--- Day changed Sat Apr 05 2008 00:00 < mechie> i had a lot of pain working with the ROHS solder 00:00 < kanzure> ROHS? 00:00 < kanzure> not resin? 00:00 < mechie> it requires such high heat and i kept cracking the resistors 00:00 < kanzure> you know, we have automation machinery for a good reason 00:00 < mechie> yeah 00:00 < mechie> but i had to mod it 00:01 < mechie> cuz our batch got messed up 00:01 < mechie> so i was the cheap labor alternative :\ 00:01 < mechie> i mostly went in for fixing things 00:01 < kanzure> you're not too bright, are you 00:01 < kanzure> joking :) 00:01 < mechie> :D 00:01 < mechie> i needed monies :> 00:01 < kanzure> for what? 00:02 < mechie> for school books 00:02 < mechie> :D 00:02 < kanzure> Download 'em. 00:02 < mechie> i just get them on half.com or w/e 00:02 < kanzure> (and leech) 00:03 < mechie> soooo 00:04 < mechie> do you make anything 00:04 < mechie> physical 00:05 < kanzure> DNA synthesizers, DNA sequencers, self-replicating machines, scanning probe microscopes, brains, bacteria, electronics, etc. 00:05 < mechie> ok 00:05 < kanzure> Artificial meat machines, 00:05 < kanzure> artificial wombs 00:05 < kanzure> cryonic suspension chambers 00:06 < kanzure> many of these projects are tentative of course 00:06 < kanzure> but it's good to have more ideas than time to implement them 00:06 < kanzure> This way I can select which ones to do. ;) 00:06 < mechie> i give up from the start :> 00:06 < mechie> EPI KNOWS 00:07 * mechie kicks epitron in the nads 00:07 < kanzure> You give up on what? 00:07 < kanzure> life? 00:08 < mechie> maybe i did. 00:08 < kanzure> You are cryptic. 00:08 < mechie> perhaps. 00:08 < mechie> i was thinking of being a surgeon 00:08 < mechie> i didn't really want to work hard through med school though 00:09 < kanzure> Med school is tanking. http://forums.studentdoctor.net/ <-- lots of morons getting into med school 00:09 < mechie> yeah i know 00:09 < mechie> my friends got in 00:09 * mechie scared 00:09 < kanzure> I am, however, interested in the medical scientist training program 00:10 < kanzure> An 8 year program to get a PhD and an MD 00:10 < kanzure> with a stipend paid by the govt 00:10 < mechie> smartypants 00:46 < epitron> kanzure: you could probably do that program a lot faster by yourself :) 00:46 < epitron> working with researchers 00:46 < epitron> with a stipend paid by the research labs 00:46 < epitron> 8 years is too much school 00:47 < kanzure> perhaps =) 00:47 < kanzure> it's not constant schooling 00:47 < epitron> toooo mucchhh schoooolll 00:47 < epitron> did you know that the guy who sequenced the human genome didn't even go to school? 00:47 < epitron> what's his name... craig ventnor? 00:49 < epitron> (ok he didn't sequence the human genome by himself.. :) but he was instrumental in its expediency) 00:50 < kanzure> he had millions of dollars 00:50 < kanzure> billions, even 00:51 < epitron> didn't the other genome project? 00:51 < kanzure> huh? 00:51 < kanzure> Craig Venter, by the way 00:51 < kanzure> J. Craig Venter 00:51 < epitron> thanks 00:51 < epitron> there were two parallel projects 00:51 < kanzure> http://venterinstitute.org/ or something 00:51 < epitron> his at celera 00:52 < kanzure> sure, there were many projects 00:52 < kanzure> check out http://bioperl.org/ for the story 00:52 < epitron> and the intergovernmental one or whatever 00:52 < epitron> what? 00:52 < epitron> :) 00:53 < epitron> what's bioperl go tto do with it 00:53 < kanzure> they have a good story on how automation saved the Human Genome Project. 00:53 < kanzure> look around on the site, the article has a lengthy title 00:53 < kanzure> and was written 1995 00:53 < epitron> so this bioperl project is old? 00:53 < kanzure> actually, no 00:53 < kanzure> but they have an old article or something 00:53 < kanzure> Anyway, I'm going to go hit bed 00:54 < epitron> i know about the basics, how venter used the shotgun approach 00:54 < kanzure> I have ~30 papers open at the moment that I still need to run 00:54 < epitron> nighty-o! 00:54 < kanzure> shotgun technique is old news 00:54 < epitron> hahah 00:54 < kanzure> http://heybryan.org/mediawiki/index.php/DNA_sequencing 00:54 < epitron> i know 00:54 < kanzure> read that and digest all of the links 00:54 < epitron> grr 00:54 < epitron> :) 00:54 < epitron> no! 00:54 < epitron> i don't need to 00:54 < epitron> semantic drift in progress 00:55 < epitron> you ever read this quote? 00:55 < epitron> "I consider that a man's brain originally is like a little empty attic, and you have to stock it with such furniture as you choose. A fool takes in all the lumber of every sort that he comes across, so that the knowledge which might be useful to him gets crowded out, or at best is jumbled up with a lot of other things, so that he has a difficulty in laying his hands upon it. Now the skilful workman is very careful indeed as to what he takes into his bra 00:55 < epitron> "He will have nothing but the tools which may help him in doing his work, but of these he has a large assortment, and all in the most perfect order. It is a mistake to think that that little room has elastic walls and can distend to any extent. Depend upon it - there comes a time when for every addition of knowledge you forget something that you knew before. It is of the highest importance, therefore, not to have useless facts elbowing out the useful on 00:56 < epitron> -- Sir Arthur Conan Doyle 00:57 < epitron> i have no trouble reading a high level summary of something 00:57 < epitron> so that i know of its existence, and can learn about it if the need arises 00:57 < epitron> but i don't bother absorbing large random research papers for no reason :) 01:04 < fenn> doyle obviously didnt know anything about data compression 01:32 < epitron> shut up noob! 01:33 < mechie> fuckers 01:33 < mechie> go to sleep 10:07 < kanzure> DNA looping? DNA-knots? 10:12 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 10:17 -!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap 10:57 < fenn> dna underwater basket weaving 11:00 < kanzure> that's what it sounds like 11:21 < kanzure> fenn 11:21 < kanzure> http://heybryan.org/mediawiki/index.php/Ellingtonia#Challenge 11:21 < kanzure> see ED3814 11:23 < kanzure> the idea is that there are biochem-networks in the databases out there on the internet 11:24 < kanzure> ideally, we can mimic the computation that those networks are doing 11:24 < kanzure> and automatically generate our own 'logic' and then have the DNA compiler implement this with transcriptional logic or whatever 11:24 < kanzure> but the problem is that the 'experimentally confirmed' biological reaction networks are messy and are defined in various ways, I think 11:24 < kanzure> I need to go look at the raw data 11:25 < kanzure> I suspect that translating that into 'abstract logic' is going to be hard 11:25 < kanzure> unless we can model complex systems in a certain way, saying "there's an information conduit between these two places' 11:25 < kanzure> a systems-diagramming method or something 11:26 < kanzure> or I guess we can just ask to model the functionality of all of the components in the network, and then we can implement this in logical terms 11:26 < kanzure> is this an impossibility? 11:56 < fenn> well, looks like you've been doing your homework 12:03 < fenn> genetic regulatory network is not logic exactly, more like fuzzy logic or analog electronic circuits 12:06 < fenn> not sure what's hard about diagramming complex systems.. isnt that the whole point of making diagrams? 15:27 < kanzure> I suppose, but can they be autodiagrammed ? 15:28 < kanzure> I mean, what is the experimental data collection format ? if it's a complex network from automated testing or something, then we're in business 15:28 < kanzure> because then we just do normal comp sci (parallel -> linear programs) 15:28 < kanzure> which, although hard, is at least studied in theoretical comp sci 15:49 < kanzure> fenn: http://www.genome.ad.jp/kegg/pathway/hsa/hsa04330.html 15:49 < kanzure> hm 15:50 < kanzure> they have a diagram, but not necessarily a format for reading this complex reaction network 15:52 < kanzure> http://en.wikipedia.org/wiki/SBML 15:55 < kanzure> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B75GS-4BP87S9-D&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=529aca035baa81bbfc382f3a52d8901a 15:55 < kanzure> BioSig: an informatics framework for representing the physiological responses of living cells 15:56 < kanzure> Subcellular experimental datasets and detailed cell models are required before modeling of whole organs. Cell modeling requires repeated interaction between simulation and experimental data. This review describes a coupled system of informatics and instrument control suitable for extracting information at the subcellular level. The BioSig informatics framework annotates time-series images with experimental variables and computed r 15:58 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1435936 15:58 < kanzure> GEM might be it. 16:07 < kanzure> http://www.cellerator.org/ ... to facilitate biological modeling via automated equation generation 16:22 < fenn> what's the point 16:22 < fenn> epicycles 16:22 < fenn> it's non-linear so your extrapolation beyond known data is probably going to be crap 16:25 < kanzure> I guess I can think of this in another way. 16:25 < kanzure> Suppose we have some differential equations that model a supercomputer, a network of Beowulf clusters or something. In our program, we can set the number of nodes on the network to N=2, and then try to map programming-instructions to those 16:25 < kanzure> two nodes to model the behavior of the ODE. If this is not the case, then we iterate over to N=3, etc., up to N=X where X is some sufficiently large number that can have enough instructions to model the ODE. 16:25 < kanzure> it doesn't matter if it's non-linear 16:25 < kanzure> supposedly our supercomptuers are nonlinear ;) 16:27 < kanzure> the fun thing is that your experimental data set is mostly 'complete' in bioinformatics 16:27 < kanzure> since you know the genes and you can trace interactions and whatever else 16:28 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1893010 " In this paper we develop tools that enable the detection of steady states that are modeled by fixed points in discrete finite dynamical systems. We discuss two algebraic models, a univariate model and a multivariate model. We show that these two models are equivalent and that one can be converted to the other by means of a discrete Fourier transform." 16:29 < kanzure> that seems to be my answer 16:30 < fenn> i have no idea what the significance of that may be 16:38 < kanzure> fixed points of finite dynamical systems -> finite field model -> Boolean model -> http://en.wikipedia.org/wiki/Boolean-valued_model 16:38 < kanzure> if you look at the article, you'll see that this is comp sci language stuff 16:38 < kanzure> meaning we have the abstract logic statements, the set of instructions basically 16:38 < kanzure> and then we can plug this into my DNA compiler. 16:40 < fenn> the 'fixed points' and 'finite dynamical systems' is just gibberish to me 16:40 < fenn> i see they have a tree of states, i guess that's the finite dynamical system 16:40 < fenn> what are the fixed points? 16:40 < kanzure> I am guessing the genes or the proteins that they express 16:40 < kanzure> but I don't know about it in a mathematical sense 16:41 < kanzure> I'm first checking it out in #math on a meta-level 16:41 < kanzure> to see if Boolean models can be symbol tables and given manipulations or whatever 16:43 < kanzure> this sounds weird though 16:43 < fenn> why not just start with the 'boolean valued model' 16:43 < kanzure> "We can show that for any n-dimensional dynamical system ... there is an equivalent one-dimensional system." 16:44 < kanzure> because you don't have that boolean valued model, you have some differential equations from cellerator ;) 16:44 < kanzure> although tracing through the software perhaps we can find a way to simplify the process 16:45 < fenn> so the point of all this is to re-create a genetic regulatory network, based on observed interactions? 16:45 < kanzure> yes 16:46 < kanzure> to extract the 'abstract logic' that evolution has come up with, in whatever fuzzy way that was 16:46 < fenn> oh.. boolean valued model is only linear interactions, right? 16:46 < fenn> p*q 16:46 < kanzure> that's what it looks like 16:46 < kanzure> but 16:46 < kanzure> that's why the "We can show ..." line looks so weird 16:46 < kanzure> it looks like the P=NP problem 16:46 < fenn> not p^q or p+q 16:46 < kanzure> or maybe I'm just seeing things 16:49 < fenn> p=np is something else 16:50 < kanzure> yes, they are hitting me over the head 16:50 < kanzure> rather rudely 16:50 < kanzure> I hate #math ... TWRBW is knowledgable, but a hardcore eugenicist/"if they can't do it, kill them" 16:50 < fenn> fuck math 16:51 < fenn> if you dont understand what something is, all the math in the world won't help 16:51 < kanzure> math and chemistry have a lot in common, in my opinion 16:51 < kanzure> while math you could supposedly do on your own, both of them require intense study of the previous literature and s oon 16:52 < kanzure> actually, that's true of much of science 16:52 < kanzure> just there it seems more stricking. 16:52 < fenn> sorta 16:52 < kanzure> hm, they also give state space diagrams 16:52 < fenn> it's just hard to communicate if you dont share the language 16:52 < fenn> and language is only got through study or proximity 16:53 < kanzure> I think I've said this before [to you], but I would really appreciate a ref book on math syntax 16:53 < fenn> heh no that was me complaining to you 16:53 < kanzure> was it you who was complaining about identity disassociation in chatting? 16:53 < kanzure> somebody who did it to you? 16:53 < kanzure> or was this epitron 16:53 < fenn> you suggested some old book and i downloaded it and never read it 16:53 < fenn> that was me 16:54 < fenn> i didnt say someone did it to me, it's just that i find myself thinking other peoples' thoughts sometimes 16:54 < fenn> not necessarily a bad thing.. i think it's how communication works 16:55 < kanzure> then it was somebody else who mentioned a bad experience with somebody who started to mistake him/her for a long-gone ex-girlfriend or something 16:55 < kanzure> Anyway, 16:56 < kanzure> since this is *not* some lunatic thinking P=NP 16:56 < kanzure> and my warning lights are not going off 16:56 < fenn> oh, yea that is me too 16:56 < fenn> i dont get the p=np problem, why is it a question? 16:56 < kanzure> it looks like I might have a vague picture from automated bioinformatics all the way down to -> automated modeling and then -> automated compiling into DNA for in vitro synthetic biology, to create systems from scratch. 16:57 < kanzure> by wrestling the insights from biology (and thus evolution) 16:57 < kanzure> so if we could just cycle through an entire database of the experimental bioinformation, we can supposedly generate all of the code to the cell, even if it is sorta fuzzy 16:58 < kanzure> although this sort of assumes we have ODEs or enough experimental data for all of the genome, so that we can do differential equations for all of the interacting genes 16:58 < kanzure> it sounds unlikely to currently exist in an easily accessible format, but it should be possible 16:58 < fenn> no, because you neglect actual interaction with the non-nucleic acid world 16:58 < kanzure> right 16:58 < kanzure> well, no 16:58 < kanzure> remember the Winfree paper on robustness 16:58 < fenn> you dont have the heuristics for protein folding 16:59 < kanzure> while there's a certain point where the cell breaks down and can't do the cascading chemical reactions 16:59 < kanzure> in general, for a normal state, they are going to work 16:59 < kanzure> you don't need protein folding 16:59 < kanzure> not by a long shot 16:59 < kanzure> the point is that we can model whatever 'normal' is 16:59 < kanzure> biology has adapted for those variety of circumstances when the environment (internal/external) gets rough 16:59 < kanzure> but that's more like filling in the gaps later 17:00 < kanzure> and tweaking the system to be able to survive in more situations 17:00 < kanzure> rather than being perfect upon the first go 17:00 < kanzure> (being perfect would involve simply replicating the DNA and doing protein biosynthesis like normal ;)) 17:01 < fenn> the point of the regulatory networks is to allow normal function even in harsh environments 17:01 < fenn> if everything is perfect, you dont need regulatory networks, you just hard-code everything 17:01 < kanzure> that's all at the edges though 17:01 < kanzure> just before the 'automated bioinformatics experimentation' stuff 17:01 < kanzure> that's where people would come up and set up a new automated experiment for a new class of genes or whatever 17:01 < kanzure> and so they would change the variables that are being tweaked and seeing how the genes react 17:02 < kanzure> I see what you mean, but I think you are assuming something that I am not 17:02 < kanzure> we'd be using this system for another purpose than modeling the cell per-se 17:02 < kanzure> suppose we run a selection experiment on bacteria 17:02 < kanzure> and they come up with a novel solution to some challenge, which would necessarily involve genetics 17:03 < kanzure> so we could characterize these new genes and they way they interact with each other -- perhaps they are a modification in the signaling network, or a new chemical synthesis, something 17:03 < kanzure> we would know where to look since we can sequence their genomes and look for the modifications, and other various DNA tech 17:03 < kanzure> we would know what conditions they were in since we were the ones who set up the selection experiment 17:04 < kanzure> it is these solutions to information-processing in whatever 'harsh' (or not) conditions we set up that we are interested in 17:04 < fenn> you mean adaptation? 17:04 < kanzure> granted, sometimes they may not be GRNs (gene regulatory networks), but we can do some interesting things to make sure their adaptations/mutations do this 17:04 < kanzure> yeah 17:04 < kanzure> this is a way to codify knowledge gathered by the evolutionary process of adaptation, into a form that humans can begin to understand 17:05 < kanzure> and then we can use this in, say, skdb, but that's another set of mental connections to make 17:05 < kanzure> the designs are abstract and do not need to be plugged into the DNA compiler 17:05 < kanzure> they could be plugged into anything, frankly 17:05 < kanzure> even gcc 17:05 < kanzure> (as long as we have a way to convert to C, of course) 17:05 < fenn> more like vhdl i think 17:06 < kanzure> but that conversion is easy, from a set of Boolean statements to C? yeah, we can do VHDL to C I think 17:06 < kanzure> there's got to be a VHDL->C translator out there, heh 17:06 < kanzure> that's just the geeky thing to do 17:06 < fenn> just so you can use gcc? sounds silly 17:06 < kanzure> well, 17:06 < kanzure> biology is software, on the hardware of reality 17:06 < kanzure> and evolution is a way of writing up new programs 17:06 < fenn> vhdl is digital logic anyway, it wouldnt work for your wacky analog interactions 17:06 < kanzure> so these new programs can be converted into software for our silicon computers 17:06 < kanzure> that's my point 17:07 < kanzure> no, this is discrete/finite points in field models, remember? (from the GRN dataset analysis, the pubmed paper) 17:07 < fenn> no i have nfc what that was about 17:07 < fenn> (i did read it) 17:07 < kanzure> it was a way of taking experimental data from bioinformatics, the automated gene analysis systems and so on, and then coming up with finite models that do the same things 17:07 < kanzure> yep 17:08 < kanzure> so anyway, my point again: nature evolves software; we translate that software into abstractions, we then can take those abstractions and test them, either in silicon or in vitro with transcriptional logic to 17:08 < kanzure> build up synthetic 'biological' systems (not necessarily cells ... but I hear Andy Ellington has an interest in nucleic acid 'origins of life' stuff) 17:09 < fenn> so this is like checking your answer by doing the problem a different way? 17:09 < kanzure> please contextualize 17:09 < fenn> in math 17:09 < fenn> two trains leave chicago and new york 17:09 < kanzure> I don't think so, I probably just don't know your question 17:10 < kanzure> let me reiterate and you can point out your questions 17:10 < fenn> the problem is 'how does this cell work' 17:10 < kanzure> biology and natural evolution comes up with new solutions to problem 17:10 < kanzure> nope 17:10 < kanzure> the problem is 'how to make it better' or 'how to get something interesting out of it' 17:10 < kanzure> cells are really good at two things in natural evolution 17:10 < kanzure> (1) genetic recombination (sex) 17:10 < kanzure> (2) mutation 17:10 < kanzure> in selection experiments, cells use both of those to come up with solutions 17:10 < kanzure> and then write them on DNA 17:11 < kanzure> these 'solutions' are quite fuzzy 17:11 < kanzure> and rely on molecular physics among other things 17:11 < fenn> your solution is modifying the DNA 17:11 < kanzure> but ultimately they are, in fact, computing 17:11 < kanzure> nope 17:11 < kanzure> hold on 17:11 < fenn> and by sheer chance the modifications end up with a solution 17:11 < kanzure> sort of, yes 17:11 < kanzure> they are in fact computing, so if we can then find out what they are doing that lets them survive the selection experiment 17:11 < fenn> it doesnt happen the other way around (as much as i would like to believe) 17:11 < kanzure> yeah :( 17:12 < kanzure> "as much as I would like to believe" 17:12 < kanzure> that's the understatement of the century 17:12 < fenn> i'm a rupert-sheldrake sympathizer 17:12 < kanzure> how so? 17:12 < kanzure> sheldrake the morphogenetic field theorist? 17:12 < fenn> i think spirits affect random chance and that's where life came from 17:12 < kanzure> I have trouble believing in randomness 17:13 < kanzure> but I do understand that you don't have all of the information 17:13 < fenn> meh 17:13 < kanzure> how can randomness ever exist, anyway? 17:13 < kanzure> for something to be truly random, 17:13 < kanzure> in my program it would have to return 'COW' or 'thing that looks like a cow, but is really an alien from 23 dimensions over' 17:13 < kanzure> but instead it just predictably spits out a number 17:13 < fenn> i didnt mean to go off on this tangent 17:13 < kanzure> sure 17:13 < kanzure> anyway, 17:14 < kanzure> the idea is to convert their programs over into a form that we can understand 17:14 < fenn> 'how does this cell work' 17:14 < kanzure> by leveraging the past 60 years of bio research to convert their 'physical language' into our abstract languages, and then we get to play around with the new components we get and see what we can do with them 17:14 < kanzure> yeah, I guess that's a good way to put it 17:14 < kanzure> but you don't have to know everything about the cell 17:14 < kanzure> there are ways to constrain selection experiments I think 17:15 < kanzure> and Andy succeeded in coming up with automatic ways of evolving nucleic acids without cells via aptamers 17:15 < kanzure> and other various biomolecules, I think 17:15 < kanzure> http://en.wikipedia.org/wiki/Aptamers (be careful, this is also somewhat of a tangent) 17:17 < kanzure> there's a limit to evolvable software, but on the other hand, it should be possible to come up with lots of interesting programs on the size of genomes ... some bacteria have genomes that are 5 to 500 times larger than the human genome, so imagine how many programs can be written and how many mutations can occur 17:20 < fenn> you dont even need a physical biological substrate to do this.. say you have a genetic algorithm, then you model it with formal models in order to abstract/extract the 'how' 17:21 < kanzure> true, 17:21 < kanzure> this is why selection experiments (whether simulated or physical) are hard to design 17:21 < kanzure> a few days ago I made the comparison of that to making ... 'shrines' for gods 17:21 < fenn> generally it just finds flaws in your selection function though 17:21 < kanzure> because that's basically the same thing 17:21 < kanzure> people were making shrines and when they did this they got new, novel mutated ideas 17:22 < kanzure> and so they thought something good must be going on 17:22 < kanzure> so they continued to make them 17:22 < kanzure> these 'shrines' are the selection experiments, but obviously in today's world we have gotten much more complex with our selections that we are making 17:22 < kanzure> haha, yes, flaws 17:22 < kanzure> suggesting your problem might suck 17:22 < fenn> why did making shrines give them novel ideas? because they're big and hard to build? 17:23 < kanzure> generally, I'd refer to the process of everything about it - what it takes to make it happen, what it's like to be in the shrine or around the shrine or whatever 17:23 < kanzure> http://en.wikipedia.org/wiki/Koans 17:23 < kanzure> it's like 'preparing to receive an insight' -- just like Feynman prepared by reading as much as he could for QED 17:23 < kanzure> as much as we'd like to do insight engineering, of course ... 17:23 < fenn> i think you might be working your brain too hard :) 17:24 < kanzure> the problem with that is that it still involves 'engineering' 17:24 < kanzure> nah, I'm pretty sure I am solid 17:24 < kanzure> that's why I have autoscholar, to prepare for insights or whatever 17:24 < kanzure> http://heybryan.org/thinking.html re: thinking/insights/incubation-theory 17:24 < kanzure> http://heybryan.org/projects/autoscholar/ - to facilitate the consumption of raw information in preparation for insights or whatever 17:25 < kanzure> http://heybryan.org/increasing_repetitive_behaviors.html for more autoscholar-like stuff, except more mental and oriented towards mental modification 17:25 < kanzure> there's a theme for a reason ;) 17:26 < fenn> why does building a shrine cause novel ideas? 17:28 < kanzure> it's permutation through possibility space, it's not the fact that the shrine 'receives godly communications' - nothing like that - but rather the opportunistic-assimilation hypothesis of incubation theory 17:29 < kanzure> Google has good results for 'opportunistic-assimilation hypothesis' 17:29 < kanzure> http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/Seabrook%20&%20Dienes%2003.pdf Incubation in Problem Solving as a Context Effect 17:30 < kanzure> (but find the occurence of the phrase within that article, you can jump to it without losing much context) 17:30 < fenn> i think you'd have a hard time convincing a molecular biologist that this is how mutations work 17:30 < kanzure> huh? 17:30 < kanzure> I am not saying this is the physics of mutations 17:31 < fenn> ok 17:31 < kanzure> shrine-making (selection-experiment making) does not make the mutations directly, but the cells are the ones that come up with the mutations 17:31 < kanzure> because however they do it, the ones that mutate or get the right recombined DNA, are the ones that survive the selection 17:31 < fenn> where is the selection in shrine-making? 17:33 < kanzure> your brain; there's another theory in incubation theory (or perhaps it's the same one) where you keep on working on the problem and literally forget how you were approaching it, so that when you come across the problem again, you get the insight to the solution, so when you make a shrine you're exhausting the contexts 17:33 < kanzure> (end of line is "so when you make a shrine you're exhausting the contexts") 17:34 < kanzure> your brain is a massive billion-something network, 'mutation' in firing patterns can easily occur (it's not solid state, after all) 17:34 < kanzure> mutation in DNA is another topic, but I think you have studied that one sufficiently (if you were going to have me complete my analogy I made above to the shrine-making and selection-experiment thing) 17:35 < kanzure> neurons are reinforced when they do something 'good' (when they contribute to a solution, i.e. various feedback mechanisms), same with bacteria (when they survive the selection) 17:35 < kanzure> anyway, I'm not trying to be pseudoscientific 17:36 < kanzure> but maybe I sound that way since I was approaching this as a bit of a tangent to the 'software from biology' idea 17:36 < fenn> i'm fine with pseudoscience as long as it's productive 17:36 < fenn> but this doesn't sound productive (maybe i'm wrong) 17:37 < fenn> tesla, fuller 17:37 < fenn> ^^pseudoscience 17:37 < kanzure> haha 17:37 < fenn> it's true 17:37 < kanzure> I think you are wrong, actually. This is the same exact problem space as skdb. 17:37 < kanzure> the problem of 'engineering knowledge' 17:37 < kanzure> you can't just derive it from first principles 17:37 < kanzure> it has to be 'evolved' 17:38 < kanzure> whether by society and trial-and-error by humans (the lab minions) (yikes) or by bacteria 17:38 < kanzure> and then we collect it and aggregate it into skdb 17:38 < fenn> i think with a good enough simulator you could build up skdb from scratch 17:38 < fenn> might take a while 17:38 < fenn> brute force vs analytical thinking 17:39 < kanzure> it's neither 17:39 < kanzure> first, I want to address your simulation hypothesis 17:39 < kanzure> you'd have to be able to simulate the world, basically 17:39 < kanzure> which means a lot of physics and a lot of computational power 17:39 < fenn> yes 17:39 < kanzure> alright, so 17:39 < kanzure> do you know Godel? 17:39 < fenn> uh huh 17:40 < kanzure> uhh, I just got interrupted, one moment 17:40 < kanzure> you can't simulate the physics of the overall system without something bigger 17:40 < kanzure> or you might as well just run the planet 17:40 < kanzure> i.e., like we are now 17:40 < kanzure> and the abstract programs that we do collect anyway, they are generalized in the first place (hurray) 17:40 < kanzure> so do we really need a simulation? 17:40 < kanzure> brb 17:41 < fenn> there is a middle ground - heuristics 17:41 < kanzure> from where? ;) 17:41 < fenn> and automated heuristic creation, like from bayesian analysis 17:41 < kanzure> hm 17:41 < fenn> it's not abstract, but it's not totally blind either 17:41 < kanzure> please explain 17:41 < fenn> say you run 100 simulations 17:42 < fenn> in all 12 of the simulations with carrots, you ended up with more rabbits at the end 17:42 < fenn> heuristic: carrot -> rabbits increase 17:43 < fenn> uh, ok i suck at explaining bayesian reasoning 17:43 < kanzure> Jef tells me I need to learn more Bayes 17:43 < kanzure> and I agree with him 17:43 < kanzure> I don't see the possibilities 17:44 < fenn> you can do experiments in the simulation too 17:44 < fenn> to test hypotheses 17:44 < fenn> like, add more carrots and see if you get more rabbits 17:44 < fenn> if you get more rabbits it will strengthen your faith in that hypothesis 17:44 < fenn> confidence i guess is a technical term in statistics 17:45 < fenn> if the simulated world is totally chaotic and acausal, you'll end up with a spread of hypotheses with near zero confidence 17:46 < kanzure> heh, my dad came in to read me a passage from 1901 - "It is in my complete and utter professional opinion, that because the power requirements scale cubically, and the wingspan requirements doubly, that aerial flight will thus remain impossible for the remainder of time. Stop bugging me." Later that year ... 17:47 < kanzure> hm 17:47 < kanzure> well, I don't really see what bayesian analysis can do to help 17:47 < fenn> i wonder why they dismissed flight so easily when there were already kites 17:47 < kanzure> my method involves automated hypothesis generation, does yours? 17:47 < fenn> yes 17:49 < kanzure> if I was going to come up with an integrative framework where I have my automated machinery setting up new selection experiments, sequencing the DNA and translating it into abstract logic 17:49 < kanzure> then you'd plug in bayesian analysis systems straight into the big pot o' algebra? 17:49 < kanzure> not algebra, sorry 17:49 < kanzure> big pot o' acquired programs 17:50 < fenn> you have to be able to modify something in order to test the hypothesis 17:50 < kanzure> how much computing hardware would be required 17:51 < fenn> ugh i dont know 17:52 < fenn> or i suppose if there's too much data to sift through you could use the search keys for your test 17:53 < kanzure> how so? 17:53 < fenn> predict levels of foo increase when bar is present; search for experiments with bar, see if foo increases vs control experiments without bar 17:54 < fenn> this is the topic of many a research paper 17:54 < fenn> but done by grad students, not a program 17:55 < kanzure> hrm 17:56 < fenn> this is all a lot easier when you say it in english of course 17:56 < kanzure> "In vitro modeling of in vivo systems" <-- this seems to be a good heading for what I have been talking to you about 17:57 < fenn> in vitro just means in a test tube, not in a cell 17:59 < fenn> knowledge representation seems to have been a big theme 18:00 < kanzure> yes 18:00 < kanzure> it is in a test tube though 18:00 < kanzure> that's the idea 18:00 < kanzure> we take in vivo circuits from cells, and then figure out new ways to run the same circuits, codify them into transcriptional logic, and run them in vitro 18:02 < fenn> i dont think that would work, since 99% of the GRN's out there are relating to keeping the cell functioning 18:03 < kanzure> haha 18:03 < kanzure> think about it, how are they doing it? 18:03 < kanzure> they are computing with biomolecules too 18:03 < kanzure> they are making decisions, but not only that 18:03 < kanzure> but the structure of the 'general network' that represents what they are doing to stay alive 18:03 < fenn> not decisions, feedback 18:03 < kanzure> is of a certain class, a certian computation 18:03 < kanzure> yes, feedback is computational 18:03 < fenn> decisions implies modeling 18:04 < kanzure> my point is that there's information routes in the cell, they are information processing entities 18:04 < kanzure> and sometimes feedback is used, yes, and these various networks for feedback or whatever, can be translated into code for our reading 18:04 < kanzure> not DNA code, but logic code stuff 18:04 < kanzure> fuzzy as it may be 18:05 < fenn> i think circuits or control system diagrams are more appropriate than code 18:05 < kanzure> circuits 18:05 < kanzure> huh 18:05 < kanzure> VHDL? 18:05 < kanzure> oh, right, VHDL -> circuits 18:05 < fenn> no, vhdl is not really circuits 18:05 < kanzure> VHDL can be converted into circuits 18:06 < kanzure> this is 'network decomposition' (circuits -> VHDL or some other language) 18:06 < fenn> yes, but the idea of vhdl is to make modular functional units 18:06 < fenn> whereas a circuit could be a big mess of interconnections 18:06 < kanzure> and is exactly related to Hamiltonian path finding, i.e. breaking down graphs into their cycles 18:06 < kanzure> I don't see how that's a problem. 18:06 < kanzure> but I understand what you mean 18:07 < fenn> vhdl coding for a messy circuit would be harder to understand than just a messy circuit diagram 18:07 < kanzure> there are some simple circuits in biology though 18:07 < kanzure> for example, the ring oscillator 18:07 < kanzure> which is basically A -> B -> C -> A 18:07 < fenn> biology tends to be messy (there are examples of modular systems too) 18:08 < kanzure> remember the paper I linked you to? there are ways to find the 'finite points' 18:08 < kanzure> or what did the paper call them? 18:08 < kanzure> fixed points 18:08 < fenn> what's a fixed point? 18:09 < kanzure> in a dynamical system, a fixed point is supposedly something that you can use to 'unravel' the dynamical system 18:10 * fenn pictures a force-directed graph layout algorithm 18:10 < fenn> sproing 18:10 < kanzure> sproing? 18:10 < fenn> its like the VSEPR model 18:10 < fenn> but with graph nodes rather than electron orbitals 18:10 < kanzure> oh, a way to minimize energy density or something 18:11 < fenn> yeah 18:11 < fenn> minimum energy diagram layout 18:14 < fenn> remember this? http://en.wikibooks.org/wiki/Circuit_Idea/Why_Circuit_Ideas_are_Hidden 18:15 < kanzure> yep 18:15 < kanzure> social knowledge, gathered from mutation/insight 18:15 < fenn> specifically, you're trying to un-hide the ideas hidden in bacterial mutations 18:16 < kanzure> yes 18:17 < fenn> a knowledge synthesizer! 18:17 < kanzure> hehe 18:17 < kanzure> accelerated, automated evolutionary engineering 18:18 < fenn> well just be glad you arent some poor sod computer programmer being given this non-specifcation 18:19 < kanzure> well, not quite a knowledge-synthesizer actually - it could gather knowledge and make up proofs and theorems involving new 'programs' that it unhides, but it's like skdb, you have to randomly try 18:19 < kanzure> out new variations in some cases, while restricting your domain (the same stuff we're doing with the computational chem programs for the replicator) 18:19 < kanzure> nah, the specification is going to be pretty easy 18:19 < kanzure> since the mathematics mentioned in that paper has a good, strong history of understanding 18:19 < kanzure> and should have some computer programs out there on the net already 18:19 < kanzure> probably open source 18:19 < kanzure> and then the bioinformatics machinery, well, that's fairly easy I think, what could they be doing in the labs to gather genetic information? And Andy has the automated aptamer stuff :) 18:20 < kanzure> automated selection experiments, I mean. 18:22 < kanzure> to answer Ellington's challenge I can just go into the databases and find some ODEs that model a particular GRN, something other than an oscillator, and just do it by hand myself 18:22 < kanzure> and then if he approves of that, I'll suggest we just automate the whole thing while we're at it 18:23 < fenn> 'do it by hand' meaning what exactly? 18:23 < fenn> put together some bio-bricks? 18:23 < kanzure> nah, he doesn't work with biobricks, thinks they're bullshit 18:23 < kanzure> I mean the transcriptional switches/logic 18:23 < fenn> well, whatever you want to call it 18:23 < kanzure> he wants an in vitro synthetic circuit 18:23 * fenn thinks they're the same thing 18:23 < kanzure> nah, they're different, but the concept of modularizing things is same across the domain 18:24 < fenn> ok, splice some genes together that behave similarly to the target circuit 18:24 < kanzure> heh, and you mentioned protein folding earlier 18:24 < kanzure> so this is where you'd need protein folding 18:24 < kanzure> unless you want to just copy the genes 18:25 < kanzure> otherwise you have to do a massive computational search for similar proteins 18:25 < kanzure> the idea was to model the basis of the circuit, the 'computational' aspects 18:25 < kanzure> anything else can be considered waste for now 18:25 < fenn> you could do a massive in-vitro search for similar proteins (artificial proteins) 18:25 < kanzure> you'd have to synthesize tons of oligonucleotides and then do transcription to 18:25 < kanzure> yeah, sure 18:25 < kanzure> that would work 18:26 < kanzure> but you'd have to separate them I think, right? 18:26 < fenn> you know about monoclonal antibodies? 18:26 < kanzure> similarities could be found via DNA hybridization and conformational stuff 18:26 < kanzure> no 18:26 < fenn> each b-cell produces a unique random-shuffled protein 18:26 < kanzure> but you'd have to make sure the proteins do not interact with each other, i.e. the set of proteins that you are testing to be similiar to the target protein 18:27 < kanzure> I think I had this same problem in another situation that I was thinking about a few months ago 18:27 < kanzure> I remember it. 18:27 < kanzure> it was the 2^(4^(N)) experimentation 18:27 < fenn> you can find the cell that makes, say, lactose-binding protein, and figure out the amino acid sequence 18:27 < kanzure> with searching for transcriptional switches and the toeholds and matches 18:28 < fenn> but you can find 50 or a zillion other different lactose binding antibody proteins 18:28 < kanzure> hm 18:28 < fenn> and isolate the cells for each of those 18:28 < kanzure> but think of it this way 18:28 < kanzure> say you have 50 million different proteins that you are matching to aptamers 18:28 < kanzure> to check if they will be anything like the one that you are targetting 18:28 < kanzure> the subset of 50 million that do not interact with each other 18:28 < kanzure> is not necessarily the subset with the best match that you want ;) 18:29 < kanzure> because everything else doesn't bind to the aptamers 18:29 < kanzure> I mean, anything that binds to each other doesn't bind to the aptamers (too large, energies, ...) 18:29 < kanzure> and you wash away the solution above the aptamers 18:29 < kanzure> and then unbind the aptamer-protein complex, and then figure out what proteins you have left, which would be your solutions that are similar to the targets 18:29 < kanzure> (I believe this has some relation to 'library testing', but I haven't explored that much, is this what the libraries are for? oligo sequences?) 18:30 < fenn> you could use 50million^2 test tubes, for every combination 18:30 < kanzure> ... 18:30 < fenn> inkjet printers! 18:30 < kanzure> to make test tubes? heh' 18:30 < fenn> yeah just drops of water on a hydrophobic surface 18:30 < fenn> with a spot of hydrophilic substrate to keep the dot still 18:30 < kanzure> not bad 18:31 < kanzure> but, what about the synthesis of the protein? 18:31 < fenn> i forget what we're trying to do 18:32 < kanzure> finding proteins that match a target circuit 18:32 < kanzure> because I need to make an in vitro synthetic circuit that matches a target circuit found in the literature (of natural organisms) 18:32 < fenn> finding proteins that bind to the same sites as other proteins 18:32 < kanzure> same sites of what? 18:32 < kanzure> I thought you were talking about a protein cascading chemical reaction network 18:32 < kanzure> isntead of a GRN 18:33 < fenn> well, it could bind to some arbitrary chemical 18:33 < kanzure> meh, I like my DNA compiler better 18:33 < fenn> there's also enzymatic action 18:34 < kanzure> yes, but I think he wants me to work with transcriptional circuits 18:34 < kanzure> which are much easier to work with in vitro 18:34 < fenn> i dont think you're going to brute-force an enzyme 18:34 < kanzure> since you can ignore transcription 18:34 < kanzure> he's done it 18:34 < kanzure> riboenzymes 18:34 < kanzure> but I don't think it's necessary here 18:34 < kanzure> we could if we wanted, but meh 18:34 < kanzure> anyway, pizza is here 18:34 < fenn> still seems unlikely 18:34 < kanzure> so I'm going to go eat 18:34 < kanzure> http://en.wikipedia.org/wiki/Ribozyme I think 18:35 < fenn> i know all about them 18:35 < kanzure> oh 18:35 < kanzure> http://en.wikipedia.org/wiki/Riboswitch 18:35 < kanzure> In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity [1][2][3]. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, depending on the presence or absence of its target molecule. 18:35 < fenn> cool 18:36 < fenn> ok so forget protein 18:43 < fenn> this is cool http://en.wikipedia.org/wiki/Spiegelman_Monster 18:44 < fenn> oh i misunderstood it. i thought the RNA sequence was also a polymerase ribozyme 18:59 < fenn> can you recommend some light reading on P/NP hard complete etc 19:00 < fenn> wikipedia provides zero examples for me to grab onto 19:04 < kanzure> no, I can't 19:04 < kanzure> I suffer from the same problem 19:04 < kanzure> however, David might be able to come in here and explain 19:04 < kanzure> or maybe Ryan Patterson 19:05 < fenn> basically it sounds like a bunch of bullshit and i'm wondering why people spend time worrying about it 19:05 < kanzure> it's for figuring out which problems can and cannot be solved 19:06 < fenn> what is "non-polynomial time"? 19:06 < fenn> i can understand polynomial time 19:07 < fenn> is it just.. everything else? 19:07 < fenn> seems like a totally useless way of describing something 19:08 < kanzure> okay, David should be appearing 19:08 < fenn> uh oh 19:08 < kanzure> why's that bad? 19:08 < fenn> i'm so not even awaky still 19:09 < kanzure> "access to channel #hplusroadmap is blocked"? 19:09 < fenn> aroo? 19:10 < kanzure> why is he on a web client 19:11 < fenn> well i think i'm going to bed soon (now) 19:11 < kanzure> uhh 19:11 < kanzure> please don't 19:11 < kanzure> he's going to appear :( 19:11 < fenn> ok ok 19:11 < kanzure> kind of like a guest lecturer :) 19:11 < fenn> i will be the guy asleep in the first row 19:12 < fenn> dont worry i'll crib the notes from someone after class 19:14 -!- davidad_ [n=me@DAVIDAD.MIT.EDU] has joined #hplusroadmap 19:14 < davidad_> kanzure: victory 19:14 < kanzure> Victory! Ha-ha! 19:14 < davidad_> the solution is to ssh to my linux box 19:14 * fenn waves the anarcho-penguin flag 19:14 < kanzure> where'd you get davidad.mit.edu ? 19:15 < davidad_> um, from MIT? 19:15 < kanzure> impressive 19:15 < kanzure> you just asked? 19:15 < davidad_> they give out three free hostnames to every student 19:15 < kanzure> so, let me explain what's been up today in #hplusroadmap 19:15 < davidad_> ok 19:16 < fenn> we talked past each other four about 3 hours 19:16 < kanzure> I've been working on some Andy Ellington stuff for biology, figuring out what software would be interesting to implement with biomolecules as the substrate 19:16 < kanzure> and somehow we got to talking about N=NP and computational complexity classes 19:16 < davidad_> that's P=NP >_> 19:16 < kanzure> djlkafjlkadjfladkjf;a 19:16 < kanzure> P=NP 19:16 < kanzure> in the context of biological computation (not computation about biology, but on biology) 19:16 < kanzure> but in general as well 19:16 < davidad_> ah 19:17 < kanzure> fenn, I think, claims that P=NP isn't much of a question/problem 19:17 < davidad_> yeah, some people think DNA computing, like quantum, does NP 19:17 < davidad_> some people think neither can 19:17 < fenn> i dont know what NP is 19:17 < davidad_> and some people think P=NP 19:17 < davidad_> basically 19:17 < davidad_> P is all the problems you can solve in polynomial time, 19:17 < davidad_> and NP is all the problems you can verify in polynomial time 19:17 < kanzure> where polynomial is the degree of the equations? 19:17 < kanzure> degree meaning exponents 19:18 < davidad_> polynomial is the big-O bound on time with respect to problem size 19:18 < davidad_> so, time = O(n^k) 19:18 < davidad_> exponential is where time = O(k^n) 19:18 < davidad_> assuming that n is the problem size 19:18 < davidad_> and k is a constant 19:18 < fenn> exponential is a subset of NP? 19:18 < davidad_> not always 19:19 < fenn> ok, just another thing to worry about 19:19 < davidad_> NP is a subset of exponential, though 19:20 < fenn> uh, no? 19:20 < kanzure> I've always referred to these computational complexity classes to the 'computational feasability' of whatever problem I am focusing on at the moment 19:20 < davidad_> any problem that you can verify in polynomial time, you can solve in exponential time 19:20 < davidad_> by just trying everything and seeing if it works 19:20 < kanzure> see, we were doing one of those methods today 19:20 < kanzure> we were suggesting a case where we deploy about 50 million different proteins 19:20 < kanzure> to test for similarities to a target protein from nature 19:21 < kanzure> which is the exponential time 19:21 < kanzure> verification would be setting up an experiment the same way as we observed the properties of the target protein the first place, I presume 19:22 < davidad_> yep 19:22 < kanzure> insert some anomalous relation to finding the longest path and Hamiltonian cycles 19:22 < kanzure> *cycles here 19:22 < davidad_> so in this case, your verification is constant-time 19:22 < davidad_> no matter how long the protein might be, 19:22 < davidad_> you can do an experiment to verify the properties in the same period of time 19:24 < kanzure> Woh, oh-oh-oh 19:24 < kanzure> Find the Longest Path 19:24 < kanzure> Woh oh-oh 19:24 < kanzure> Find the Longest Path 19:24 < kanzure> If you said P is NP tonight 19:24 < kanzure> There would still be papers left to write 19:24 < kanzure> I have a weakness 19:24 < kanzure> I'm addicted to completeness 19:24 < kanzure> And I keep searching for the longest Path 19:24 < kanzure> The algorithm I would like to see 19:24 < kanzure> Is of Polynoimal Degree 19:24 < kanzure> Buts its elusive, 19:24 < kanzure> Nobody has found conclusive 19:24 < kanzure> Evidence that we can find the Longest Path 19:24 < kanzure> I have been hard 19:24 < kanzure> Working for so long 19:24 < kanzure> I swear its right, 19:24 < kanzure> But he marks it wrong 19:24 < kanzure> Somehow I'll feel sorry when its done 19:24 < kanzure> GPA 2.1, 19:24 < kanzure> Is more than I hoped for 19:24 < kanzure> Garey, Johnson, Karp and other Men (and Women) 19:24 < kanzure> Try to make it Order n log n. 19:24 < kanzure> Am I a math fool 19:24 < kanzure> If I spend my life in Grad School 19:24 < kanzure> Forever following the Longest Path. 19:24 < kanzure> Woh oh-oh-oh 19:24 < kanzure> Find the longest path 19:24 < kanzure> Woh oh-oh-oh 19:24 < kanzure> Find the longest path 19:24 < kanzure> (Dan Barrett) 19:24 < davidad_> ..ok 19:25 < kanzure> Anyway, 19:25 < fenn> words! yeah 19:26 < kanzure> there was something else 19:26 < fenn> are you sure NP is a subset of exponential? what if there is an infinite number of combinations? 19:27 < davidad_> well, complexity classes are defined for decision problems 19:27 < davidad_> where the output is only YES or NO 19:27 < fenn> well, say you want to pick two real numbers 19:27 < davidad_> you can't 19:27 < davidad_> you can never finish outputting a real number 19:28 < davidad_> the best you can do is output an algorithm that represents a real number, 19:28 < davidad_> and algorithms are countable 19:28 < fenn> you can verify 2.1000... + 3.900... = 6 19:29 < fenn> but what are the real numbers adding up to 6 that fenn likes? 19:29 < davidad_> hahah 19:29 < fenn> you cant try all of them 19:29 < davidad_> you can't verify them in polynomial time, either 19:29 < fenn> do i at least have a grasp of what it's all about? 19:29 < davidad_> I think so 19:29 < davidad_> the formal definition of an NP problem 19:30 < davidad_> is a decision problem that is solvable in polynomial time on a non-deterministic turing machine 19:30 < davidad_> which means it can "split" and do computations in parallel 19:30 < davidad_> but it can't split infinitely many times, because that would take longer than polynomial time 19:31 < davidad_> if, however, there's a reasonable number of possibilities, it can split and check all of them and be done in polynomial time 19:31 < kanzure> hm 19:31 < kanzure> splitting is interesting 19:31 < fenn> oh fuck N is non-deterministic? now i really want to kill some comp-scientists 19:31 < kanzure> considering we do self-replication here 19:32 < davidad_> yeah, the N is non-deterministic 19:32 < davidad_> lucky you can't kill people over IRC 19:32 < davidad_> (for me) 19:32 < davidad_> another way of thinking about splitting 19:32 < davidad_> is that the machine is the luckiest possible guesser 19:33 < davidad_> at any time, it can guess a number and be guaranteed to guess the right one if there is a right one 19:33 < fenn> like a quantum computer 19:35 < kanzure> huh? 19:35 < kanzure> quantum, why? 19:35 < fenn> because it exists in all possible states 19:35 < fenn> it runs through all possible program paths, if you will 19:36 < kanzure> oh, right, I remember some hype a few months ago about quantum programs and their 'fantastic possibilities' 19:36 < kanzure> but I also remember Slashdotters fairly correctly refuting those ideas for quantum Traveling Salesman. 19:40 < fenn> hmm why's that? 19:40 < fenn> because the weights are real numbers and not quantized? 19:41 < kanzure> http://science.slashdot.org/article.pl?sid=07/08/09/1535231 19:42 < kanzure> http://science.slashdot.org/comments.pl?sid=265375&cid=20172049 in particular 19:42 < kanzure> ah, that's Engel 19:42 < kanzure> I think he's on freenode somewhere 19:43 < kanzure> http://science.slashdot.org/comments.pl?sid=265375&cid=20172269 19:43 < kanzure> haha - feasability calculations - http://science.slashdot.org/comments.pl?sid=265375&cid=20172747 19:45 < kanzure> this one is good - http://science.slashdot.org/comments.pl?sid=265375&cid=20172137 19:49 < fenn> sometimes in these computer science discussions the concept of 'good enough' gets lost entirely 19:51 < fenn> i.e. would take the salesman less time traveling than it would take to optimize his route 19:51 < kanzure> no 19:51 < kanzure> the idea is that there may be a solution algorithm 19:51 < kanzure> that will tell you the shortest path instantly 19:51 < kanzure> 'instantly', i.e. within one step 19:51 < fenn> ya 19:51 < kanzure> and then that's it -- you just use that as long as you want :) 19:51 < fenn> its just huge for high levels of complexity 19:52 < fenn> but with the optical experiment, you'd get some halfway decent answers early on 19:52 < kanzure> maybe 19:52 < fenn> statistically speaking, 'probably' 19:52 < kanzure> the optical solution is something like 1E167 years to come up with enough photons or something 19:52 < kanzure> per that last slashdot link I gave up there ^ 19:53 < fenn> that's to go through all possible permutations 19:53 < fenn> its not like you're going to put 1e200 photons in a box 19:54 < fenn> and then the answer pops out 19:54 < fenn> anyway it's not a quantum computer 19:56 < kanzure> I'd like to see somebody try to do 1E200 photons in a box 19:58 < fenn> the box would explode :) 19:59 < fenn> i wouldnt like to see it, my local parsec would be converted to plasma 20:01 < kanzure> in ##neuroscience I just linked a person over to http://www.dbc.uci.edu/neurobio/Faculty/Lynch/lynch.htm after her expression of interest in the (bullshit) "holographic brain theory" (Pietsch stuff) 20:01 < kanzure> ooh 20:01 < kanzure> I also picked up some books today 20:02 < kanzure> Microbiology, 5th ed., Prescott, Harley, Kim 20:02 < kanzure> The Cartoon Guide to Genetics, Larry Gonick & Mark Wheelis 20:02 < kanzure> Making PCR: A Story of Biotech, Paul Rabinow 20:02 < kanzure> The Most Beautiful Molecule: The Discovery of the Buckyball, Hugh Aldersey-Williams 20:03 < fenn> i think you could do the 100 city hamiltonian cycle with a reasonably small number of q-bits (not that i know what i'm talking about) 20:03 < kanzure> practicality? 20:03 < kanzure> do you remember D-Wave? 20:03 < fenn> no 20:03 < kanzure> they are the quantum computing guys 20:03 < kanzure> they were making their rounds a few months ago 20:03 < kanzure> getting about $40 million in funding overall 20:03 < kanzure> they do supercold quantum computing and things seem to be looking strong for them 20:04 < kanzure> they claim they'll be doing 256 qbits sometime this year 20:04 < kanzure> and maybe 1024 qbits by the end of the year 20:04 < fenn> that's impressive 20:04 < kanzure> I was talking with the CEO a few months ago 20:04 < fenn> all entangled? 20:04 < kanzure> only to learn the next day that my dad has some money invested in them O.o 20:04 < kanzure> I would've invited him to the chat if I had known that 20:05 < kanzure> anyway, in terms of practicality 20:05 < kanzure> I think that carbon might offer some interesting solutions 20:05 < kanzure> for quantum computing 20:05 < kanzure> since we can get quantum tunneling and the field effect on graphene 20:05 < kanzure> plus semiconductor effects in buckyballs/CNTs 20:05 < fenn> er... no 20:05 < kanzure> no? 20:05 < fenn> quantum tunneling is just one electron hopping over an energy barrier 20:06 < kanzure> right 20:06 < fenn> quantum entanglement is that one electron spread in 50 places at once 20:06 < fenn> or two, if you're a physicist 20:07 < kanzure> sure, but I'm just saying that graphene allows us to investigate quantum effects 20:07 < kanzure> and it allows us easy access and manipulation 20:07 < fenn> ok, but so do copper wires 20:07 < kanzure> so it seems like an interesting platform to paly with 20:07 < kanzure> *play with 20:07 < kanzure> really? 20:07 < fenn> ya 20:08 < kanzure> so can it do entanglement? 20:09 < fenn> there's too much noise in room temperature systems 20:12 < fenn> scroll down to 'So how big is an electron?' http://laputan.blogspot.com/2003_09_21_laputan_archive.html 20:13 < kanzure> heh, I am glad that he does not agree with Copenhagen 20:13 < kanzure> I like the Feynman/von Neumann interpretations 20:13 < fenn> i can never keep all those dead guys straight 20:14 < kanzure> Feynman isn't dead. Not yet, anyway. 20:15 < fenn> copenhagen = the electron could be anywhere but it is definitely somewhere, we just dont know? 20:16 < kanzure> no 20:16 < kanzure> Copenhagen is stuff like "view it and you kill babies in another universe" 20:16 < kanzure> MWI shit 20:16 < kanzure> haha, Mead studied under Feynman 20:16 < kanzure> good 20:17 < fenn> heh "Shut up and calculate!" 20:23 < kanzure> "the electron is its own medium" 20:23 < kanzure> hm 20:41 < fenn> many worlds is its own interpretation.. copenhagen is observer-centric 20:44 < kanzure> ah, that's right 20:44 < kanzure> statistics and so on 20:44 < epitron> omg observing particles kills babies?! 20:44 < kanzure> I still need to finish reading that link, but it's good stuff 20:44 < epitron> how do i stop! 20:44 < kanzure> epitron: haha :) 20:44 < fenn> epitron: cats, not babies 20:44 < epitron> fenn: IT SAYS BABIES 20:44 < kanzure> how do you know it was a cat? 20:44 < kanzure> it's only a cat if you observe it to be a cat 20:45 < kanzure> until then it has a 50/50 chance of being a baby 20:45 < fenn> kanzure: schrodinger said it was a cat 20:45 < epitron> schrodinger has cat-hater bias 20:45 < kanzure> schrodinger didn't know what life was ;) 20:45 < epitron> you cannot trust anything schrodinger did 20:45 < kanzure> and there's a broadcast premiere of Star Wars on at the moment 20:45 < kanzure> so please excuse me, I have an addiction to work on 20:46 < epitron> haha 20:46 < fenn> me too (sleep) 20:46 < epitron> hey kanzure 20:46 < kanzure> yes? 20:46 < epitron> did you ever see the fanedit of Espiode IV? 20:46 < kanzure> No? 20:46 < epitron> you ever seen fan edits? 20:46 < kanzure> nope 20:46 < epitron> lemme find ya some 20:46 < kanzure> whole movies? 20:46 < epitron> yeah 20:46 < kanzure> delicious 20:47 < epitron> http://fanedit.org/wpTF/?p=29 20:47 < epitron> Star Trek - Kirkless Generations 20:47 < epitron> http://fanedit.org/wpTF/?p=495 20:47 < epitron> STAR WARS: EP IV 2004 Special edition REVISITED 20:47 < epitron> http://fanedit.org/wpTF/?p=485 20:47 < epitron> THE MATRIX EVOLUTIONS 20:47 < epitron> http://fanedit.org/wpTF/?p=521 20:47 < epitron> Army of Darkness - Primitive Screwhead Edition 20:47 < epitron> :D 20:47 < epitron> (and of course, the classic jar-jar-less Episode I) 20:48 < epitron> i'm downloading the first 3.. i've seen the 4th 21:56 < kanzure> Jar-jar-less? Awesome. 23:01 -!- Aulere [n=dragon_d@131.229.176.252] has joined #hplusroadmap 23:02 < kanzure> Welcome, dragon. 23:59 < epitron> http://funtarded.com/pics/show/2641