 - limit cycle oscillators 19:52 < kanzure> Pivosky - 1996 - synchronization among chaotic oscillators (what's a chaotic oscillator supposed to do?) 19:52 < kanzure> Josephson semicondcutor junctions 19:58 < kanzure> http://heybryan.org/mediawiki/index.php/Cell_oscillators 20:10 < kanzure> http://heybryan.org/mediawiki/index.php/Nucleic_acid_architectures 20:12 < fenn> kanzure: know about the lorentz attractor? 20:12 < fenn> i think that's a chaotic oscillator 20:12 < kanzure> http://en.wikipedia.org/wiki/Lorenz_attractor 20:13 < fenn> http://mysite.mweb.co.za/residents/cyb00746/chaos/chaos.htm 20:14 < fenn> looks amazingly similar 20:19 < kanzure> http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome 20:33 < kanzure> http://heybryan.org/mediawiki/index.php/Models_of_cell_signaling_pathways 20:39 < fenn> entrainment makes me think hypnosis and steam injector pumps 20:42 < fenn> what's with the references that are just numbers in []'s? 20:42 < kanzure> woah, they all crashed 20:42 < kanzure> huh? 20:42 < kanzure> well, I don't grab the references at the end of the article 20:43 < kanzure> for some reason - usually it's because the PDF file sucks 20:43 < kanzure> http://heybryan.org/mediawiki/index.php/Engineering_of_GRNs mentions some good references 20:43 < kanzure> but then the PDF viewer crashed and I have now lost track of which papers I was going to read and not going to read etc 20:43 < kanzure> hrm 20:44 < fenn> i'm confused.. the wiki says * blah blah [123] 20:45 < fenn> shouldnt it have a link instead of a number? 20:45 < kanzure> oh 20:45 < kanzure> right, well 20:45 < kanzure> I just type [123] 20:45 < kanzure> and then I'd go back at the end and find which reference 123 is in that paper 20:45 < kanzure> since I'm reading them linearly 20:45 < kanzure> I don't go to the references section immediately 20:45 < Enki-2> http://hakware.oopsilon.com/poetry/Rainbow's%20End.txt 20:46 < kanzure> that would involve too much scrolling and frankly too much refreshing of the pages (PDF viewers suck like this) 20:46 < kanzure> dianetics? 20:46 < fenn> rhymes with memetics 20:47 < fenn> hey you could change that to autogenix 20:47 < kanzure> http://dna.caltech.edu/DNAdesign/ DNA design toolbox -- beta beta beta version 20:48 < fenn> Enki-2: if you have a few days to kill.. http://vrinimi.org/rainbowsend.html 20:50 < kanzure> if you have a few weeks to kill. http://heybryan.org/docs/Zindell,%20David%20-%20Neverness%20(v1.0).txt 20:50 < fenn> crystal palaces indeed 20:50 < kanzure> I remember seeing vrinimi.org =) 20:51 < kanzure> too much chatting for me though 20:51 < fenn> looks like vernor vinge's site 20:52 < kanzure> lots of scifi pretends to be about talking 21:25 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 21:31 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap 21:33 < kanzure> fenn 21:33 < kanzure> http://kurtz-fernhout.com/oscomak/index.htm 21:33 < kanzure> Open Source Community on Manufacturing Knowledge 21:36 < kanzure> http://openvirgle.info/ 21:38 < fenn> the sad thing is google and friends probably could do it if they tried 21:40 < kanzure> http://www.openvirgle.info/wiki/index.php/Martian_Oxygen_Production 21:40 < kanzure> Google has the money, certainly 21:40 < kanzure> but the thing is 21:40 < kanzure> they have the brains to do it with no money in the first place 21:41 < fenn> that's what i mean, they dont have as much money as nasa (or do they?) 21:41 < kanzure> uhh 21:41 < kanzure> NASA has a cap of $1 billion 21:41 < kanzure> Google has a few hundred billion 21:42 < fenn> google revenue $16b assets 25b 21:42 < fenn> nasa budget 16b 21:43 < fenn> thing is, nasa gets to spend it all on space projects, whereas google actually has to spend it on making money 21:43 < fenn> google net income 4b 21:44 < kanzure> hm 21:49 < kanzure> http://www.chaordic.org/who_we_are.html huh? 21:50 < fenn> New Open Source Confucianism (TM) 21:50 < kanzure> I see. 21:51 < kanzure> Charlton Heston passed away? 21:53 < kanzure> woah, they killed AP CS AB? WTF? http://news.slashdot.org/article.pl?sid=08/04/06/1916242 21:56 < fenn> meh 21:57 < fenn> by the time it trickles down to AP tests it would be laughably out of date anyway 23:08 -!- Netsplit niven.freenode.net <-> irc.freenode.net quits: epitron, Enki-2, kanzure 23:09 -!- Netsplit over, joins: epitron 23:11 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap 23:11 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has joined #hplusroadmap 23:11 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has quit [Connection reset by peer] 23:12 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap 23:12 < kanzure> I'm pretty sure I wrote this 23:12 < kanzure> http://kurtz-fernhout.com/oscomak/need.htm 23:12 < kanzure> not entirely sure though 23:13 < kanzure> hm 23:13 < kanzure> fenn: http://kurtz-fernhout.com/oscomak/index.htm 23:40 < fenn> i've never heard you use the word sustainable 23:42 < kanzure> ah 23:42 < kanzure> but surely you see the equivalence 23:51 < kanzure> Huh. What's the chances of listening to a song on repeat for three hours only to have it show up on the first internet radio station you plug in to? 23:52 < Aulere> :) 23:52 < fenn> you probably just fell through a time portal without realizing it 23:53 < kanzure> it's Lain over at AnimeNfo 23:55 < kanzure> fenn: where were we with autogenix 23:56 < kanzure> are we ready to deploy the wiki? 23:56 < fenn> no 23:56 < kanzure> what's first? 23:56 < kanzure> I remember the package format being a good start 23:56 < fenn> figure out what's built in and what's part of modules 23:56 < kanzure> well, 23:57 < kanzure> I've been thinking abotu that and I've realized that you can't expect there to be total centralization really 23:57 < kanzure> except that it's all on the same server 23:57 < kanzure> so we just have to account for many software libraries/helper-programs to work with a standard interface 23:57 < fenn> of course 23:57 < kanzure> and these programs would separately process different types of packages 23:57 < kanzure> for example, a program to try to assemble the packages on oxygen reactions will be somewhat different from the package doing automobiles 23:57 < kanzure> *from the software packaging automobile packages 23:57 < kanzure> or dealing with its interface 23:58 < kanzure> so I think what we need is, at its root, something like a "unit testing framework" 23:58 < kanzure> does that make sense? 23:58 < fenn> they would use the same package format, but each code module will deal with a different specialized element in that package 23:58 < kanzure> right 23:59 < kanzure> parsing is not necessarily the same all around, but the point is that they are standardized somewhere 23:59 < fenn> i'm not sure if unit test is the right word, maybe 'compliance test' or 'interoperability test' 23:59 < kanzure> http://en.wikipedia.org/wiki/Unit_testing 23:59 < kanzure> ah 23:59 < fenn> no, parsing should be the same 23:59 < kanzure> nono 23:59 < fenn> otherwise it turns into a Perl clusterfuck 23:59 < kanzure> perl clusterfucking works for APT 23:59 < kanzure> but I was not suggesting parser errors 23:59 < kanzure> you'd be stupid to put that as a spec requirement 23:59 < kanzure> heh