| --- Day changed Sun Apr 06 2008 | ||
| mechie | hahaha | 00:04 |
|---|---|---|
| kanzure | What is it? | 00:07 |
| mechie | a black man | 00:21 |
| mechie | in a tshirt | 00:21 |
| kanzure | I see it. | 00:25 |
| 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 | 00:26 |
| 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 | 00:27 |
| 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 | 00:28 |
| epitron | that's a sha1 hash | 00:29 |
| epitron | so, however many bits those are | 00:29 |
| epitron | anyhow | 00:29 |
| 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 | 00:30 |
| epitron | if you make enough waves, people will have to let you go | 00:31 |
| epitron | especailly if you didn't do anything wrong :) | 00:33 |
| 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 | 00:50 |
| kanzure | because you don't necessarily need all of the logic gates on a microprocessor | 00:51 |
| kanzure | terahertz/gigahertz doesn't matter | 00:51 |
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| epitron | are you trying to figure out how much molecule-processing it'll take? | 01:58 |
| 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 | 01:59 |
| 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 | 02:09 |
| 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? | 02:24 |
| kanzure | it bumps around | 02:25 |
| kanzure | however, | 02:26 |
| epitron | i see | 02:26 |
| 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 | 02:27 |
| 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 | 02:28 |
| epitron | hahah | 02:29 |
| 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 | 02:30 |
| 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? | 02:31 |
| 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 | 02:32 |
| 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 | 02:33 |
| epitron | i'll look into nanotube computing perhaps | 02:34 |
| epitron | then i will share the info | 02:34 |
| 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 | 02:37 |
| 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 | 02:38 |
| 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 | 02:39 |
| 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 | 02:40 |
| 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") | 02:41 |
| 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 | 02:42 |
| 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 | 02:43 |
| 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 | 02:44 |
| 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 | 02:45 |
| 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 | 02:46 |
| 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 | 02:47 |
| 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 | 02:48 |
| 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 | 02:49 |
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| kanzure | http://glofish.com/ | 03:02 |
| kanzure | is somebody around to do a bullshit analysis on an email I'm about to send? | 04:09 |
| kanzure | http://heybryan.org/mediawiki/index.php/BS-analysis-requests | 04:26 |
| fenn | explain how it will do something you cannot predict - is that possible? | 08:44 |
| fenn | you need to explain more on part 1 | 08:45 |
| 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 | 09:14 |
| kanzure | hm | 10:12 |
| kanzure | something that I can't predict | 10:13 |
| kanzure | so maybe I just need to fake it | 10:13 |
| fenn | maybe i'm a cranky old goat, but why would unpredictable outcomes be desirable? | 10:20 |
| fenn | that's no way to build useful systems | 10:21 |
| kanzure | :( | 10:32 |
| kanzure | http://www.diybio.org/ <-- Boston group, new, announcement was sent this morning | 10:32 |
| fenn | maybe i would be excited if school hadn't beaten the soul out of me | 10:35 |
| kanzure | that bad? | 10:37 |
| fenn | he's right about tech culture | 10:39 |
| fenn | how can you do anything with bio without arousing suspicion and fear? | 10:39 |
| fenn | desktop-STM's is one thing, de-brained mice is another | 10:40 |
| fenn | probably the only 'safe' area is plant genetics | 10:41 |
| fenn | the hypocrisy is amazing | 10:42 |
| fenn | we need an institutional review board to do mouse behavior experiments, but then people go and slaughter chickens and cows by the billions | 10:43 |
| fenn | kanzure ever think about using animals as containers for your brain-pods? | 10:49 |
| fenn | i'm reading this: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2220020 | 10:51 |
| kanzure | I don't really want to have to do deal with meat-bodies for brains | 11:14 |
| 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 | 11:15 |
| fenn | scientific discussions of morality always leave a lot to be desired | 11:16 |
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| kanzure | the qual-chicken stuff looks interesting | 11:18 |
| kanzure | quail* | 11:19 |
| kanzure | but I don't know about "conferring humanity on mice" - what the hell? | 11:19 |
| kanzure | who were you talking about when you said "he's right about tech culture" ? | 11:22 |
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| 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 | 11:25 |
| 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 | 11:27 |
| 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 | 11:28 | |
| kanzure | no feces throwing in here | 11:29 |
| fenn | digital feces? | 11:29 |
| kanzure | ok, fine | 11:29 |
| kanzure | but not the wet ones | 11:29 |
| 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 | 11:30 |
| fenn | one man's emergence is another man's magic | 11:31 |
| 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. | 11:32 |
| 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? | 11:33 |
| 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 | 11:34 |
| 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 | 11:35 |
| 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? | 11:36 |
| kanzure | get access to scientific databases | 11:37 |
| fenn | diy doesn't help there | 11:37 |
| kanzure | right | 11:37 |
| fenn | unless you propose building entirely new databases from amateur experimental results | 11:38 |
| fenn | that's a bit beyond "diy" tho | 11:38 |
| kanzure | http://www.eminerals.org/ | 11:42 |
| kanzure | for the sciencey stuff - http://www.eminerals.org/ | 11:43 |
| kanzure | erm | 11:43 |
| kanzure | http://www.eminerals.org/highlights/index.html | 11:43 |
| fenn | oo structured water | 11:46 |
| 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. | 11:49 |
| kanzure | How is this an example of emergence?? " Robots play soccer or build heaps of collected items (cf. Figure 2)." | 11:50 |
| 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 | 11:51 |
| 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 | 11:54 | |
| kanzure | nonlinear systems from discrete components? | 11:55 |
| kanzure | "intrinsic emergence" | 11:59 |
| kanzure | "the system itself capitalizes on the patterns that appear" | 11:59 |
| kanzure | "novel causal powers coming into being at specific levels of ontology" | 12:00 |
| fenn | hurr | 12:01 |
| fenn | self-assembly maybe | 12:01 |
| 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 | 12:02 |
| 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.” ` | 12:05 |
| kanzure | so how would I do that without predicting P | 12:06 |
| 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.` | 12:08 |
| 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 | 12:09 |
| fenn | well duh, the point of a GRN is to ensure the stability of a cell | 12:11 |
| 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. | 12:21 |
| 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 | 12:22 | |
| 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? | 12:23 |
| 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 | 12:24 |
| 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 | 12:25 |
| fenn | yep | 12:26 |
| fenn | creativity, not motivation | 12:26 |
| fenn | motivation is simple neurotransmitter circuits i think | 12:26 |
| fenn | a knowledge synthesizer! | 12:27 |
| fenn | hidden in plain sight | 12:27 |
| 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 | 12:28 |
| 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 | 12:29 |
| 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) | 12:30 |
| 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 ;) | 12:32 |
| 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 | 12:33 |
| kanzure | http://heybryan.org/edeism.html not related | 12:39 |
| fenn | the edeist stuff is painfully immature sci-fi | 12:40 |
| 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 | 12:45 |
| 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 | 12:46 |
| 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 | 12:47 |
| 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. | 12:48 |
| kanzure | So there's ways to work with it, I guess. | 12:49 |
| fenn | they're talking about Ede? | 12:49 |
| fenn | at what point does Nick Ede become the Solid State Entity? | 12:50 |
| kanzure | Edge is another god | 12:50 |
| kanzure | *Ede | 12:50 |
| 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? | 12:52 |
| kanzure | eh, yes, Zindell stumbles on a few points like that | 12:54 |
| 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 | 12:55 |
| 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. | 13:05 |
| fenn | a sphere isnt really a good shape for high-energy stuff | 13:15 |
| fenn | hint: dont draw inspiration from science-fantasy :) | 13:16 |
| kanzure | heat-dissipation | 13:25 |
| kanzure | I'm pretty sure there's been lots of calculations on this | 13:25 |
| kanzure | esp. Anders Sandbergs - Physics of Intelligent Superobjects, 1999 | 13:26 |
| kanzure | Anders Sandberg, woops | 13:26 |
| fenn | planets are round because they have wimpy compressive strength | 13:36 |
| 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 | 13:37 |
| 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 | 13:38 |
| fenn | you could have a 'colloidal suspension' of asteroids but they would just bounce IR back and forth between each other | 13:39 |
| fenn | high surface area, but poor heat emitter | 13:40 |
| fenn | with reversable computing, heat dissipation might not be important at all | 13:41 |
| kanzure | hm | 13:41 |
| fenn | reversible* | 13:41 |
| fenn | i note that biology is quite stingy with irreversible operations | 13:43 |
| fenn | most enzymes function in a state of equilibrium | 13:43 |
| fenn | there's no direction, except there's more of the input type of molecule than the output | 13:44 |
| 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 | 15:19 |
| 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? | 15:20 |
| 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 | 15:21 |
| 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 | 15:22 |
| fenn | phun is like my "smirf" idea: http://www.phun.at/ | 15:31 |
| fenn | except it's not an mmo (yet) | 15:31 |
| fenn | needs more fluid dynamics from the looks of it | 15:33 |
| fenn | i've been playing xmoto a lot, it's basically phun, but you're a guy on a dirtbike | 15:38 |
| kanzure | xmoto? | 15:48 |
| 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 | 15:49 |
| 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 | 15:50 |
| kanzure | how do I play | 15:56 |
| 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' | 15:57 |
| fenn | green hill zone act 1 is cool too | 15:58 |
| 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. | 16:03 |
| 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 | 16:08 |
| 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 | 16:10 |
| 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 | 16:11 |
| fenn | hence why i suggested 'nicest levels' | 16:12 |
| kanzure | I still like Icy Tower and Mario Arena. if I had a windows machien. | 16:19 |
| kanzure | or Alex the Allegator | 16:19 |
| 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 | 16:44 |
| kanzure | What's up with Phil Ken Sebben? | 16:49 |
| fenn | theres a lot of stuff on that list, what's the goal? | 17:13 |
| 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 | 17:31 |
| fenn | er.. pipette is all about repeatability and accuracy | 17:40 |
| 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 | 17:41 |
| kanzure | I have lost all concentration. I need to go. | 17:42 |
| kanzure | http://heybryan.org/mediawiki/index.php/In_vitro_liquidwars | 18:28 |
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| 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/ | 19:09 |
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| kanzure | Hey Aulere. | 19:14 |
| Aulere | hey | 19:15 |
| kanzure | http://www.ustream.tv/channel/immortality-update <-- Immortality Institute board meeting | 19:15 |
| Aulere | cool | 19:15 |
| 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. | 19:18 |
| fenn | that's the most blippy staticky digital radio i've ever heard | 19:33 |
| Aulere | yeah | 19:36 |
| Aulere | I'm having streaming trouble too. | 19:36 |
| 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) | 19:40 |
| 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 | 19:42 |
| kanzure | about the same time that they did animated GIFs, I'd guess | 19:43 |
| 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. | 19:45 |
| 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 | 19:46 |
| kanzure | need a list of plasmid types | 19:47 |
| kanzure | Picogreen kit? | 19:47 |
| kanzure | three-stage transcriptional cascade, but no gain independent of the instruments used since there's no energy source really | 19:48 |
| 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 | 19:49 |
| kanzure | http://neb.com/ | 19:50 |
| kanzure | 1967 - Arthur Winfree - phase oscillators equation/modeling | 19:51 |
| kanzure | Kuramoto universality of phase oscillator models | 19:51 |
| 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 | 19:52 |
| kanzure | http://heybryan.org/mediawiki/index.php/Cell_oscillators | 19:58 |
| kanzure | http://heybryan.org/mediawiki/index.php/Nucleic_acid_architectures | 20:10 |
| 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 | 20:12 |
| fenn | http://mysite.mweb.co.za/residents/cyb00746/chaos/chaos.htm | 20:13 |
| fenn | looks amazingly similar | 20:14 |
| kanzure | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome | 20:19 |
| kanzure | http://heybryan.org/mediawiki/index.php/Models_of_cell_signaling_pathways | 20:33 |
| fenn | entrainment makes me think hypnosis and steam injector pumps | 20:39 |
| 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 | 20:42 |
| 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 | 20:43 |
| fenn | i'm confused.. the wiki says * blah blah [123] | 20:44 |
| 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 | 20:45 |
| 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 | 20:46 |
| fenn | hey you could change that to autogenix | 20:47 |
| kanzure | http://dna.caltech.edu/DNAdesign/ DNA design toolbox -- beta beta beta version | 20:47 |
| fenn | Enki-2: if you have a few days to kill.. http://vrinimi.org/rainbowsend.html | 20:48 |
| 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 =) | 20:50 |
| kanzure | too much chatting for me though | 20:51 |
| fenn | looks like vernor vinge's site | 20:51 |
| kanzure | lots of scifi pretends to be about talking | 20:52 |
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| kanzure | fenn | 21:33 |
| kanzure | http://kurtz-fernhout.com/oscomak/index.htm | 21:33 |
| kanzure | Open Source Community on Manufacturing Knowledge | 21:33 |
| kanzure | http://openvirgle.info/ | 21:36 |
| fenn | the sad thing is google and friends probably could do it if they tried | 21:38 |
| 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 | 21:40 |
| 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 | 21:41 |
| fenn | google revenue $16b assets 25b | 21:42 |
| fenn | nasa budget 16b | 21:42 |
| 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 | 21:43 |
| kanzure | hm | 21:44 |
| kanzure | http://www.chaordic.org/who_we_are.html huh? | 21:49 |
| fenn | New Open Source Confucianism (TM) | 21:50 |
| kanzure | I see. | 21:50 |
| kanzure | Charlton Heston passed away? | 21:51 |
| kanzure | woah, they killed AP CS AB? WTF? http://news.slashdot.org/article.pl?sid=08/04/06/1916242 | 21:53 |
| fenn | meh | 21:56 |
| fenn | by the time it trickles down to AP tests it would be laughably out of date anyway | 21:57 |
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| 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 | 23:12 |
| kanzure | hm | 23:13 |
| kanzure | fenn: http://kurtz-fernhout.com/oscomak/index.htm | 23:13 |
| fenn | i've never heard you use the word sustainable | 23:40 |
| kanzure | ah | 23:42 |
| kanzure | but surely you see the equivalence | 23:42 |
| 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? | 23:51 |
| Aulere | :) | 23:52 |
| fenn | you probably just fell through a time portal without realizing it | 23:52 |
| kanzure | it's Lain over at AnimeNfo | 23:53 |
| kanzure | fenn: where were we with autogenix | 23:55 |
| 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, | 23:56 |
| 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 | 23:57 |
| 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 | 23:58 |
| 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 | 23:59 |
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