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10:48 < kanzure> Hey.
10:48 < kanzure> So I had an idea yesterday.
10:48 < kanzure> I want to run it by you guys.
10:48 < kanzure> http://heybryan.org/self_replication.html
10:49 < kanzure> What I've been mentioning is that self-replication is kind of like a single point-of-failure. It doesn't fail, but I mean that if your system component isn't integrated into everything else, it's not going to be self-replicating. 
10:49 < kanzure> Two howevers:
10:50 < kanzure> (1) What if the parent unit did a secondary construction process that gave the child unit more functionality? For example, a human -> baby, but the hu gives the kid <something that the hu parent makes>.
10:50 < kanzure> (2) And what if anything that isn't fully integrated into the self-replication process was completely "replaceable", in the sense that "I can use my arms to take them off and replace them with something else" ? Would that be a way to cheat the definition of self-replication?
10:51 < kanzure> It occured to my sometime yesterday, so I threw up the web page and ran off.
11:04 < kanzure> Since the real self-replicator in the organism is the ribosome, I was wondering how to compartmentalize the ribosome. At the moment there's the nascent chain stopping techniques in ribosome display, as well as various emulsion techniques, lysosome techniques, but those don't really interest me. 
11:05 < kanzure> I came up with a list of all possible ribosome compartmentalization techniques: have it output into a shell that is directly attached; have it attach to a surface that has deposition holes in it; have it make its own shell that wraps completely around it; 
11:05 < kanzure> All of these require molecular mechanisms that are, frankly, too hard to come up with. It would be great if we could have a ribosomal machine that makes its own buckyball to sleep in, but I'm not sure I want to go yakshaving on that.
11:07 < kanzure> Also, the fact that it's all protein folding really, really sucks, and means that you're not really going to be laying down exact wires for electronics ever, that's unacceptable. But one possible method -- if we really, really wanted the self-replicable, evolvable ribosomal manufacturing unit, is to use an STM tip to inject mRNA into a ribosome at the end of the tip, and then the output channel would go into another nanotubule as 
11:08  * kanzure is flipping through some notes
11:09 < kanzure> Since we can do electromechanical integration pretty well (brain interfaces aren't impossible, we can get a few bits out of the system, things are looking good), and when we considering physical manufacturing, where's the crossover? The best answer I can come up with is "your hydraulics system" (motors that pump water through pipes). We can work with electricity and magnetism pretty well, but not 
11:09 < kanzure> mass/matter, which I'm still stuck on. Supposedly the answer would be the ribosome (digital (DNA) data => physical manufacturing with mass/matter (the amino acids)), but you lose the precision that is required.
11:10 < nsh> precision is an artifact
11:10 < kanzure> meh?
11:10 < kanzure> the context that I'm considering is, say, electrical wiring
11:10 < nsh> it is part of a paradigm that is untenable in the biological domain
11:10 < kanzure> right
11:10 < kanzure> well,
11:10 < kanzure> not without some very fancy evolutionary experimentation
11:11 < kanzure> i.e., see spirals
11:11 < kanzure> but that's not going to help me here
11:11 < nsh> our understanding of engineering is distinctly idiosynchratic to the various accidents of our development (paper, metal, steam, etc.)
11:11 < kanzure> while their discovery and applications are accidental,
11:11 < kanzure> our ability to go dig a trench and make a brick wall 
11:11 < kanzure> is not.
11:11  * nsh nods
11:12 < nsh> but the underlying metaconcepts are not as amenable on the nanoscale as they are on the mesoscale
11:12 < kanzure> meh, I don't care much about that
11:12 < kanzure> the scale doesn't matter that much to me
11:12 < nsh> unfortunately, physics does :-)
11:12 < kanzure> The reason why I was thinking about ribosome is because it's the interface between digital information and manufacturing
11:12 < kanzure> but I'm not in love with ribosomes.
11:13 < kanzure> So, one idea that I have had in the back of my head that might be worth mentioning :-)
11:13 < kanzure> have you heard of a protein array?
11:13 < kanzure> I think it's just this giant 2D array of proteins tied on to a surface
11:13 < kanzure> and then there's some way to do interaction studies
11:13 < kanzure> Usually this is paired with mutagenesis to see what changes might do to the proteins and the interactions and whatever.
11:13 < kanzure> That sounds cool. ;-)
11:13 < kanzure> What I'm considering is exploding the ribosome into its subunits (it's made up of other proteins that bind together)
11:13 < kanzure> and then from the action sites that we have determined from the literature, split those up as well
11:14 < kanzure> and then I want to individually test all of the action sites with a big, giant repetitive experiment
11:14 < kanzure> i.e., I want to reverse engineer the ribosome
11:14 < kanzure> and see what problem space that evolution was playing around with
11:14 < nsh> interesting idea
11:14 < kanzure> so, instead of proteins on an array, we have partially folded polypeptides, maybe some proteins sometimes, mutated proteins to see what the differences would be, etc.
11:15 < kanzure> I'm assuming that there's -- to some extent -- a mapping between the physical interactions and the actual problem that evolution struggled with
11:15 < kanzure> but all of this isn't a guarantee at all -- it's kind of a last resort scenario
11:15 < kanzure> I'm pretty sure there should be some way to do this on the macroscale, ignoring biology completely. 
11:16 < kanzure> where 'this' = that interface between digital/computation and manufacturing
11:17 < kanzure> frankly I find it odd that the interface is "the ribosome" -- a named, single unit
11:18 < kanzure> Shouldn't the design of the ribosome be implementable on a larger scale too?
11:18 < kanzure> http://www.google.com/search?q=%22design+of+the+ribosome%22 grr, first result is Kurzweil
11:21  * nsh chuckles
11:22 < nsh> a potential problem is that much of the historical context to the evolutionary development may be lost
11:22 < kanzure> technically the proteins fold mostly /outside/ the ribosome, so maybe my talk of ribosomes is not needed
11:22 < kanzure> yep
11:22 < nsh> as the environment has changed along with the organism
11:22 < kanzure> the problem that evolution was solving probably wasn't protein folding
11:22 < kanzure> since protein folding is of the amino acids themselves, no?
11:23 < kanzure> and "solving" protein folding would mean something like being able to digitally specify what protein to make
11:23 < kanzure> and as far as we know, no biological system does this
11:23 < kanzure> (not even us unfortunately)
11:23  * nsh smiles
11:24 < nsh> it's dangerous to implicitly imagine a biological 'problems' in the same manner as problems solved by conscious agents
11:24 < nsh> s/a //
11:24 < kanzure> of course
11:24 < kanzure> on that note, of dangerous things with bio, http://heybryan.org/evolution.html
11:24 < nsh> there is usually no knowledge of the challenge, nor what would consitute success, save that ones genes are around where they might not have bind
11:25 < nsh> aparatus has no perspective
11:25 < nsh> mm
11:26 < kanzure> why is polymerase and ribosome two separate entities?
11:26 < kanzure> besides the obvious locality issues?
11:26 < nsh> because we define entity based on a molecular bias?
11:26 < kanzure> not entirely, the ribosome is made up of multiple proteins for example
11:26  * nsh is always dubious about entities and discrete components
11:27 < kanzure> if you can show me somebody who has a nondiscrete, but completely usable interpretation of molecular biology, please :) be my guest
11:27  * nsh smiles
11:27  * kanzure realizes that saying 'molecular biology' is against the idea of nonentitious interpretations
11:28 < kanzure> so maybe call it nondiscrete nonentititous process-theoretic nanoscale biology
11:28 < kanzure> or maybe information theoretic, whatever
11:29 < kanzure> Yep, I was wrong.
11:30 < kanzure> I forgot that the coding elements themselves are really the special features here -- the code specifies the proteins, everything else is just facilitation
11:30 < nsh> hmm
11:30 < kanzure> so, escaping the biological domain, let me pull out a little bit
11:31 < kanzure> the important aspect is that mass/material can be integrated because of the digital specifications (coding)
11:31 < kanzure> that's what I'm trying to capture here too; it's directly applicable to the design compiler and the other ideas that float around in this channel
11:31 < nsh> "Those original emergent chemical conditions were dependent on the environment -- which we can determine from the rock records to some extent -- as well as by the fact that we figure they would have to be fairly simple, not some monstrous process more complicated than current organisms [although this alternative hasn't been extensively explored to my knowledge]."
11:31 < kanzure> :)
11:31 < nsh> i like that you considered that.
11:33 < kanzure> I can do electrical interfaces very, very well -- computation, discrete stuff, it's all good
11:33 < kanzure> but /me just can't figure out how to deal with mass/material
11:33 < kanzure> it just kind of sits there
11:33 < kanzure> and you need to pick it up
11:33 < kanzure> but to pick it up you need a motor
11:33 < kanzure> but to get that motor in the first place you need that mass
11:35 < kanzure> I suppose it's an "all or nothing principle" -- the food for an organism supplies every single aspect of it, right on down to the nucleic acids. Whereas the supplies to a manufacturing process are just 'touched'.
11:35 < nsh> i'm not sure i follow
11:35 < nsh> you're referring to consumption vs. manipulation?
11:36 < kanzure> perhaps; ultimately what I am trying to do here is escape object-orientation in manufacturing
11:36 < kanzure> fenn mentioned a few days ago the idea of having constraints and genetic algorithms and other evolutionary techniques so that "something like a spoon" could be manufactured for a process,
11:36 < nsh> that'd be nice
11:36 < kanzure> but that's still object-orientation, no? 
11:36 < kanzure> yes, it would be :)
11:37 < kanzure> I thought about it later that day and I kind of just sat there for a while until I came to a lengthy conclusion
11:37  * kanzure takes a deep breath
11:37 < kanzure> So, it kind of relates back to my two approaches to brains at this point
11:37 < kanzure> as you might know, I like the idea of self-augmentation http://heybryan.org/recursion.html
11:38 < kanzure> but at the same time I am also a programmer and know when the hell to sandbox changes
11:38 < kanzure> don't want to run around deleting neurotransmitter receptors, do we? ;-) BAD, BAD
11:38  * nsh smiles
11:38 < kanzure> at the same time it also kind of sucks
11:38 < kanzure> since we can't get much information out of these brains
11:38 < nsh> well, maybe could freeze a few...
11:38 < kanzure> yes, we can try freezing them, we can try implants, we can try augmentation their structures and so on
11:38 < kanzure> yes
11:38 < kanzure> but I'd rather have something more guaranteed
11:39 < kanzure> we've frozen cat brains before (7 years); and they did show electrical activity
11:39 < kanzure> and I'd be willing to do that, but in the mean time I'd rather also try some other solutions
11:39 < kanzure> anyway, we're basically screwed like that
11:39 < kanzure> which is fine, I'm okay with that, because there are some ways that I can cope with that (freezing, implants, whatever)
11:39 < kanzure> but what about a brain that isn't so majorily screwed?
11:40 < kanzure> that's the "next generation" stuff -- the "building brains", neurofarms, neuropods, using Markram's simulations and so on
11:40 < kanzure> which, coincidentially, are very useful for figuring out what changes to make per http://heybryan.org/recursion.html
11:40 < kanzure> *cough* it's not a coincidence
11:40 < nsh> hmm
11:40 < nsh> what are markram's simulations?
11:40 < kanzure> whole brain simulations
11:40 < kanzure> he has accurate simulations of cortical columns
11:41 < kanzure> i.e., he throws all of these molecular, neurophysiological, ion channel, all of these models together
11:41 < kanzure> http://heybryan.org/mediawiki/index.php/Henry_Markram
11:41 < kanzure> there's an amazing video fi you haven't seen it yet, it's on the second link on that page, and then click the 'talk' link (it might be the first) on the resulting page
11:41 < nsh> oh, this was in the google video linked here a while back, right?
11:41 < kanzure> yes
11:41 < nsh> right, cool
11:41 < nsh> never got around to giving that my full attention
11:41 < kanzure> okay, so we can build brains :) cool
11:41 < fenn> yak yak yak yak
11:41 < kanzure> heh, that's partly my point in all of this -- attention, etc.
11:41 < kanzure> fenn: bah, hold on
11:41 < fenn> ribosome is 98% RNA
11:42 < fenn> the protein is just there to stabilize it
11:42 < kanzure> grr, train of thought is crashing
11:42 < kanzure> anyway, my idea was that those brains that we could supposedly build
11:42 < kanzure> the ones that won't be screwed
11:42 < kanzure> the ones that could be compartmentalized and digitized
11:42 < kanzure> that's where we'd need that computation-manufacturing interface, no?
11:42 < kanzure> that's where losing object-orientation would be a Good Idea.
11:43 < kanzure> especially if the brains are able to manufacture themselves, or if the brain farm is completely self-replicable
11:43 < kanzure> brains can already self-replicate to some extent, no? 
11:43 < nsh> agency problems again
11:43 < kanzure> hm?
11:43 < nsh> is it the brain self-replicating, or the toenails
11:43 < nsh> or the genome
11:43 < kanzure> no, hold on
11:44 < kanzure> so adding in machinery (like a petri dish + MEA + other equipment) or infrastructure (to manage a huge farm) ... which can't make itself much? That's not a good idea.
11:44 < kanzure> I think I have a better reason somewhere 
11:44 < kanzure> better than "it's not a good idea"
11:44 < kanzure> oh,
11:44 < kanzure> it was the issue that (1) the brains can do electromechanical interfaces very, very well already
11:44 < kanzure> but (2) dealing with mass/matter on a scale other than "it's what sustains life and all of the nucleic acids and all of the damn proteins in the body, you fool" is the difficult part
11:45 < kanzure> and where I suspect the lack of object-orientation can help out.
11:45 < kanzure> aha. there we go.
11:45 < nsh> what are you defining mass/matter in opposition to?
11:45 < nsh> information?
11:45 < kanzure> fenn: by 'ribosome is 98% RNA' does that mean mRNA or ribosomal RNA (rRNA) ?
11:45 < fenn> ribosomal rna
11:45 < fenn> ribozyme
11:45 < kanzure> nsh: well, I'm just considering it in opposition to electricity for example
11:45 < kanzure> which I know is bad
11:45 < kanzure> since the electron does in fact have mass
11:45 < nsh> hmm
11:45 < kanzure> but consider E=MC^2 or something silly like that
11:46 < kanzure> I hate to bring that up, but the mass-energy equivalencies for example
11:46 < kanzure> while they might be 'equivalent', they are of different forms
11:46 < fenn> a topological defect in the fabric of spacetime
11:47 < nsh> but is the difference 'fundamental', or merely a product of our perceptual and conceptual dichotomising?
11:47 < nsh> afaik, there is no evidence that nature necessarily conforms to a binary logic
11:47 < kanzure> there has to be some way to integrate manufacturing in a /useful/ way without shoving it into the 'fundamental food' of the system (by this I mean, bio's food, which fuels the whole damn system)
11:47 < fenn> occasionally subatomic particles decay into pure energy
11:48 < fenn> i'm not sure about the reverse
11:48 < kanzure> if the design of the system doesn't incorporate the variety that we need it to execute, does it mean that the system can't effectively deal with that variety? by this I refer to the variety from the periodic table
11:48 < kanzure> *need it to execute/implement
11:48 < kanzure> that's where I came up with the original statements in here today
11:48 < kanzure> the idea of 'replaceable components'
11:49 < kanzure> or the idea of 'the parent self-replicates, but then adds in some componentry as well' 
11:49 < kanzure> and whether or not those can meet the definition of self-replication
11:49 < kanzure> http://heybryan.org/self_replication.html
11:49 < kanzure> nsh: so, is the difference fundamental?
11:49 < kanzure> I'm wondering if I'm going to randomly run into a roadblock due to a lack of understanding of gravity or something :-p
11:49 < kanzure> I hope not :)
11:50 < fenn> you've been treating a replicator as a particle when it's really a wavicle
11:50  * nsh smiles
11:50 < fenn> i.e. some things are more strongly associated with perpetuating the system than others
11:50 < kanzure> okay, sure
11:50 < fenn> the wave 'passes through' the steak you had for dinner
11:50 < kanzure> huh?
11:51 < fenn> is the cow part of kanzure?
11:51 < kanzure> how could a dependency loop include processes that are not depended on?
11:51  * nsh decides to walk home, thinking on these things
11:52 < fenn> you hjust set your sights too narrow
11:52 < fenn> ever heard of the gaia hypothesis?
11:52 < kanzure> yes
11:52 < fenn> well, even earth isnt a closed system
11:52 < fenn> we wouldn't be here if it weren't for water comets bombarding the earth for billions of years
11:52 < fenn> so, where's the replicator?
11:53 < kanzure> but you said it's a wavicle, implying that it's somewhat like a particle
11:53 < kanzure> what about this notion?
11:53 < kanzure> screw the replicator as an object, just imagine it's untouchable in that sense
11:53 < fenn> indeed, most of the functionality is in a nice little package you can send up to a space station and around the edge of infinity and back
11:54 < kanzure> it has some functionality that we may or may not know about
11:54 < kanzure> but the only things that might be 'objects' are the decisions that we make in order to interface with it or hack it
11:54 < kanzure> would that be appropriate?
11:54 < kanzure> fenn: no, your example of a cow disagrees with the edge of infinity journey
11:54 < kanzure> i.e., dependency on the biosphere processes
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11:55 < kanzure> and autotrophs and whatnot to gather energy
11:55 < fenn> hm i guess
11:55 < kanzure> but I'm not so much concerned about "where's the replicator"
11:55 < kanzure> oh
11:55 < kanzure> well, I guess you were asking that wrt my question of whether or not it's okay to have "replaceable parts" or something
11:55 < kanzure> i.e., hu makes a kid, but kid doesn't have arms, hu makes arms, gives kid the arms later
11:55 < kanzure> and then if the kid can do the same, then it's a replicator
11:56 < kanzure> this is my way of getting around the manufacturing problem
11:56 < fenn> i dont get the analogy
11:56 < fenn> what manufacturing problem?
11:56 < kanzure> we can do electromechanical interfacing stuff very, very well, but managing materials -- without having them implemented in our food and abilities to eat food and turn them into our own bodies -- is foreign so far.
11:56 < kanzure> the bootstrapping problem
11:56 < fenn> what's "electromechanical interfacing"?
11:56 < kanzure> many things:
11:57 < kanzure> your interface with your arm
11:57 < kanzure> my interface with the computer
11:57 < fenn> my arm doesnt have an interface
11:57 < kanzure> you have neurons to it
11:57 < kanzure> to the muscles
11:57 < kanzure> brain implants would also be appropriate
11:57 < fenn> i can solder wires to random points in a circuit, that doesn't make it an interface
11:58 < kanzure> semantics
11:58 < kanzure> suggest another word for it
11:58 < fenn> i use my arm to do stuff?
11:58 < fenn> like press buttons
11:59 < fenn> but my arm isn't well suited for manipulating molecules, is that what you're getting at?
11:59 < kanzure> not quite?
11:59 < kanzure> maybe this is a better way to put it
11:59 < kanzure> you can retool your arm, or various parts of your brain
12:00 < kanzure> but if we wanted the hu embryo to grow into a human + spaceship, we'd only have one option at the moment
12:00 < kanzure> basically hoping that the hu child would make it
12:00 < kanzure> i.e., CAN make it versus IT WILL make it
12:00 < kanzure> whereas, if we are to take the approach of a self-replicator, isn't it supposed to be completely integrated into the design of the system? I mean, isn't it supposed to be automatic and not something left up to chance?
12:00 < kanzure> this is hard to explain
12:01 < kanzure> I really thought that this was the same thing as the bootstrapping problem that we face
12:01 < kanzure> we have implementation ideas, but now we need the matter/energy in order to make it happen
12:02 < kanzure> (bootstrapping of autogenix and the actual, physical manufacturing)
12:05 < kanzure> I don't want wavicles, I want just 'waves' (I'd rather call it processes, computation, etc.). 
12:05 < kanzure> there's no reason manufacturing must be object-oriented
12:05 < fenn> OT i'm concerned about how i didn't notice anything weird about this guy when he was at my house last week, talked to him for a couple hours and he seemed totally normal, although according to others he was abnormal: http://www.idsnews.com/news/story.aspx?id=51308&comview=1
12:07 < fenn> supposedly he had been strung out on acid for several weeks
12:07 < kanzure> huh
12:09 < kanzure> here's the challenge:
12:09 < kanzure> figure out a way to consider mass/materials/matter without object-orientation
12:09 < kanzure> for example, a rock
12:09 < kanzure> the context is it's on my front lawn
12:12 < kanzure> with energy like electricity we can run around collecting it and charging batteries, running motors and generators and do whatever we like 
12:12 < kanzure> with mass, though, what does it do but sit there? Some of the materials could be used to make the electrical systems that we need,
12:12 < kanzure> but those systems aren't self-replicating (argh!)
12:12 < kanzure> "Hi RepRap! Here's the rock from my front yard!."
12:13 < kanzure> <reprap just sits there>
12:14 < kanzure> the typical case in the biosphere is for the hundreds of trillions of prokaryotes to run around and possibly integrate the new mass/material into their systems
12:14 < kanzure> and then you can trace them through the ecosystems and food chains
12:15 < kanzure> but surely there's a way to do it without aggregating organisms like that ?
12:15 < fenn> and then hopefully the prokaryotes are easier to digest than the rocks
12:15 < kanzure> and without integrating it into the fundamental-food-of-the-system
12:15 < fenn> plants do it all the time
12:16 < kanzure> it's basically (1) organism eats some stuff it doesn't know about, something that could be toxic on a large scale or something
12:16 < kanzure> (2) the organism has some evolutionary pressure to mutate, or it just does so anyway
12:16 < kanzure> and then by the grace of #2, #1 might come into use
12:16 < kanzure> it's all an accident
12:17 < kanzure> whereas our brains seem to acknowledge these materials and objects that we have around us
12:17 < kanzure> maybe I should just ignore it all
12:17 < kanzure> but then how would you ever extend your functionality beyond your hands ?
12:17 < fenn> one aspect of intelligence is modeling things outside experience
12:18 < kanzure> naughty
12:18 < kanzure> you know I don't like the I word
12:18 < fenn> too bad
12:18 < kanzure> heh
12:18 < fenn> i was going to say "brain" but that was too narrow
12:18 < fenn> and inaccurate in any case
12:19 < fenn> so, it seems you want a "theory of everything" really a model of everything
12:19 < kanzure> I hope not
12:19 < kanzure> if that's the case then I can accept the errors of my thoughts :)
12:20 < fenn> "with mass, though, what does it do but sit there?" is what made me think that
12:20 < kanzure> sometimes people treat 'whole systems' as if its own 'process'
12:20 < kanzure> as if its own 'spirit' or 'soul' or 'directed action' or something
12:20 < fenn> sure, "om" is the sound of the entire universe
12:20 < kanzure> I don't know how to say that and I haven't considered if it's bunk
12:21 < kanzure> so, that 'holism'/emergence works in a number of interesting cases
12:21 < kanzure> ant colonies, the brain and especially intelligence, etc.
12:21 < kanzure> and maybe even debian
12:21 < fenn> cybernetic systems hah
12:22 < fenn> let the buzzwords fly
12:22 < kanzure> sure, cybernetic systems
12:22 < kanzure> okay
12:22 < kanzure> so given those buzzwords
12:22 < kanzure> blah, I guess the real problem is that I don't actually have much of a problem that I am trying to solve here
12:22 < kanzure> I'm losing my train of thought
12:23 < kanzure> I really thought that the bootstrapping problem was a serious one
12:23 < fenn> we're still alive mate, no worries :)
12:23 < fenn> its 99% done because of that
12:23 < fenn> its the old 99/1 problem
12:24 < fenn> i think you're butting heads with the replicator myth
12:24 < fenn> there is no replicator
12:25 < fenn> we're the all-singing all-dancing crap of the world
12:25 < kanzure> it also might be my distinction between electricity/energy and mass/materials
12:25 < kanzure> or the distinction between process and object
12:26 < kanzure> oh
12:26 < kanzure> I guess objects could just be aggregated skdb files in the end anyway
12:26 < kanzure> and some of these might come with a physical ,actual attachment
12:26 < kanzure> i.e., "download chair;" "are we still in Austin, Texas?" "yes" "supplies negotiated and will arrive by noon"
12:27 < kanzure> (that's assuming a social backbone to that individual's system)
12:27 < fenn> your naive conception of 'electricity' as a thing shows that you havent worked with it much
12:27 < kanzure> or something :-/
12:27 < kanzure> what do you mean though?
12:27 < kanzure> I mena, the brain is able to interface with electrical systems, but we can't interface with a rock
12:27 < fenn> you cant just run any old voltage through the tubes
12:27 < kanzure> without busting our heads open :)
12:27 < kanzure> that's true
12:27 < fenn> likewise, where does that electricity come from?
12:28 < kanzure> well, do we mean the flow of electrons?
12:28 < fenn> it's the result of charged or magnetic masses moving about
12:28 < fenn> there's also the photoelectric effect, but those photons are the result of masses oscillating
12:29 < kanzure> I guess I could make an analogy to molecular computation
12:29 < kanzure> most of our computation and so on is done in terms of energy, processes, and information
12:29 < kanzure> I haven't seen an information theoretic approach to matter
12:29 < fenn> anyway, you say 'we can use electricity to run motors and stuff' but its sorta like saying 'we can use water to turn turbines to make electricity'
12:30 < kanzure> ok
12:30 < kanzure> yes, you're right
12:30 < fenn> do i get a cookie?
12:30 < kanzure> so my interface distinction is null and void
12:30 < kanzure> but then why is it that we can program and make digital circuits
12:31 < fenn> because the mathematical models for electrical circuits are very simple, linear, and predictable
12:31 < kanzure> and yet our 'circuits' with matter (I'm imagining either manufacturing facilities or giant chemistry lab setups) aren't similarly programmed?
12:31 < kanzure> and why can't this programming be integrated into my own programming
12:31  * kanzure whines
12:31 < fenn> you cant integrate digital circuits either
12:31 < kanzure> hm?
12:31 < kanzure> brain implants?
12:32 < fenn> you can't just stick a DIP package into your skull and be done with it
12:32 < kanzure> AND gates made out of neurons?
12:32 < kanzure> heh :)
12:32 < kanzure> http://heybryan.org/docs/neuro/
12:32 < fenn> even if you had a brain implant, you couldnt 'download' procedural memory
12:32 < kanzure> right
12:32 < fenn> this is why we have dreams
12:33 < fenn> the temporary storage buffer neurons have to 'teach' the long term memory neurons how to do stuff, and the only way is to re-live the experiences needed to use those procedures
12:33 < fenn> er, experiences that cause those procedures to be used
12:34 < fenn> so, you'd have to have a programmable dream machine i guess
12:34 < kanzure> you're working off of your statmeent of 'modeling things that haven't happened yet' ?
12:34 < kanzure> I'm guessing.
12:34 < fenn> i didnt quite say that
12:34 < kanzure> erm
12:35 < fenn> modeling things outside of our experience
12:35 < kanzure> yes, I realize I butchered that
12:35 < fenn> like, i can picture you sitting there in front of your computer
12:35 < fenn> cat on the bed, too many books on the floor
12:36 < kanzure> I do not want to have 'intelligence' as a requirement of skdb
12:36 < kanzure> ever.
12:37 < kanzure> blargh, as a fundamental requirement
12:37 < kanzure> as an optional requirement in some random package or whatever, meh
12:37 < fenn> what are the fundamental goals of skdb?
12:37 < kanzure> well, originally it was to bootstrap a self-replicating machine, namely its design
12:37 < kanzure> and this was because of the requirements for recursion.html
12:38 < kanzure> at least from my perspective
12:38 < kanzure> plus all of the extras that it offers, like DIY manufacturing and such
12:38 < fenn> 'plus' is not a fundamental goal is it?
12:38 < kanzure> nope
12:38 < fenn> so, you have to define what  self replicating machine is
12:39 < fenn> don't feel bad if you can't come up with an answer, i dont think biologist can define life either
12:39 < kanzure> my ability to recombine my genome with a woman's
12:39  * kanzure cheated
12:39 < fenn> yeah that has nothing to do with self replication
12:39 < kanzure> I took 'self' seriously
12:40 < kanzure> okay, so the idea was to get exponential replication 
12:40 < fenn> in any case, your child would be only halfway you (and none of your environmental influences)
12:40 < kanzure> or at least exponential duplication or whatever
12:40 < kanzure> most manufacturing and building is n^2 and I want 2^n
12:41 < fenn> exponential growth
12:41 < kanzure> yes
12:41 < fenn> in that case the only 'self' is the whole growing system
12:41  * kanzure wonders if the definition of 'growth' is important here
12:41 < fenn> yep
12:42 < fenn> growth is based on functionality i think
12:42 < kanzure> when I was thinking about exponential self-replication for making brain farms and brain simulations I was thinking of clanking replicators
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12:42 < kanzure> but that's object-oriented
12:42 < kanzure> how about a nonobject-oriented definition of growth?
12:42 < kanzure> uhm
12:43 < fenn> well, an increase in the number of functions possible would be considered growth
12:43 < kanzure> well, the goal was to do lots of simulations of brains or at least physically implemented neural tissue slices for experimentation
12:43 < fenn> this reminds me of the AI "hard takeoff" bootstrapping scenario
12:43 < kanzure> so as long as that goal references objects, the definition of growth will be object-oriented
12:43 < kanzure> sure
12:44 < kanzure> linux treats procs as objects
12:44 < fenn> they are objects, because if linux didnt herd them around they'd die
12:45 < fenn> that didnt come out right
12:46 < fenn> i dont like this obsession about whether something is object oriented or not
12:46 < fenn> it seems to be religiously motivated
12:46 < kanzure> it's shorthand for a deeper issue
12:47 < kanzure> we don't care about the objects, we care about the functionality
12:47 < fenn> when you speak of 'a rock' the object is the model used to represent the rock, right?
12:47 < kanzure> the object is the rock
12:47 < kanzure> it's right there
12:47 < kanzure> sitting there
12:47 < kanzure> (on my lawn)
12:47 < fenn> but its just a bunch of atoms and energy
12:47 < kanzure> right, so what the hell are we going to do with ti
12:47 < kanzure> *it
12:48 < kanzure> especially with respect to our exponential growth system
12:48 < fenn> you dont care about the absolute positions of all the electrons in the rock at a particular time
12:48 < kanzure> right
12:48 < fenn> (unless you do)
12:48 < kanzure> I don't think I do
12:48 < kanzure> what is your statement trying to say?
12:48 < kanzure> is it asking if I do?
12:49 < fenn> but what if the rock had consciousness and you wanted to do a 'rock scan' so you can upload it into rock heaven?
12:49 < kanzure> gah?
12:49 < fenn> object orientation is mainly a way to organize data by relevance
12:49 < kanzure> context flip for a sec
12:50 < kanzure> do you recall my work on a matter beam?
12:50 < fenn> not really
12:50 < kanzure> ok, well, laser beams we have
12:50 < kanzure> we also have matter beams
12:50 < kanzure> http://heybryan.org/projects/atoms/
12:50 < fenn> ok, ion laser, big deal
12:50 < kanzure> no
12:50 < kanzure> Bose-Einstein Condensates
12:50 < kanzure> it's where matter functions as a wave
12:50 < kanzure> you have to get it ultracold
12:50 < fenn> yeah i know, and then you can slap a hologram onto it and a puppy coalesces out of the mists
12:51 < kanzure> something like e-9 torr
12:51 < fenn> that's pressure
12:51 < kanzure> ignore the hologram shit
12:51 < fenn> why? it makes sense
12:51 < kanzure> I don't care
12:51 < kanzure> my point is that the matter is a beam/wave
12:51 < fenn> uh, sorta
12:51 < fenn> it's a coherent system
12:51 < kanzure> for some reason the temperature difference forces us to treat it differently when it's at room temperature or something
12:52 < kanzure> whereas we get to treat the flow of electrons as a, well, flow
12:52 < kanzure> but a flow of rocks on a conveyor belt has to be a flow of rock-objects, :-/
12:52 < kanzure> I guess we could replace flow-of-rock-objects with a differential equation
12:52 < kanzure> that describes the damage done to the walls of the conveyor belt system or something
12:52 < kanzure> right?
12:52 < kanzure> and then we could just aggregate these models together in the typical skdb sense that we've considered before 
12:53 < fenn> no, an equation is not a real thing
12:53 < fenn> you can model the rocks with a differential equation
12:53 < kanzure> how the hell do you model a lump of matter with a diff-eq?
12:53 < kanzure> it's mostly constant
12:53 < fenn> i dunno, what's a diff-eq
12:53 < kanzure> "yep, still sitting there"
12:53 < kanzure> differential equation
12:54 < fenn> did you pay attention to what i said earlier about why we use electronics for digital logic circuits?
12:54 < kanzure> modelability?
12:55 < fenn> the models correspond to observations very well, and it makes using electronics very predictable
12:55 < kanzure> oh, and then we get to the dream machine because observations and model making requires the intelligence 
12:55 < fenn> the dream machine is just a way to get knowledge into a brain
12:55 < kanzure> or at least some sort of genetic algorithm for model construction (where the scoring function is of the new phenomenon that we're dealing with, yadda yadda)
12:56 < fenn> a genetic algorithm for model construction might work ok for many situations
12:57 < fenn> i'd go so far as to call it intelligence
12:57 < fenn> why did you bring up bose einstein condensates?
12:58 < kanzure> trying to get matter as a wave
12:58 < fenn> i think it's still more complex than a simple EM wave
12:59 < fenn> rubidium is still rubidium when it comes out, not gamma rays or whatever
12:59 < kanzure> I think the fundamental issues are solved though
12:59 < fenn> i think of it as something like a crystal in the aether
13:00 < kanzure> the solution was social aggregation, just like before
13:00 < kanzure> just like we determined before
13:01 < kanzure> plus some way to do mutagenesis on brains or something so that we can do more pre-emptive modeling
13:01 < fenn> instructables is 'mere' social aggregation
13:01 < kanzure> or GAs for model construction
13:01 < fenn> we're adding a formal system on top of that to allow computer manipulation of knowledge
13:01 < fenn> a grammar if you will
13:01 < kanzure> programming is like manipulating all of those experiences that resulted in nuggets of knowledge and applying the 'gist' of the situation to a new ant mound
13:02 < fenn> eh, i think programming is really the reverse of that
13:02 < kanzure> debuggign?
13:02 < kanzure> *debugging?
13:02 < fenn> taking the generalized 'law' and turning it into discrete, specific cases
13:02 < kanzure> so which one is the skdb package
13:02 < kanzure> is it the generalization
13:02 < kanzure> or is the case-package ?
13:03 < fenn> the specific case
13:03 < fenn> with varying levels of specificity
13:03 < kanzure> ok
13:03 < fenn> spoon, wooden spoon, silver spoon, utensil
13:04 < kanzure> but then why is it that I seem to be able to construct simple objects like that in my mind
13:04 < kanzure> without having to rely on experimentation and testing
13:04 < kanzure> making a new type of eating utencil, for example
13:04 < fenn> uh, who says you dont have to rely on experimentation and testing?
13:04 < kanzure> every four year old has their idea of an awesome new spork with extra wings or something
13:04 < fenn> go try it, make a new eating utensil and see if it works
13:05 < kanzure> I can see a way to fold a food-scooping mechanism with paper and tape
13:05 < fenn> the difference between theory and practice is muh greater in practice
13:07 < fenn> the concept of 'data point' is useful here
13:07 < kanzure> now how the hell do we write code for all of this
13:07 < kanzure> design compiler, inventory (data point? :p) management, blargh
13:07 < fenn> meh
13:07 < kanzure> I have to go back and trace the ideas here and recombine them with the arguments I was presenting earlier
13:08 < kanzure> oh
13:08 < kanzure> a package of tools for the modeling of new experiences or materials or things
13:08 < fenn> no
13:08 < kanzure> which would then be submitted back to an skdb aggregation system
13:08 < kanzure> no?
13:08 < fenn> that's AI
13:08 < kanzure> nononono
13:08 < kanzure> consider bacteria
13:08 < kanzure> they can integrate new materials into their system
13:09 < kanzure> like randomly coming across an awesome metal or something
13:09 < kanzure> without ai
13:09 < fenn> they do it with evolution which is a form of intelligence
13:09 < kanzure> don't tell me that the Cherbnoyl reactor bacteria were intelligent ;-)
13:09 < kanzure> (it might have been fungi, and fungi does weird shit, so maybe they /were/ intelligent)
13:09 < fenn> they dont make any models of the metal and decide it might be a good idea
13:09 < kanzure> right, and we can do evolution with software to some extent
13:09 < kanzure> like modeling and equations software and so on
13:09 < kanzure> GAs too
13:10 < fenn> so feed the software and magically it pops out a set of formulas describing the system?
13:10 < kanzure> nah
13:10 < kanzure> what I'm thinking is that there are some tools and methods that we can use to model systems to some extent
13:10 < kanzure> and then finding the right combination or sequence is the trick
13:10 < fenn> what's the context here?
13:11 < kanzure> that's difficult to say
13:11 < kanzure> consider a new chemical reaction ?
13:11 < kanzure> or maybe consider a new thing that would be socially aggregated
13:11 < kanzure> one of those buzzword situations, where something 'new' has been found
13:11 < fenn> a new thing
13:11 < kanzure> and it needs to be 'crystalized'
13:11 < fenn> not much semantic content
13:11 < kanzure> so that other skdb users can go around using it
13:11 < kanzure> right, but the semantics could be developed over time or something
13:12 < fenn> are you just talking about the process of creating a formal grammar for describing systems?
13:12 < fenn> because computers are notoriously bad at that
13:12 < kanzure> no, I was thinking of the case where you're out "on the field" and you have a computer, a something 'new', and you have some tools, like a GA and some information on similar things or context-related packages or whatever, so now you're going to plug things together and try to constrain possibility space to get models or something that can be packaged for skdb
13:13 < kanzure> the intelligence could be used for constraints on the possibility space that would be explored
13:13 < fenn> a robot scientist
13:13 < kanzure> but otherwise, the system should be able to, say, automatically build that lab 
13:13 < kanzure> http://expo.sf.net/ re robot scientists, who we need to go talk with eventually
13:13 < fenn> i dont think it's part of the fundamental 'what makes skdb skdb'
13:13 < kanzure> they have university funding so they might be another case of reprap, but they are of the bio community and so might be more friendly (if not territorial like biobarcamp)
13:13 < fenn> and i stick by my assertion that it's AI
13:13 < kanzure> it's definitely not a fundamental component
13:13 < kanzure> however
13:14 < kanzure> you pointed out 'just' a while back
13:14 < kanzure> when I mentioned that it was social aggregation
13:14 < kanzure> and so I was providing a few ideas on making the social aggregation actually happen
13:14 < kanzure> making some tools that allow new things to be thrown into the database would be a good idea methinsk
13:14 < kanzure> *methinks
13:17 < fenn> i find myself clinging to the cathedral style of development
13:17 < fenn> not wanting a bunch of machine generated junk dropped into the system
13:17 < fenn> but humans will do that anyway
13:17 < kanzure> debian has quality assessment teams
13:17 < kanzure> that guard the gateways
13:18 < kanzure> I thought we were going to do something like that anyway ?
13:18 < fenn> yeah but it's not all designed to work together
13:18 < kanzure> it harms nobody since they git-clone the whole thing anyway
13:18 < kanzure> hm?
13:18 < kanzure> oh
13:18 < kanzure> from the ground up
13:18 < fenn> it just happens to work after some massaging and cooddling
13:18 < kanzure> refactoring sucks
13:18  * kanzure suspects it's why firefox still sucks
13:19 < kanzure> the code base I mean
13:19 < kanzure> everything else about it is pretty awesome
13:19 < fenn> firefox is developed as a cathedral.. i'm not following
13:19 < kanzure> oh
13:20 < kanzure> well, I was referring to the nasty codebase and how it would be a good idea to refactor it
13:20 < kanzure> so that it doesn't have the issues that I've been pointing out for a while now (re: my tab addiction problem)
13:20 < kanzure> and I mentioned that refactoring sucks
13:20 < kanzure> not so much the cathedral distinction
13:20 < fenn> but nobody else has that problem so it isnt aproblem
13:20 < kanzure> simply that refactoring a large code base because something was wrong in the beginning, really, really sucks
13:20 < kanzure> bah
13:20 < fenn> dammit the wireless works fine when i'm the only person awake
13:21 < kanzure> that's like saying just because you're sick but nobody else is, means that you're therefore not sick
13:21 < kanzure> I think I once theoretically solved the refactoring problem
13:22 < kanzure> I don't remember how.
13:22 < kanzure> I wish I had some notes on that.
13:22 < fenn> if the system as a whole does what it was designed to do, then it doesnt matter if i'm upset that there's a bunch of crap floating around the skdb intarweb
13:22 < kanzure> I was complaining about it a lot one or two months ago, and I mentioned to somebody my plans about it
13:22 < kanzure> it might have involved my brain plans
13:22 < kanzure> sure
13:22 < fenn> sounds like a bad plan then
13:22 < kanzure> fenn: but the data that you /do/ receive might have to be refactored anyway
13:22 < kanzure> especially if the people that are submitting it do it their own way
13:23 < kanzure> see, it's still cathedral 
13:23 < kanzure> since they have to agree on the standards and whatever
13:23 < fenn> that's a lot of work
13:23 < kanzure> of course, automatic filtering of noncompliant package
13:23 < fenn> you cant just turn everything away because it's not your way
13:23 < kanzure> right :(
13:23 < fenn> see how far that got stallman :P
13:23 < kanzure> or can I?
13:23 < kanzure> get lost
13:23 < kanzure> heh
13:23 < kanzure> well, he's not dead yet
13:24 < kanzure> 99 percent, remember?
13:24 < kanzure> :P I kid
13:24 < fenn> yeah maybe he'll finish hurd by the time he's dead
13:24 < fenn> or maybe he'll take some acid and realize he's not interested in software anymore
13:25 < fenn> do you believe in self determination?
13:25 < kanzure> what the hell does that mean
13:26 < kanzure> :)
13:26 < fenn> are we just particles banging around probabilistically, all of our desires simply a result of chance
13:26 < fenn> no blame, no credit
13:26 < kanzure> this is a complicated issue
13:26 < kanzure> and I thought we went over it before
13:26 < kanzure> brb
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15:37 < kanzure> fenn: so, to answer your question
15:38 < kanzure> "I am physics"
15:38 < kanzure> perhaps not all of it
15:38 < kanzure> and really only a quite limited subset of the possible combinations of phenomena
15:42 < kanzure> and I don't understand probability/statistics. Or at least people's reliance on it. It's an easy way to 'get around' some problems. It's not so much getting around as ignoring ...
15:51 -!- Splicer [n=p@h77n3c1o261.bredband.skanova.com] has joined #hplusroadmap
15:52 < kanzure> Hey Splicer.
15:52 < kanzure> hm
15:52 < Splicer> hi 
15:53 < kanzure> So if I go do laundry, I get to go order that new computer
15:53 < kanzure> hm
15:53 < kanzure> What a deal.
15:54 < Splicer> a man can never have too many computers
15:54 < kanzure> And in the background I'm backing up all of my data. I think the total is coming out to close to 300 GB. 
15:54 < kanzure> It's interesting to see cp in the background there and all of the old, old folders and packages of stuffs that I've made.
15:55 < kanzure> like what the hell is /mnt/edmini/books/2008-06-21_server/home/bbishop/new_logdir2/cyanopicapica/
15:55 < kanzure> oop
15:55 < kanzure> 2008-02-21_server
15:56 < kanzure> Anyway, with any luck my cache will be web accessible soon.
16:22 < kanzure> 452 days remaining. Geesh. And I'm being kicked out, I think.
16:23 < nsh> hrm?
16:39 < kanzure> nsh: I'm not sure.
16:40 < kanzure> But I was told that it would be a "good idea". And that arrangements have already been made.
16:45  * nsh frowns
16:48 < Splicer> ... it's alive
16:56 < kanzure> Hm.
16:57 < kanzure> Oh well. I think it might be alright. There might be some free food out of it.
16:57 < kanzure> And faster pipes.
17:02 < nsh> pipes are always a bonus
17:13 < kanzure> http://heybryan.org/buildingbrains.html
17:16 < kanzure> Oops, refresh.
17:24 < kanzure> I seem to be on 11 day cycles.
17:24 < kanzure> (when it comes to documents)
17:51 < nsh> hrm
17:52 < nsh> this channel just went back in time by half an hour
17:52 < nsh> ah, no. t'was ##neuroscience
17:52 < kanzure> haha :)
18:01 -!- willPow3r [n=will@cpe-66-75-6-181.san.res.rr.com] has joined #hplusroadmap
18:04 < kanzure> Hey willPow3r.
18:04 < kanzure> Lemme upload today's logs.
18:04 < willPow3r> cool
18:05 < kanzure> http://heybryan.org/chats/2008-06-24_hplusroadmap.html
18:42 < kanzure> http://linuxpmi.org/trac/wiki/OpenMosixPatchCommentaries commentary on the linux kernel
18:42 < kanzure> got this from #openmosix
18:42 < kanzure> an impressive woman wrote the page
18:51 < willPow3r> i didn't think there was such thing as an "impressive woman"
18:52 < nsh> that might be a self-fulfilling assessment
18:54 < willPow3r> if you tend to disagree, you should come on out to san diego and check out the STI incubators that attend vernor vinge's SDSU
18:57  * nsh smiles
18:57 < willPow3r> i'm biased in my view. please forgive me for my misogyny.
18:58 < nsh> it don't confront me; long as i get my money next friday
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19:11 < kanzure> nsh: Not self-fulfilling really, but by 'impressive' I mean to say she's not transexual and i.e., really a guy
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19:18 < kanzure> nsh: Not self-fulfilling really, but by 'impressive' I mean to say she's not transexual and i.e., really a guy
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19:40 < kanzure> Uhm. I lost a train of thought.
19:40 < kanzure> What am I doing?
19:56 -!- fenn_ [n=pz@adsl-76-251-85-53.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap
19:56 -!- 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/
19:56 -!- Topic set by kanzure [] [Sun Jun  8 13:00:15 2008]
19:56 [Users #hplusroadmap]
19:56 [ fenn ] [ freer  ] [ percent_] [ Splicer  ] [ wrldpc] 
19:56 [ fenn_] [ kanzure] [ procto  ] [ willPow3r] [ ybit  ] 
19:56 -!- Irssi: #hplusroadmap: Total of 10 nicks [0 ops, 0 halfops, 0 voices, 10 normal]
19:56 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
19:57 -!- Irssi: Join to #hplusroadmap was synced in 37 secs
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20:08 < willPow3r> taking your adhd medication?
20:08 < kanzure> willPow3r: Hm?
20:09 < kanzure> Yes, today at least.
20:09 < willPow3r> heh ;)
20:09 < kanzure> The reason my output has decreased is somewhat because I've been doing only half my dosage recently since I've been at the lab and not at home, but I'm fixing that starting tomorrow. It's too stupid losing so many nights just because I can't reach a cabinet fast enough.
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20:09  * kanzure wasn't at the lab today.
20:10 < willPow3r> what are you taking?
20:10 < kanzure> Adderall.
20:10 < kanzure> And it /works/. Off of the medication, one minute I can be as I am now, the next minute I find myself playing in the grass outside.
20:10 < willPow3r> inattentive type
20:11 < willPow3r> i used to take adderall, but this new med came out
20:11 < willPow3r> called vyvanse
20:11 < kanzure> Yeah, I tried that too.
20:11 < willPow3r> its a prodrug, lisdexamphetaime
20:11 < willPow3r> i really like it
20:11 < kanzure> patch form.
20:11 < kanzure> marketed towards kids
20:12 < willPow3r> yes, thats usually where adhd medication is aimed when it comes to market
20:12 < kanzure> I went in to the doc's office in late 2007 and the guy basically told me that I had Hitler syndrome, so he took me off Adderall for a week and put me on vyvanse. Blargh. Didn't go well.
20:12 < kanzure> I didn't want to kill jews, so I don't think I had Hitler syndrome ;-)
20:13 < kanzure> I'm actually more the H in ADHD.
20:13 < willPow3r> you were going the way of pinky and the brain then?
20:13 < kanzure> No, there's some other things going on, other than just ADHD.
20:13 < kanzure> I'm suspecting some Aspergers.
20:13 < kanzure> http://heybryan.org/intense_world_syndrome.html
20:13 < willPow3r> class in 15. bbl
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20:37 < kanzure> willPow3r: Just say when you're back.
20:48 < kanzure> http://en.wikipedia.org/wiki/Intensive_Care_Unit
20:48 < kanzure> I want one.
20:54 < kanzure> http://en.wikipedia.org/wiki/DO-178B ' standard methods for producing life-critical avionics software'
21:22 < wrldpc> what was that?
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21:25 < kanzure> Hm?
21:25 < kanzure> wrldpc: What?
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21:26 < wrldpc> did you just receive the system-wide message?
21:26 < wrldpc> I glanced at it.
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21:29 < kanzure> wrldpc: No, I didn't.
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