| --- Day changed Tue Jun 10 2008 | ||
| fenn | its not even up to date.. kurzweil already demonstrated his 'pocket sized reading machine for the blind' | 00:02 |
|---|---|---|
| kanzure | it's very focused on Kurzweil | 00:04 |
| fenn | kurzweil is amazingly accurate | 00:04 |
| kanzure | I wonder why Kurzweil is so popular | 00:04 |
| kanzure | really? he completely ignores so much though | 00:04 |
| fenn | clarke has some really weird predictions | 00:06 |
| kanzure | ' | 00:06 |
| kanzure | Immediately forget any preconceptions you may have about Salman Rushdie and the controversy that has swirled around his million-dollar head. You should instead know that he is one of the best contemporary writers of fables and parables, from any culture. Haroun and the Sea of Stories is a delightful tale about a storyteller who loses his skill and a struggle against mysterious forces attempting to block the seas of inspiration fro | 00:06 |
| fenn | Largest living creature filmed: a 75-metre octopus in the Mariana Trench. [Clarke99] | 00:06 |
| kanzure | :) | 00:07 |
| fenn | compared to something you might actually expect a futurist to say, like "2012: billion digital video cameras posting online realtime, personal privacy is history" | 00:07 |
| kanzure | I don't know about the 'idle predictions' thing though | 00:09 |
| kanzure | "the best way to predict the future is to create it" | 00:09 |
| kanzure | I'm not feeling good recently | 00:09 |
| kanzure | have not had enough time to express all that I really should be | 00:09 |
| kanzure | for example, it may appear that I do not know about GPL licensing | 00:09 |
| kanzure | but that's really just my laziness showing | 00:09 |
| kanzure | too much time in the lab probably :) I get more work done juist sitting alone in five minutes. | 00:10 |
| * kanzure needs to go read up on the latest in filesharing | 00:13 | |
| fenn | look at distributed hash table on wikipedia | 00:13 |
| kanzure | I mean actual networks :) | 00:14 |
| kanzure | hurray for lists | 00:15 |
| kanzure | http://www.zeropaid.com/bbs/showthread.php?t=38811 | 00:15 |
| fenn | coral cache isnt an actual network? | 00:15 |
| kanzure | http://www.coralcdn.org/ | 00:16 |
| kanzure | ? | 00:16 |
| fenn | nevermind | 00:16 |
| kanzure | ? | 00:17 |
| fenn | i thought you were talking about the implementation, not just what's available and popular at the moment | 00:18 |
| kanzure | I'm either shutting down or completely confused now. | 00:22 |
| kanzure | re: the lab work, I think I'm going to possibly insert the complaint that since they don't know how to do the manufacturing, it's all bunk | 00:22 |
| kanzure | unless they want to propose the crazy idea of doing the chemistry from scratch | 00:22 |
| kanzure | which is a very big task that I am not too sure about ... wouldn't somebody have done this by now ? heh' | 00:22 |
| fenn | reinventing biochem? why bother | 00:23 |
| fenn | it already works | 00:23 |
| kanzure | I'm not too certain about the protein engineering stuff | 00:24 |
| kanzure | and again | 00:24 |
| kanzure | you mention that the writozyme (or just general easy DNA synthesizer) proliferation might help that out | 00:24 |
| kanzure | but I'm not quite sure how, other than letting lots of people tinker and try new stuff out :) | 00:24 |
| fenn | yep, pretty much | 00:24 |
| kanzure | I suppose it has to be ultimately tractable | 00:24 |
| kanzure | protein folding, I mean. | 00:24 |
| fenn | i think a system of legos could be built, even using standard biotech tools | 00:26 |
| kanzure | http://heybryan.org/mediawiki/index.php/Wittig_cohort#2008-06-09 <-- meeting with Zack, the guy who shows up and likes amorphous computing stuff | 00:26 |
| kanzure | he seems to be fairly knowledgable about the general space of stuff that this involves | 00:26 |
| kanzure | and isn't exactly a biochemist-specialist, so he looks like he's from the software side | 00:26 |
| fenn | but if you have to do some nobel-prize-winning effort every time you want to build something with those lego's, its no good | 00:26 |
| kanzure | system of legos? so, a new biochemistry though? | 00:27 |
| kanzure | I mean, that sounds nasteh | 00:27 |
| fenn | no | 00:27 |
| fenn | i mean sticking protein blobs together | 00:27 |
| kanzure | oh | 00:27 |
| kanzure | puzzle pieces? | 00:27 |
| fenn | right | 00:27 |
| kanzure | or lego | 00:27 |
| kanzure | right | 00:27 |
| kanzure | heh' | 00:27 |
| fenn | not artificial amino acids or whatever | 00:27 |
| kanzure | I see | 00:28 |
| kanzure | that's structure, not necessarily function | 00:28 |
| fenn | you can have functional subunits though | 00:28 |
| fenn | turn them into engineering blackboxes | 00:28 |
| fenn | with levers and buttons | 00:28 |
| kanzure | okay | 00:28 |
| kanzure | I guess I just have to get over the fact that coming up with new blackboxes isn't going to be the same as writing a new function | 00:29 |
| kanzure | (in terms of code) | 00:29 |
| kanzure | unless we solve some other problems re: protein folding of course | 00:29 |
| fenn | if my humble opinion is worth anything, i dont think compartmentalization is going to go much anywhere | 00:30 |
| kanzure | how are you going to get evolution? | 00:30 |
| kanzure | the idea is to get "genotype and phenotype in the same place" | 00:31 |
| kanzure | one way that this might happen is Mike's, uh, "RNA polymerase + biotin + attach it to the strand of RNA" - which isn't a compartment, but it's functionally equivalent | 00:31 |
| fenn | yes, perhaps you'll demonstrate a "DNA computer" but it'll be slow and require external 2d patterning | 00:31 |
| kanzure | attaching the two components together. | 00:31 |
| fenn | eh, i'm talking past you i think. sorry | 00:32 |
| kanzure | it might be, I'm falling asleep | 00:33 |
| kanzure | maybe you mean the problem with compartments and how you're just creating lots of problems | 00:33 |
| kanzure | like communication barrier stuff | 00:33 |
| kanzure | I've been listening to these guys boast about emulsions | 00:33 |
| kanzure | and it sounds like painfully, retardingly intense work | 00:33 |
| kanzure | for minimal returns that are barely related to the ideals of amorphous fabrication and their other dreamgoals | 00:33 |
| fenn | did my comment about wifi networks and noise threshold make sense? | 00:34 |
| kanzure | no, unless you meant that only a certain number of the packets (signal) get to the more distant wifi nodes and thus those get to be counted as noise | 00:35 |
| fenn | yes, that's what i meant | 00:35 |
| kanzure | I'm guessing it's dependent on 802.11b | 00:35 |
| kanzure | so, ok | 00:35 |
| fenn | but instead of a bunch of houses with transmitters on the roof, you have a microarray with transcriptional switch genes | 00:35 |
| kanzure | right | 00:35 |
| kanzure | this scenario has shown up a number of times | 00:36 |
| kanzure | it's even what I recommended a few months ago | 00:36 |
| fenn | so, you can re-use the same toehold sequence if they're far enough apart | 00:36 |
| kanzure | http://heybryan.org/mediawiki/index.php/In_vitro_liquidwars | 00:36 |
| fenn | but you lose the whole amorphous part | 00:36 |
| kanzure | aha! | 00:36 |
| kanzure | you see | 00:36 |
| kanzure | they don't agree with me on that | 00:36 |
| kanzure | they tell me that it's ok for it to be attached | 00:36 |
| kanzure | that "everything has to do symmetry breaking" | 00:36 |
| kanzure | but I keep pointing out that it's not amorphous if it's attached | 00:37 |
| fenn | well, its certainly easier than building a chip fab | 00:37 |
| fenn | but not amorphous | 00:37 |
| kanzure | the idea is that you have *both* (1) you don't know their location, and (2) NEITHER DO THEY. | 00:37 |
| kanzure | except relative concentration gradients and so on | 00:37 |
| kanzure | and whatever established relative axises between each other etc. | 00:37 |
| fenn | it doesnt matter if you dont know the location, the point is you have to pattern this microarray thingy to do anything | 00:37 |
| kanzure | right, I don't like the prospects of losing the biological advantage | 00:38 |
| fenn | heh you could make a DNA origami array :) | 00:39 |
| kanzure | ruthemund's work involves self-assembling structures based off of a scaffolding system, so that's close, I guess | 00:40 |
| kanzure | I wonder if building stuff from DNA like that is worth it? | 00:40 |
| kanzure | http://dna.caltech.edu/ | 00:40 |
| * fenn pats self on the back | 00:40 | |
| kanzure | eh? | 00:40 |
| fenn | 100% DNA computer | 00:40 |
| kanzure | well, are you trying to lead back to the DNA FPGA idea? | 00:40 |
| fenn | you heard it here first | 00:40 |
| fenn | sorta.. but instead of using semiconductors you use transcriptional switches | 00:41 |
| fenn | and that way the complexity is already programmed in | 00:41 |
| fenn | the problem of course is that you can't reprogram it | 00:41 |
| kanzure | yeah .. | 00:41 |
| kanzure | I'm still not quite convinced | 00:41 |
| kanzure | DNA is not the best substrate for much | 00:41 |
| fenn | cant work around defects in tile crystal growth | 00:41 |
| kanzure | I mean, it degrades in all sorts of weird shit | 00:41 |
| kanzure | there are ways to do "checks" on tile growth | 00:42 |
| fenn | DNA doesnt normally degrade | 00:42 |
| kanzure | that Ruthemund has apparently implemented | 00:42 |
| kanzure | eh, I guess I just need to give up on the idea of semiconductors being so solid state | 00:42 |
| kanzure | but I guess I could argue something about DNA having lots of repair enzymes to help fix it, does that count? | 00:42 |
| fenn | DNA is not a semiconductor (yet) | 00:42 |
| kanzure | you think that could change ? how ? | 00:42 |
| fenn | well, i read it was superconducting somewhere.. that sorta blew my mind | 00:42 |
| kanzure | hrm | 00:43 |
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| fenn | at 1 kelvin | 00:44 |
| kanzure | at 1 kelvin | 00:44 |
| kanzure | heh' | 00:44 |
| fenn | yeah :( | 00:44 |
| kanzure | I'm sure we could throw in some salts or phase change stuff | 00:45 |
| fenn | http://www.physics.ucla.edu/research/biophysics/news/pdf/outlook.pdf | 00:46 |
| fenn | first time i've seen a retraction of prior unlikely claims in the new scientist | 00:47 |
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| -!- 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/ | 01:05 | |
| -!- Topic set by kanzure [] [Sun Jun 8 13:00:15 2008] | 01:05 | |
| [Users #hplusroadmap] | 01:05 | |
| [ fenn ] [ kanzure] [ parodyoflanguage] [ pupnik ] [ wrldpc] | 01:05 | |
| [ fenn_] [ nsh ] [ procto ] [ Splicer] | 01:05 | |
| -!- Irssi: #hplusroadmap: Total of 9 nicks [0 ops, 0 halfops, 0 voices, 9 normal] | 01:05 | |
| -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008 | 01:05 | |
| kanzure | fenn_: you still need a surface with your dna assemblers | 01:05 |
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| kanzure | why do the Wachowski brothers spell 'woah' as 'whoa' ? | 01:09 |
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| ybit | internet connection issues all day while i was at work it seems | 02:01 |
| ybit | so what'd i miss? :) | 02:01 |
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| wrldpc | fnord | 05:22 |
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| faceface | anyone seen a guy called don in here? | 10:59 |
| faceface | don / mindreck | 11:00 |
| kanzure | Nope. | 11:09 |
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| cis-action | ping | 17:02 |
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| * procto is at the cambridge semantic web gathering | 18:14 | |
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| kanzure | Hey all. | 19:45 |
| * kanzure got his radiation training done today. | 19:45 | |
| kanzure | The whole "don't be a terrorist" thing. | 19:45 |
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| kanzure | fenn: So I put some thought into it, and I think I can get their 'amorphous fabrication' goals via ribosome+polymerase+switches all hopelessly tied together. However, it requires the same writozyme/polymerase ideas. The good news is that ribosomes have been very well characterized. | 20:35 |
| * kanzure feels a stroke of evil genius coming along | 20:41 | |
| kanzure | I just found a paper that explains how to couple mRNA, ribosome, and the protein output together. | 20:42 |
| kanzure | i.e., chemically/physically | 20:42 |
| Splicer | are you talking about a bacterial amorphous computer project? | 20:46 |
| kanzure | "coupled transcription-translation" | 20:49 |
| kanzure | Yes. | 20:49 |
| kanzure | But it's not bacterial. | 20:49 |
| kanzure | In the lab we're doing transcriptional switches that we hope will one day ("a very long time from now") can lead up to amorphous computation+fabrication (an intersection of the two). The writozyme idea and some others kind a jump the gun and say "screw a long time, let's do it now." | 20:50 |
| Splicer | how would a transcriptional switch work? | 20:52 |
| kanzure | Splicer: Imagine a DNA fragment. A polymerase would bind, during a run through a PCR protocol, and copy a portion which would then go off to promote the transcription of another part of the switch, which would then ... :) | 20:53 |
| kanzure | Splicer: http://heybryan.org/mediawiki/index.php/Wittig_cohort <-- notes from the cohort. | 20:54 |
| Splicer | checking | 20:55 |
| kanzure | uh, well, technically we don't necessarily want polymerase bound to the ribosome display techniques | 21:08 |
| kanzure | simply a transcriptase | 21:08 |
| kanzure | DNA -> mRNA converter | 21:08 |
| kanzure | so, RNA polymerase. | 21:09 |
| Splicer | but how is the switching done?... I mean the polymerase follows the singlestranded DNA so either that has to contain the blueprint or the polymerase has to be modified? | 21:19 |
| kanzure | The polymerase copies a part of the DNA molecule which then goes off to signal a "neighboring" (one that matches) strand. | 21:20 |
| Splicer | you mean you steer what gene to read? | 21:21 |
| kanzure | There are inhibition regions and promoter regions. So what if the promoter region is blocked? Suddenly the strand doesn't transcribe. :) | 21:22 |
| kanzure | (the small signaler portion, at least) | 21:22 |
| Splicer | the promroter/inhibitor regions are gene wide? | 21:24 |
| kanzure | What? | 21:26 |
| Splicer | mmm... i have to read up on this... i thought they regulated the whole gene, so the mRNA is a separate piece ending in the STOP. | 21:26 |
| Splicer | wait.. you are building a single logic gate? | 21:27 |
| Splicer | not a program | 21:28 |
| kanzure | It's just an oscillator. | 21:28 |
| kanzure | but that's basically a flip flop, if you can get some hooks into it and so on | 21:28 |
| kanzure | and from flip flops you can build gates | 21:28 |
| Splicer | ah.. cool | 21:28 |
| kanzure | well | 21:28 |
| kanzure | no | 21:28 |
| Splicer | fuck... i have a lot to learn | 21:29 |
| kanzure | http://en.wikipedia.org/wiki/NOT_gate :) | 21:29 |
| Splicer | shut up | 21:29 |
| Splicer | hehehe | 21:30 |
| kanzure | not sure how to implement NOT on transcriptional switches really | 21:30 |
| kanzure | in fact, I'm still working through the entire scheme myself | 21:30 |
| kanzure | to see what we actually have | 21:30 |
| kanzure | it's kind of weird that the other students that I am working with seem to have it nailed down, but when I actually try to ask them about any of the computational aspects or the meaning of any of the certain aspects, they just kind of go walk off :-p | 21:31 |
| Splicer | wans't there an iGEM team who built an oscilator... it blinked 10 times i think | 21:31 |
| kanzure | Maybe. | 21:31 |
| Splicer | maybe cause you are a high profile guy | 21:32 |
| Splicer | ( http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator ) | 21:32 |
| kanzure | I think it's because I know the grad student is a comp sci guy, I'd like to think I know how these guys work. We get along pretty well. But then they shush me when they think he's mad (just getting excited about a certain aspect of a system, really), etc. | 21:32 |
| Splicer | you do get excited | 21:34 |
| kanzure | No, not me, him. | 21:36 |
| Splicer | you meant mad mad? | 21:36 |
| Splicer | like nuts? | 21:37 |
| kanzure | No. | 22:10 |
| kanzure | I don't know how to characterize it. I'll get back to you on that. | 22:11 |
| procto | kanzure: re the cybernetic view of models: http://pespmc1.vub.ac.be/MODEL.html | 22:41 |
| kanzure | Principia Cybernetica gets *close* to some pretty awesome insights. | 22:41 |
| procto | more stuff here: http://pespmc1.vub.ac.be/EPISTEM.html | 22:42 |
| procto | and on the sidebar on the right | 22:42 |
| procto | yes, certainly | 22:42 |
| procto | I'm trying to remember where I saw some other really interesting stuff on cybernetic modelling but it's elluding me | 22:42 |
| procto | soon as I remember a keyword other than "cybernetics" and "world models" i'll google it | 22:43 |
| procto | I'm not sure I'm totally with the cybernetic epistemology, though | 22:57 |
| kanzure | How so? | 22:59 |
| procto | you could say i'm epistemologically agnostic, but not because I don't want to commit, but rather because I don't feel I know enough as yet to properly defend a position to myself | 23:06 |
| procto | at the same time, I rather like the cybernetic framewolk | 23:06 |
| procto | framework* | 23:06 |
| procto | much od my conception of epistemology I derive from decision theoretic semantics, which is a sort of meta-semantic theory. that is, it subsumes within it referential and possible world models | 23:07 |
| procto | and utilizes decision theoretic and game theoretic techniques | 23:07 |
| procto | claiming that this models the way humans decide on consensus meaning | 23:08 |
| procto | i.e. a meaning of an utterance is ascribed on the basis of maximizing utility | 23:08 |
| procto | and in a conversation, some sort of game theoretic approach may be used to decide on the equilibrium point, which is the then decided upon meaning | 23:09 |
| kanzure | who cares if it models 'consensus' ? | 23:10 |
| procto | some prefer a cooperative approach. i.e. in your head, you are modeling the decision problems of the person your are speaking to, and thus an utterance is an answer to a hypothetical question one might ask to increase the utility of that model person in your head | 23:10 |
| procto | well, by "consensus" I mean a situation where in the process of an interaction, clashes are minimized | 23:11 |
| procto | myself, I prefer an adversairal approach | 23:11 |
| procto | adversarial* | 23:11 |
| procto | if we are talking together about how much we love mashed potatoes in standard informal english, we have little to no misunderstanding | 23:12 |
| procto | and you can model the way in which we would both ascribe the word "potate" to the same-ish category of tuber in the decision theoretic semantics framework | 23:13 |
| procto | potato* | 23:13 |
| fenn | mashed potatoes are awesome | 23:14 |
| fenn | i'm glad you guys can udnerstand | 23:14 |
| * Splicer wonders if nsh speaks finnish | 23:15 | |
| procto | kanzure: although the epistemology derived from this is quite similar to the cybernetic one, the difference is that the cybernetic framework indicates that the internal representation is created through interaction with the environment | 23:17 |
| procto | kanzure: whereas I currently prefer a framework where the internal representation is created by internal evaluation of the environment in terms of relative value | 23:19 |
| procto | the difference is subtle and i have not plumbed its depths. it could be a non-existant one, since my feeling of distinction could be wrong | 23:20 |
| procto | perhaps to illustrate what I percieve to be the difference I can use an example | 23:22 |
| procto | take Searle's Chinese Room (I am assuming familiarity) | 23:22 |
| procto | searle's argument is that it lacks semantics, that is, meaning | 23:22 |
| procto | hmmm | 23:24 |
| procto | actually | 23:24 |
| procto | scratch all that | 23:24 |
| procto | (I am expressing ideas and such that are relatively nebulous in my head, so revision once they are regurgitated is a welcome side effect) | 23:24 |
| procto | it seems that i was anthropomorphizing systems | 23:25 |
| procto | i.e. robbing non-value laden systems such as searle's chinese room of the ability to practice an epistemological process | 23:25 |
| procto | that is, "if it doesn't have a mind it can't know things" | 23:27 |
| procto | but cybernetics says nothing of minds | 23:27 |
| procto | (my initial thurst was, rephrased, that minds are born when a cybernetic system becomes value-laden) | 23:28 |
| procto | definition of value-laden: able to ascribe utility to "stuff" | 23:29 |
| procto | (this utility can be ordinal or cardinal, not picking a system) | 23:29 |
| * procto takes a deep breath | 23:31 | |
| procto | was my train of thought followable? (it's ok if there was no desire to follow it :>) | 23:31 |
| procto | sleep times now | 23:45 |
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