##hplusroadmap

<@kanzure> it's not constantly replicating (is it?)
fennhmm18:23
fennmaybe18:23
fennif it has no other leaf nodes, yes18:23
@kanzureit has to wait for resource accumulation, you realize18:24
@kanzureso it can't constantly be replicating, it will hit run-time errors18:24
fennyes, that's part of replication18:24
@kanzureokay18:24
fennit won't assemble the new unit until the parts are built18:25
@kanzureso,18:25
@kanzure(1) can skdb and autogenix do the package/functionality requirements we need to be able to specify?18:26
@kanzureand (2) can we do a small proof of our 'fishing' method for some other design project?18:26
@kanzurealso, it looks like for each package and functionality we add, we have to include everything that it could possibly be used to do 18:26
@kanzureand mention its relationships to all existing functionality18:26
fennfishing the ring out of the swamp?18:27
@kanzureright18:27
fennthere arent any replicators18:27
fennor do you mean just fake it, and prove the algorithm works?18:27
@kanzurethe algorithm for fishing?18:27
fenns/prove/demonstrate/18:27
fennyes18:27
@kanzureyes, I suppose18:27
@kanzurebut with packages and functionality in there18:28
@kanzurewhere *we* know a solution18:28
@kanzurebut we want the computer to find it18:28
fennre:1, skdb/autogenix only exist in our minds right now ;)18:28
@kanzureyes, but I mean to say that we get to do functional specs for skdb/autogenix and make sure the file formats could possibly define all of this information that we need18:28
@kanzureI guess this is going to be ad-hoc really18:29
@kanzuresince there's all sorts of variables we will want to include18:29
fennthe design can change if it's needed18:29
@kanzureperhaps we will make it abstract18:29
fennwe can do .agx version 1, version 2, etc18:29
@kanzurein the sense that we can "include package-required-for-electricity-variables"18:29
@kanzureand then other variables can be further subunits which will each add functionality to the overall project18:29
epitronhttp://kol.coldfront.net/thekolwiki/index.php/Time_sword18:30
fennwhat variables? diesel for your diesel generator?18:31
@kanzurefenn: as well as flow and other information about that fluid18:31
@kanzurethere's tons of information that CRC keeps on such stuff18:31
@kanzurebut we can't know all of these variables from first principles18:31
fenntrue18:31
@kanzureso when we want to include a new variable for a new functionality18:31
@kanzurewe should be able to just add a new 'library' addon thing18:31
@kanzureor extension18:31
@kanzurewhich would include subcomponents that would be called upon during simulation18:32
@kanzureI think this is the 'virtual function' idea in C/C++18:32
@kanzureor template factory18:32
@kanzurenot sure.18:32
fennterminology update: streams are run-time capabilities/requirements, packages are build-time, packages can provide streams18:32
@kanzurepackages still vertices?18:33
fennyes18:33
@kanzurepackages deliver streams to the new unit?18:34
fenni guess i wasnt specific enough18:34
@kanzureno, I think you were18:34
fennstreams are things like materials, energy, information18:34
fenni havent figured out if they're vertices or edges yet18:34
fennthere's going to be a lot of streams that have no package providing them, like sunlight, air18:35
fennthe aluminum smelter relies at run-time on the clay processor to provide bauxite18:36
fennsmelter, processor = packages18:36
fennclay, bauxite = streams18:36
@kanzurestreams sound kind of like vectors18:37
fennthen you can have a factory object that makes packages18:37
fenna package that makes packages18:37
@kanzureincluding itself?18:38
fennlet's not go there :)18:38
@kanzureisn't that what we wanted in the first place?18:38
fennyes of course18:38
fennbut there are lots of intermediate packages that make other packages (i guess)18:39
fennmaybe that's just poor refactoring on society's part18:39
@kanzurethat was my 'criss-crossing' example: where package X requires stream Y during build-time to reproduce package X in the new unit, but in normal operations, package Y would require stream X, or something18:39
@kanzureerm18:40
@kanzurecriss-crossing:18:40
@kanzureNote that the "sand-processing subsystem" need not be made out of sand. The "sand-processing subsystem" needs to be made out of X mineral where there exists in the design "X-processing subsystem" which, again, is not necessarily made out of X, but it has to be made out of something like "X" that eventually makes it full circle back to sand.18:40
fennah a sub-loop18:40
@kanzureso, package X (which processes Y) needs to be made out of stream L where stream L is 18:40
@kanzureI am having trouble variabilizing it, because it's a hard statement to make18:40
fennthe loop is in stream-space, whereas the package tree is very linear and loop-free18:41
fennmaybe draw a diagram18:41
epitronTIME SWORD!18:41
@kanzurethe dependency loops are important, of course18:41
@kanzurelet's see18:41
fennthe subtle knife18:42
@kanzure(($mineralX)-processing-subsystem) can be made out of $mineralY, where there exists in the overall design a (($mineralY)-processing-subsystem), which either must immediately be made out of ($mineralX) or some (($mineralI-don't-care)-processing-subsystem) which eventually is made out of ($mineralX)18:43
@kanzurewhere:18:43
@kanzureyou would probably say the mineralX-processing-subsystem is a package, yes?18:43
@kanzureand then streams would be tapped during build-time by a certain package to manufacture a new package, for the replicated entity to have.18:44
fenni'm not convinced this is a problem we have to worry about18:46
@kanzurehow so?18:47
fenndo you think a loop will kill the dependency resolution code?18:47
@kanzureno?18:47
@kanzureit's not a problem18:48
@kanzurewe're just formalizing what we need18:48
@kanzureright?18:50
fennyah18:54
fennits funny, usually i'm trying to cut apart dependency loops, but for self-replication they're quite useful18:58
@kanzurethe more the better (in terms of design)18:59
@kanzurebut the more the worse, in terms of implementation18:59
fenngrr do they really expect me to pay money for nasa publications?19:09
@kanzurehere's my attempt at defining a package:19:11
@kanzurea package must (1) be made of a certain material, (2) has an input stream that gives it a material to make, (3) this input material is different than the material in #1, and (4) a package must make *some other package* with the input stream material.19:11
fennpackage must make a package?19:12
@kanzureyep19:12
@kanzuremust make *another* package19:13
fennwhat about instruments19:13
@kanzureand that other package might end up making the original package19:13
@kanzurea package might be a fabricator, and that fabricator, by coincidence, can make extra stuff19:13
@kanzurelike an instrument19:13
fenni mean sensors, like an oscilloscope or something19:13
fenna spectrometer19:13
fennwhat does the spectrometer make?19:14
@kanzureright, it makes nothing19:14
@kanzureso these are your leaves19:14
@kanzureleafs19:14
fennit makes information, which is necessary for replication19:14
@kanzureinteresting19:14
fenni feel funny calling data a package19:14
@kanzureinstrument == package?19:15
fennwell sure, it's a collection of components that performs a function19:15
fennand there are control instruments that dont produce 'information' exactly19:16
fennthe computer that's directing operations19:16
@kanzurearrgh19:17
@kanzureI just wrote down "Reverse Method of Making a Fabricator"19:17
@kanzure(1) start with a fabricator19:17
@kanzure'erm, replicator19:17
@kanzure(2) Break it down into its components.19:17
fennwell gee with #1 we're already done :)19:17
@kanzure(3) Make a machine to do the reverse. Done.19:17
@kanzureheh'19:17
@kanzureyeah :(19:17
@kanzureman, relying on biology really helps though19:17
@kanzureit gives you something to start with19:18
@kanzurebecause if you want to be able to create enough for a human to live and grow19:18
@kanzurethen you can just require your materials for self-replication rely on that same stuff19:18
fennhuman is too complex, start with a minimal bacterial cell19:18
@kanzureokay, what's agar made out of?19:18
@kanzureunbranched polysaccharide?19:18
fenninput streams: amino acids, sugar, nucleic acids, lipids, salts19:18
@kanzure`Agar is a heterogeneous mixture of two classes of polysaccharide: agaropectin and agarose`19:19
fennnow we need proteins to import each of those streams into the cell19:19
fennthen there are assemblies of proteins that turn those streams into higher order molecules, like proteins and nucleic acids19:19
@kanzurehuh?19:20
fennnucleic acid polymers :)19:20
@kanzurewe don't need those proteins, do we?19:20
@kanzurejust make agar for the bacteria and that's it19:20
fenni'm talking about how the bacterium works19:20
@kanzurehell, I am sure we can make bacteria that can eat moon rock19:20
@kanzurethat's hacking the bacterium19:20
@kanzurenot really necessary IMO19:20
fennno, as a model for how replicators work in general19:20
@kanzureah19:20
@kanzureokay, so then the packages that we would define19:21
@kanzurewould they be genes and protein expressions ?19:21
fenntake te bacteria apart, abstract and generalize the functions and structure, put it back together using other technologies19:21
@kanzureremember the Minimal Cell Project?19:21
fenni've heard of it, not read much though19:21
@kanzurehttp://heybryan.org/mediawiki/index.php/Minimal_cell_project19:21
@kanzurelucky for you, I have a page19:22
@kanzurewe could try to model the whole damn cell, I guess19:22
@kanzureand then figure out how to apply our terminology to it19:22
fennyeah19:22
@kanzureisn't that kind of cheating, shouldn't we be able to come up with the model ourselves?19:25
@kanzureand why can't we use von Neumann's work on theoretical self-replicators?19:25
@kanzuresurely there must be somebody who has been exploring the mathematics of this topic19:25
fenni was just trying to make sense of your 'reverse method'19:25
@kanzurewe're operating on many different levels here19:26
@kanzureah19:26
@kanzurewell, I see what you mean in that case19:26
@kanzurethe other reverse methods that I have been proposing are different of course19:26
@kanzuresuch as starting with a fabricator arm that can move "completed components" to assemble the fabricator arm itself19:26
@kanzureand then adding in the closed-form dependency loops to make all of the components on the shelf19:27
@kanzurewhich is a reverse recursive definition method, but not quite the same thing as starting with a cell instead19:27
fennthat's the reprap way, but unfortunately plastic goo isnt good for shit19:27
fennso you have to start with something that has potential19:27
fennand legos, have you ever tried to manufacture something using only legos?19:28
@kanzurenope19:28
@kanzurebut19:28
@kanzureI wonder if it would be possible to make a lego factory out of legos19:28
fenni saw a youtube where a 'factory' was assembling legos.. looked godawful inefficient19:28
fennthe factory was made of legos too19:29
@kanzureit surely had some electronics or someting19:29
@kanzure*something19:29
fennyes there's an electronics brick19:29
fenni guess you could use control cams like in a screw machine (not that legos lend themselves to that method)19:29
@kanzureGoogle isn't being kind to me - not much info on synthesis of agar 19:30
@kanzureor agarose for that matter19:30
fennagar is made of agarose :)19:30
@kanzurebut it occurs to me that there does exist such things as aerobic bacteria 19:30
fennits refined from seaweed, fuchus i think19:30
@kanzurehrm19:30
@kanzurethat's not good19:30
fennagarose is not a nutrient19:30
@kanzurehow does fuchus make it?19:30
@kanzureooh19:30
fennit's used for bacteria because they can't digest it19:30
@kanzurewell, we can just have giant water tanks pointed at the sun19:30
@kanzureoh?19:30
fennso you get a nice smooth plate with bumps sitting on top19:31
fenninstead of having the bacteria forming branching colonies inside the agar19:31
fennwell, they do that too, but it doesnt break down at least19:31
fennif the agar broke down it would turn into a pool of slime19:31
fennlego factory: http://www.youtube.com/watch?v=GQ3AcPEPbH019:33
fennwith some odometry that whole thing could be replaced by a car with a gripper19:37
fennthe minimal cell project has too much information processing in the form of molecules, it's like a factory made of cams and levers19:40
fennso it's a bad model to follow for macro-scale replicators19:41
@kanzuretake a look at this19:41
@kanzurehttp://heybryan.org/mediawiki/index.php/Self-replication#Sipper_excerpt19:41
@kanzurehttp://en.wikipedia.org/wiki/Langton's_loops19:42
fennsure but it relies on the cellular grid being just right19:42
fennthe rules of the universe, if you will19:42
fennvon neumann's design separates structure from information, which is desirable when dealing with a fuzzy non-digital universe19:45
@kanzurehttp://ti.arc.nasa.gov/people/jlohn/bio.html <-- good guy to know19:46
fennso now we have DNA and proteins, instead of an RNA-based ribozyme mishmash19:46
@kanzure"the rules of the universe, being just right" --> With any sufficient preparation ...19:46
fennneat stuff19:47
@kanzurehttp://lslwww.epfl.ch/pages/embryonics/ interesting19:48
fennevolution is good at circuit-hiding :\19:50
@kanzureit doesn't look like anybody has actually focused on the mathematics of self-replication, away from cellular automata19:51
@kanzurein fact, why the hell has cellular-automata been used in the first place19:51
@kanzurethis should have been graph based since the beginning19:51
fennbecause cellular automata is a math-based representation of 'the real world'19:51
@kanzureso if we had a cellular automata configuration file that was a self-replicator19:52
fennalso because, in math you can just say 'a = b' and you're done19:52
@kanzurehow would we use that to help us find a material implementation19:52
fennwell, remember they came up with the information tape before DNA was discovered19:52
@kanzureso?19:53
fennwhat if we hadn't discovered DNA?19:53
@kanzureheh, we'd still be stuck on CAs.19:53
fenni guess they had paper tape already19:54
fennanyway, i dont know what the CA simulation is good for19:54
@kanzurenothing as far as I can tell19:54
@kanzurelooks like we were going in the right direction with our definitions/graph-theory approach19:54
@kanzurewith the extendible simulator to generate posisble reactions and interactions between streams so that we can figure out if we have missed any optimizations19:55
fennbtw have you ever seen animations of the vonneumann replicator? it's really cool to watch19:56
@kanzurenope20:01
fennwell too bad, you probably never will :P20:01
@kanzurehm, this is interesting -  1. W.M.Stevens "NODES: An Environment for Simulating Kinematic Self-Replicating Machines" Proc. of the Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9) 39-44, 2004.20:03
@kanzurethe guy's web site - http://www.srm.org.uk/home.html20:03
fennyep found it20:04
fennlooks quite biological20:07
fennhavent any of these guys heard of a tape reel? :)20:08
@kanzurehttp://www.landesbioscience.com/books/special/id/91220:10
@kanzure$150. I may just have to go beg Freitas.20:10
@kanzureOr maybe Max can lend me his copy, if he has it.20:10
fennit's on his website20:12
fennhttp://www.molecularassembler.com/KSRM.htm20:13
fenni need to read that too20:13
@kanzurelet's wiki it20:13
fennwiki what? the whole thing? :)20:14
fenngosh there are a lot of citations20:15
@kanzureyep20:16
@kanzurehttp://heybryan.org/mediawiki/index.php/KSRM20:26
@kanzuremy start to it20:26
fennthis book must be rather heavy20:26
@kanzureFreitas is a peculiar fellow. I saw him on video once, he had no clue as to how to run a presentation. He was reading straight from a transcript, looking down, was not energetic, very monotonous tone. But if he's really all that he's cracked up to be ...20:27
@kanzurefenn: http://heybryan.org/mediawiki/index.php/KSRM/321:18
@kanzureit's getting all messed up21:18
@kanzurehttp://heybryan.org/projects/ksrm/output.txt has the entire wiki code for the book, sort of21:19
@kanzurebut it's all out of order I think21:19
@kanzureoh wait, nevermind21:19
@kanzurehm,21:37
@kanzureFreitas cites Winfree.21:37
@kanzure1175. Brent A. Ridley, B. Nivi, Joseph M. Jacobson, “All-inorganic field effect transistors fabricated by printing,” Science 286(22 October 1999):746-749; http://www.media.mit.edu/molecular/Science10-99.pdf21:38
@kanzure1987. Kinneret Keren, Rotem S. Berman, Evgeny Buchstab, Uri Sivan, Erez Braun, “DNA-templated carbon nanotube field-effect transistor,” Science 302(21 November 2003):1380-1382, 1310 (comment). See also: “DNA used to create self-assembling nano transistor,” ISRAEL21c, 23 November 2003; http://www.israel21c.org/bin/en.jsp?enPage=BlankPage&enDisplay=view&enDispWhat=object&enDispWho=Articles%5el557&enZone=Technology&enVersion=21:39
@kanzurefenn: it occurs to me that we can use humans as the 'black box' for as long as we want for self-replication, slowly porting over certain functions to the actual hardware, until eventually the machine replicates on its own22:03
fennreading the printed FET paper.. i wonder if the nanocrystals could be aligned by an externally applied electric field22:05
fennkanzure: it's more than just 'humans' it's industrial civilization22:06
@kanzureas long as we can move all of the functionality over to the human, we're good22:06
fenni dont know how to make aluminum from scratch :P22:06
@kanzurewhat printed FET paper?22:06
@kanzureare you reading my nanocrystals page?22:06
fennall inorganic field effect transistors fabricated by printing22:07
fennyou just linked to it22:07
@kanzureoh22:09
@kanzurewell22:09
@kanzuremore on semiconductor nanocrystals - http://heybryan.org/alternate_transistors.html22:09
@kanzurei.e., printed FETs.22:09
@kanzurebut this isn't the DNA-based FETs.22:09
fenni cant load the israel21c.org url22:10
@kanzurehttp://web.archive.org/web/*/http://www.israel21c.org/bin/en.jsp?enPage=BlankPage&enDisplay=view&enDispWhat=object&enDispWho=Articles%5el557&enZone=Technology&enVersion=0&22:11
fenndid you ever read about qtc pills?22:11
@kanzure"The DNA serves as a scaffold, a template that will determine where the carbon nanotubes will sit," Braun said.22:14
@kanzurehmm22:14
@kanzurenope22:14
@kanzurelooks like pressure-based switches?22:15
fennyes22:15
fennthey're rubber-state switches22:15
fennwell, variable resistors22:16
fennthe fabrication sounds really low tech22:17
fennmix nickel powder and adhesive22:17
@kanzurewoah22:18
@kanzurethat's definitely worth it22:18
@kanzurewhy haven't I seen more of this22:18
@kanzuresearching for 'qtc pills' doesn't show up much but a single company's website22:18
@kanzurecan you get me some other links or something ?22:18
fennit's fairly new, and there's only one company developing it (the inventor)22:18
fennhell if i know why it isnt more widespread22:19
fennpopular article on the history of qtc http://www.sep.org.uk/catalyst/articles/catalyst_18_1_333.pdf22:34
@kanzurehm22:40
fenni wonder if you could make a composite material that was both a qtc-resistor and a piezo actuator22:42
fennso a small electric field would change the conductivity22:42
fennit would probably have to be anisotropic, like a fiber embedded in silicone rubber22:42
@kanzurehow does a piezo actuator work? 22:42
fenngood question22:43
@kanzureis it just a simple case of applying a current and making it move?22:43
@kanzureI am pretty sure piezo actuator == piezo buzzer22:44
@kanzure`http://www.sep.org.uk/catalyst/articles/catalyst_18_1_333.pdf`22:44
@kanzureoops22:44
@kanzureInkjet printers: On some inkjet printers, particularly those made by Epson, piezoelectric crystals are used to control the flow of ink from the inkjet head to the paper.22:44
fenni think piezoelectric materials deform due to voltage, but there is a certain amount of charge that must be transfered (as if it were a capacitor)22:44
@kanzurePiezoelectric motors: piezoelectric elements apply a directional force to an axle, causing it to rotate. Due to the extremely small distances involved, the piezo motor is viewed as a high-precision replacement for the stepper motor.22:45
fennyeah the piezo inkjets physically squirt the ink onto the page22:45
@kanzureyes, piezoelectrics work just like that22:45
fennugh, no, ignore the piezoelectric motor snippet22:45
@kanzurebut I have not figured out how that applies to piezo steppers / actuators22:45
@kanzureoh?22:45
@kanzurebecause that doesn't make sense22:45
@kanzureif you apply a voltage22:45
@kanzureit will deform and push the axil22:45
@kanzurebut then when you stop the voltage22:45
@kanzureit should just move back to where it started22:45
@kanzurewhich makes no sense :)22:46
fennyou can cause rotational motion, but not _continuous_ rotation22:46
fennunless you have some ratchet mechanism or something22:46
@kanzureI doubt they are using ratchets22:46
@kanzurebecause you're using twice the energy22:46
@kanzurethat you need.22:46
@kanzurewhere's Superkuh when you need him? heh'22:47
@kanzurehe's a self-made expert in piezos last time I checked22:47
@kanzurewas designing a piezo-based particle accelerator22:47
fennyou could use a piezo actuator as the replacement for a piston in an engine (sorta)22:47
fennah i bet he was doing something with fusion22:47
fennlithium deuteride crystals yes?22:48
@kanzureso how would you cause rotational motion with piezos?22:48
@kanzurelet me chekc22:48
@kanzureFerroelectric/pyroelectric particle accelerators and research with homebrew methods.22:48
@kanzure[context pressure ~=10^-3 Pa] Has anyone considered using pyroelectric crystal mediated acceleration of charged particles (spontaneous polarization of voltage oriented through the c-axis crystal faces (when heating the , +z surface has a negative potential and the -z surface has a positive potential, reverse for cooling) as the result of shifting ions in the crystal shape/lattice combined with funky dilute gas charge masking behav22:48
@kanzure Particle (electrons or ions depending on the crystal face and heat/cool cycle) energies up in the 150keV+ range are very doable (or 200kev+ with dilute light gases and a bipolar setup). Plus with cylindrical crystals the beams are self focusing. A common choice for this is Lithium Tantalate, and making thin films and stacking this material is possible, but there are lots of tricks involved (and making crystal boules is a magnitud22:48
fennthat's pyroelectric, not piezoelectric22:49
@kanzureyeah .... oops.22:49
@kanzurebut 22:49
@kanzurehe's the guy that introduced me to piezoelectricity22:49
fenni see22:49
fennwell, anyway, there are piezoelectric polymers (kynar/polyvinylidene)22:50
@kanzurehm, that's convenient22:51
fennbut the most promising are ceramic22:51
@kanzurebut how does the rotational motion work that you were mentioning?22:51
fenna piston in a car engine goes up and down, so replace the piston with a piezo actuator22:51
fennthe crank turns reciprocating motion to rotation22:51
fennthere's more ways to do it22:52
@kanzurehuh22:52
fennlike a clock wheel, hit each tooth with a hammer as it goes by22:52
@kanzureso if you just do rapid voltage pulses22:52
@kanzureyou'd convert this into rotational motion with a crank22:52
fenni saw a 'wiggle motor' somewhere22:52
fennit's a piezo rod that wiggles its way around, using a gearing principle similar to harmonic drives to provide a decent output torque22:53
fennit was about 5mm wide 20mm long22:56
fenncylinder22:56
@kanzurenot much turning up on Google.22:56
fennhttp://www.newscaletech.com/squiggle_overview.html22:58
@kanzurethat's really convenient23:01
@kanzureI wonder how we could make it.23:02
@kanzureIt looks like just a piezo + voltage + ... I don't know what.23:02
@kanzureeither a rachet or a crank23:02
@kanzurefrom Superkuh's bookmarks - http://www.pollin.de/shop/shop.php?cf=detail.php&pg=NQ==&a=MDA5OTQ3OTk= giant piezo crystals23:03
@kanzurehttp://www.chem.pacificu.edu/Johnson/JohnsonResearch/STM/PIEZO.HTM piezo tube23:04
@kanzurehttp://www.colomar.com/Shavano/mini_piezo_tweeter.html DIY mini piezo tweeter23:04
@kanzureHm, in my trash I apparently have a Google search for pyroelectrical transistors - 23:04
http://www.google.com/search?client=opera&rls=en&q=pyroelectric+transistor&sourceid=opera&ie=utf-8&oe=utf-8
fennwow that's cheap (pollin.de)23:05
@kanzuremaybe we should stock up ;)23:07
fennthe piezo tube looks like what the squiggle motor uses23:09
fennheh, go back on that page it says 'inchworm motor housing' for STM23:10
@kanzurethe piezo tube is for motion in x/y/z directions, not up/down, although ... if we could find a piezo that could change shape by say, 5 mm or something, that would be great23:11
@kanzureor I guess it doesn't have to be too much23:11
@kanzureit could just be a rubber band stretching system23:11
fennoh i guess 'inchworm motor' is the stick-slip thing i keep reading about23:11
@kanzurehttp://en.wikipedia.org/wiki/Inchworm_motor23:12
fennwhy 5mm? what do you plan to do with it?23:12
@kanzurewell23:12
@kanzurea 1 m piezo would be great23:12
@kanzureas a piston or something :)23:12
@kanzurehttp://www.physikinstrumente.com/en/news/fullnews.php?newsid=123&Wiki_iw I hate this website, but it's about the principles of the inchworm motor23:13
@kanzurephysikinstrumente spams all over the place23:13
@kanzuretons of domain squatting23:13
@kanzureif this piezo motor can scale from 1 Newton to up to thousands of Newtons that'd be great23:14
fenna motor might have force and speed but not at the same time23:15
fennbut why does it matter? what are you going to use it for?23:15
@kanzurehuh?23:16
@kanzureI was assuming you had a few ideas23:16
@kanzurefor using it in a replicator23:16
fennwell, i never considered piezo's to be useful for producing mechanical power23:16
fennthat might be a mistake on my part23:16
@kanzureit looks fairly convenient23:17
fenndid you notice the efficiency chart? looks like they are much less efficient when size goes up23:17
@kanzurehrm23:18
@kanzureqtc-resistor + piezo would be really useful though23:18
fennon the right side of here http://www.newscaletech.com/doc_downloads/SQUIGGLE_Overview_2-18-08.pdf23:18
@kanzurecombines a lot of parts23:18
fennyes, i was thinking mainly piezos for squeezing qtc's to control a more conventional motor23:19
fennlike, a pancake motor or switched reluctance23:19
fennvoltage is easy to get from a tiny computer chip23:20
fennanyway this all needs some empirical data23:20
fenni've never used either qtc's or piezo's23:21
@kanzurethe qtc research group should be responsive23:24
@kanzurehttp://www.dur.ac.uk/psm.group/qtc.html23:24
fenni'd like to know if there are other metals besides nickel that form nano-spikes23:26
@kanzureI need to take a break from this stuff and go figure out a circuit for Andy ... he wants me to come up with something that has an emergent property23:27
@kanzurebut this is pretty hard23:27
@kanzureI am thinking about telling him about my 'evolvable DNA logic circuits' idea, but I think that's sidestepping his request23:27
fennsomething with an emergent property eh23:28
@kanzureheh'23:28
fenncats and dogs and buttered toast!23:28
@kanzurehe cited the ring oscillator as the "classic example"23:28
@kanzureindeed23:28
@kanzurethe oscillator example is really simple and takes up a huge class of possibilities23:29
@kanzureso I can't do anything that oscillates23:29
@kanzureI was thinking about trying to implement sine23:30
@kanzurebut that's analog, whereas this is discrete-state23:30
fennforget about emergence, come up with something that has 'a spiritual property'23:30
fennthey're both meaningless words23:31
@kanzurethen what should I implement23:32
@kanzurecalculations are mostly meaningless in this context23:32
@kanzurealthough the prospects are interesting for large-scale computing really23:32
@kanzurebecause if you have a few million gates for a single circuit23:33
@kanzureand want to do simultaneous computation all at once23:33
@kanzurethen you have them all extremely localized23:33
@kanzureif you have it acting in a centrifuge then it would be interesting to store the result of the computation eventually, but I don't see how23:33
@kanzuremaybe a flip flop system23:33
@kanzurebut there's no guarantee of saturation or propagation of all of the same states to all of the flip flops23:34
@kanzurehrm23:34
@kanzuremaybe a massive cellular automata implementation23:35
@kanzurewhere the logic gates are the cells23:35
@kanzureeach logic gate has four neighbors, and they are all executed in parallel, so what would happen?23:36
fenn*drool* http://sourceforge.net/projects/xandra23:36
@kanzureawesome23:36
fennhow do you connect the neighbors? through winfree's toehold addressing mechanism?23:38
@kanzureyes23:44
@kanzureand in this scenario,23:44
@kanzureyou don't have to be too specific either23:44
@kanzuresince you can have four neighbors for each 'cell'23:45
@kanzureheh23:45
@kanzureso that means I don't have to be as strict when selecting the toeholds and the recognition sequences23:45
@kanzuresneaky, isn't it?23:45
fennscreenshot from xandra showing a hexaglide actuator: http://imagebin.org/1516423:46
fenni dont get it. the reason you have to be strict when selecting toehold sequences is to reduce crosstalk23:48
@kanzureyes23:48
@kanzurewell23:48
@kanzurenot only that23:48
fenncrosstalk will bunch up your fabric23:48
@kanzurebut you also don't want one toe-hold to match for the wrong logic gate23:48
@kanzureit's kind of like a lock-and-key method23:48
@kanzurewhere the logic gate output is a key to the next one in the pathway23:48
@kanzureso if your key unlocks the 4 neighboring cells ..23:48
@kanzurewhere 'cells' are really just gates23:48
fenn'cell' as in cellular automata right? not bacterial cell23:50
fennblah my brain is hurting23:51
@kanzureright23:52
fennanother xandra screenshot http://imagebin.org/1516523:52
@kanzureheh23:52
@kanzureso what does it simulate23:53
@kanzurejust a 3D visualization?23:53
fennmachine tool kinematics23:53
@kanzureooh23:53
fennwindows only right now or i'd be playing with it23:54
@kanzurewine?23:54
Day changed to 23 Mar 2008
@kanzurefenn: you wouldn't happen to remember how to use the X11 screenshot feature to take a snapshot of a particular program?00:04
fenni use ksnapshot00:05
@kanzureI need to automate it. I think there was a program named xsd or something.00:05
fenntry `man import`00:05
@kanzureokay00:06
fennwith import you have to click on the window..00:06
fennxwd is what you're remembering00:09
@kanzureyes00:12
@kanzurethank you00:12
@kanzureturns out xplanet ( http://xplanet.sf.net/ ) does image output itself00:12
@kanzureso all is good00:12
@kanzurea guy from the Moon Society wants me to write a quick script to show the earth from the moon at the given moment00:13
@kanzurehe said his web dev team has been at it for two years00:13
@kanzureI laughed and set it up in 2 minutes :(00:13
fenntwo years!00:13
@kanzurescript kiddies do better than two years ...00:14
fenni feel like i've been doing JITT (just in time training) for a few years now00:18
fennexhibiting symptoms of 'jitt-stick'00:19
fennwikipedia overdose00:19
@kanzureJITT indeed00:24
@kanzurebut what can be done about that00:24
fennmobile computing for exercise (faster removal of brain waste products, increased oxygen)00:27
fennmight cause more harm than good though, you could walk into the street or something00:27
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fennLight from the sun hitting lunar dust causes it to become charged through the photoelectric effect. The charged dust then repels itself and lifts off the surface of the Moon by 05:07
electrostatic levitation.
fennIt is thought that the smallest particles are repelled up to kilometers high, and that the particles move in "fountains" as they charge and discharge.05:07
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-!- [freenode-info] if you're at a conference and other people are having trouble connecting, please mention it to staff: http://freenode.net/faq.shtml#gettinghelp05:23
-!- Channel #hplusroadmap created Sat Mar 22 15:44:12 200805:23
kanzurehttp://archives.seul.org/geda/dev/Nov-1999/msg00120.html13:26
kanzureEDIF 2 format13:26
kanzureoh13:26
kanzureheh13:26
kanzuregood old ~rcary13:26
kanzurehttp://www.rdrop.com/~cary/mirror/tools_htmlized.html13:26
kanzureThis guy is a god.13:27
kanzureDavid Cary.13:27
kanzurehttp://www.rdrop.com/~cary/html/idea_space.html <-- read this like a bible13:27
kanzurehttp://www.geda.seul.org/wiki/geda:icarus_xnf13:31
kanzuregEDA can do XNF.13:31
fennheh i'm reading ~cary and he's slipping into orion's arm lingo13:32
kanzureyes13:32
kanzureI've emailed him over the years. He doesn't seem to exist any more.13:33
fennreduced information diet13:35
kanzureFrom #electronics13:38
kanzure(2008-03-16 12:39:35) gordboy: i'd like to see store "disloyalty" cards. you pop in your card and it injects a virus into the system and causes all the wheels and dials to spin 13:38
hopelessly out of control, while technicians with suspiciously german-sounding accents rush around shouting "gott und himmel. donner und blitzen"
kanzurescrew it, I could have been done by now with a 'logic' grammar13:39
kanzurejust need something that can do "output1 = input1 xor input2 xor input3"13:39
fennum, how bout C?13:39
kanzurebut it compiles into bytecode13:39
fennwhat kind of bytecode?13:39
kanzureI mean, the machine code for the specified architecture13:40
kanzureoh13:40
kanzureI wonder how to specify the architecture13:40
kanzureand the specified architecture would thus be DNA13:40
fenni think that's the hard part13:40
kanzureQuick! to #gcc !13:41
kanzuremaybe it would be technically smarter to 13:43
kanzuremake an assembler13:43
fennassembler assumes a linear sequence, whereas what you are building is inherently parallel execution13:44
kanzurenopre13:44
kanzure*nope13:44
kanzuresurprisingly not13:44
kanzureassume one DNA molecule per cell13:44
kanzureand the gene, the nucleotides on the molecule, *that's* the gate13:44
fenn:313:44
kanzurebwahah13:45
kanzureso now I just need to look for a simple assembly language13:45
kanzureI will _not_ implement x86 or MIPS. Screw that.13:45
fennsomething's walking down the molecule though, recombining at various places13:45
kanzureso?13:45
fennyou can have more than one of those13:46
kanzureyeah, but there's only one gate13:46
kanzureit's just asynchronous logic13:46
kanzureit's a bottleneck13:46
fennwhat is the 'something'?13:46
kanzureyour 'something'? 13:46
kanzureI thought it was RNA polymerase13:46
kanzureor DNA polymerase13:46
fennso, the state of the logic gate's inputs are blobs of protein stuck to the dna, and the 'flow' is whether the gene is transcribed.. got it13:47
kanzureright, because when you transcribe the gene, you're making the "output" of the gate, which then becomes the input to the next gate13:48
fennthis is much simpler then :)13:48
kanzureso I just need to write a DNA assembler.13:48
fennso you need a library of transcription factors and inhibitors13:49
fennthat's your 'cache'13:49
kanzurethere are rules for making those library-items13:49
kanzureso automatic generation of those is important13:49
kanzuresince you might have a circuit with a few thousand components13:49
kanzureand you want your output going to the right place13:49
fennhas that been proven in a lab?13:49
fenncreating new transcription factors13:49
kanzureyep, I'm pretty sure13:50
kanzurehttp://www.dna.caltech.edu/DNAresearch_publications.html13:50
kanzuresee Construction of an in vitro bistable circuit from synthetic transcriptional switches.13:50
kanzureit does not specifically imply that they have done this, but it is clear that they are using a mechanism so that logic does not 'jump'13:51
kanzurealso see Enzyme-Free Nucleic Acid Logic Circuits.13:51
kanzureah, shit: Protein Design is NP-Hard.13:52
fennyou could do a combinatorial approach, tying known-to-work blobs together13:53
kanzurewait, why do I want an assembler13:54
kanzurean assembler works off of an ISA13:54
kanzureand the ISA is for using the hardware13:54
kanzurebut we are writing the hardware, no?13:54
kanzurethis is confusing13:54
fennyou want to generate the 'bitstream' i believe13:54
kanzure?13:54
fennwhich is where your netlist gets turned into hardware state13:54
fennin FPGA's there is some data which initializes the hardware into the state you want it to be (your circuit)13:55
fennit's called a bitstream13:55
fennVHDL/verilog describe the desired state in an abstract sense13:55
fennthis gets turned into something made of slightly more concrete elements (logic gates and digital devices like flipflops)13:56
fennthat's your xnf file13:56
kanzureeh13:56
kanzurelet's modularize this13:56
kanzurethe basic output of this program should be a single logic gate13:57
kanzureas in, the DNA13:57
kanzureso, program xxdna should output DNA + information on "output specs" ... the parameter to xxdna should be (1) the logic gate needed and (2) the input-key that it should read (i.e., it 13:57
can't just accept anything)
kanzurethe space is limited obviously, so if you need 2^8 gates, you need something like 4 nucleotides for the 'key'13:58
kanzureor something like that, 4^4 should be 2^813:58
kanzureanyway, the input parameter to xxdna (the second parameter) should actually be a file name13:58
kanzureand in this file we can store all of the input keys already used13:58
kanzureso it just uses the next one13:58
fennit might be too hard to recognize DNA sequences, you will probably have to use combinations of proteins that bind together13:59
kanzureand then it makes up its own output-key, which becomes the parameter for the next call to xxdna13:59
kanzurenope,13:59
kanzureas it turns out that's well studied13:59
kanzureI need to go back and read the papers, but it looks pretty well studied13:59
fennah that's good14:01
kanzureI need to go find the algorithm.14:01
kanzurebecause if I can find the algorithm14:01
kanzurethis is a very simple perl scripot14:01
kanzure*script14:02
fennso you can just change the protein sequence to recognize a differen dna sequence?14:02
kanzureno proteins involved14:02
fennoh? it's RNA transcription factor?14:02
kanzureall mRNA strands :)14:02
kanzureyep14:02
fennnice14:02
kanzureprotein folding is NP-hard, remember? hehe14:02
fenni think that's a myth, but i digress14:03
kanzureit's a paper on their site14:03
kanzureheh14:03
kanzurethe papers talk about a "toetail" which is what we want to algorithmically change14:05
kanzurebut they do not mention where this is in the actual sequence of the gates and so on14:05
kanzurethey give 8 different DNA sequences, I need to go back and map these out to what each of them are supposed to do14:06
kanzureI have the sequences at the end of the page over here -- http://heybryan.org/winfree.html14:06
fennthe output from the gate is tagged with the 'address' of the next gate14:11
kanzuresort of, yes14:11
fennis there a 'packet diagram' somewhere or do they just list the raw sequences and hope you can read AGTAGAACCATAACACAAGGGTTCTCAAGAA14:14
kanzurepacket diagram?14:14
fennhttp://www.media.mit.edu/physics/publications/papers/04.10.sciam/barcode.jpg14:16
kanzureogh14:17
kanzureheh14:17
kanzureso in other words, a packet diagram of each of the DNA sequences14:17
kanzure[this part should be changeable][READ ONLY!!] etc.14:17
fennright14:17
kanzure--> The sequences of all DNA molecules and expected RNA transcripts14:20
kanzurewere chosen to minimize the occurrence of alternative secondary14:20
kanzurestructures, checked by the Vienna group’s DNA and RNA folding14:20
kanzureprogram (Flamm et al, 2000). All DNA oligonucleotides were14:20
kanzurepurchased (Integrated DNA Technologies, Coralville, IA). T21-nt is14:20
kanzurehmm14:20
kanzureI guess I need that program14:20
fennflim flamm folding fun14:21
kanzureFlamm's papers14:22
kanzurehttp://www.tbi.univie.ac.at/~xtof/papers.html14:22
kanzureVienna RNA secondary structure server -- Hofacker 31 (13): 3429 ...The Vienna RNA package (12) is a free software package that implements a variety of ...... A. Weixlbaumer, A. Werner, 14:22
C. Flamm, E. Westhof, and R. Schroeder ...
kanzurenar.oxfordjournals.org/ cgi/content/full/31/13/3429?ck=nck - Similar pages14:22
kanzure(behind a paywall)14:22
kanzureah14:22
kanzureRNAcofold14:22
fennit doesn't matter so much if you can't get the papers (if you have the source)14:23
kanzurehttp://www.tbi.univie.ac.at/~ivo/RNA/14:23
kanzurehaha, bitches!14:23
fenngoogle ftw14:23
kanzureactually :( http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software14:24
kanzure`Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).`14:25
kanzurehttp://rna.tbi.univie.ac.at/cgi-bin/RNAinverse.cgi <-- Web interface :)14:25
kanzureso now I am confused14:27
kanzurethe RNA inverse input is not a nucleotide sequence14:27
kanzuretherefore RNA folds too?14:27
fenni think you want the other direction to figure out what those sequences do14:27
kanzureyou have to come up with a sequence in the first place14:28
fennrna and dna can fold up, depending on their sequence14:28
fennthat web program takes a structure (a shape) and spits out a sequence that will give that shape14:28
kanzureokay, then I want RNAup14:28
kanzureThe RNAup program for computing RNA-RNA interactions is now included.14:28
fennyes14:28
kanzureso, if we want the logic gate to go through with the operation14:28
kanzurethe two RNA sequences must bind14:28
kanzureor actually14:28
kanzurethe RNA output sequence (from the last gate)14:29
fennand relplot.pl14:29
kanzurehas to bind with the DNA14:29
kanzureso this is RNA-DNA interaction14:29
kanzurenot RNA-RNA.14:29
fennyou need both? the mRNA will interact with itself14:29
kanzurehuh?14:30
kanzurethat's true14:30
kanzureso this is to check RNA-RNA interactions14:30
kanzureoh14:30
kanzurethe RNA output has to bring in a sequence14:30
kanzurethat will complete the DNA for the next logic gate14:30
kanzureso the RNA has to be able to "bring/tug/port" an oligonucleotide sequence over to the next logic gate14:30
kanzurehm14:31
kanzureI wonder if we can make it so that 14:31
kanzureyeah, it has to be made so that when the oligonucleotide sequence is wrong (the wrong key) the RNA does not deposit the oligonucleotides into the logic gate14:32
kanzurebecause that would 'block' the logic gate14:32
fennone problem i can think of is sequence specificity.. a partly-mismatched 'address' will still bind somewhat14:34
kanzurenope14:34
fennso you're still dealing with analog 'fuzzy' logic somewhat14:34
kanzureI got it14:34
kanzureDNA repair mechanisms14:34
kanzureyou have only one strand of the DNA logic gate there14:34
kanzureand the RNA transcribers bring in the complement14:34
kanzureyeah, wait a second14:35
kanzurehow do they unbind14:35
kanzureor, why doesn't the DNA repair mechanisms just fill in the gaps14:35
kanzureI think it's at "run time" where everything happens14:35
kanzureso that only at run time, when the logic gate is being transcribed, is it on or off14:35
fennyou lost me with the DNA repair stuff14:35
kanzurewell14:35
kanzureI am now very confused14:36
kanzureI was thinking that it may be using strand complements14:36
kanzurefor the on/off property14:36
kanzurebut that would mean that DNA repair mechanisms could just come in and add the right nucleotides and make it blocked14:36
kanzurebut I realize now that it has to be more "run time" than that14:36
kanzurei.e., the actual magic happens during transcription14:36
fennthis is complex..14:36
kanzureyes14:36
fennthe dna structure exposes certain regions of DNA14:37
kanzureno, it can't do that14:37
kanzurebecause DNA repair guys would come around and fix it14:37
fennin a double helix14:37
kanzurethink of this: AATTGGTTT[where you need your gate output to fit]TTCCCATTGTAC and then this is attached to a complete compliment14:37
kanzurethe DNA proteins would fix the gap14:37
kanzuretherefore this is not how it works.14:38
fenneverything's hunky dory, but 5% of the time (or whatever, depending on the binding strength of the DNA sequence) the double stranded structure comes apart and allows transcription factors 14:38
to bind
fennAT pairs are stronger than GC pairs14:38
kanzurehm?14:38
fennit comes unzippered14:38
fennit's all jumbling around in a soup of brownian motion14:39
kanzureyes14:40
fennso you can think of it like quantum mechanics, it's in suchnsuch state 20% of the time,14:40
kanzurebut I am having trouble parsing what you are saying14:40
fennthe DNA repair mechanisms only detect certain types of structural abnormalities, they won't bind to partially open sequences like when it comes a bit unzippered14:40
fennwhen something 'binds' to a sequence, it's sometimes there and sometimes not there14:41
kanzureoh14:41
kanzureoh14:42
kanzurealso, 14:42
kanzurepage 4 is good 14:42
kanzureConstruction of an in vitro bistable circuit from synthetic transcriptional switches - bistable_switch2006.pdf14:42
kanzurethat's a lot of dense information14:45
kanzureI need to diagram it or something14:45
kanzurefor some reason I keep on reading that paragraph over and over again, but it's not getting any better -- I think that they are giving the packet specification there, but I don't know how 14:49
they figured out what sequence to put in it
fenntheir diagram sucks14:49
fennoh boy the waveforms are plotted in hours14:51
kanzurethat's not good, is it?14:52
fennthis is in vitro, it could mean anything14:54
fennhttp://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software#_note-book114:57
kanzure?14:57
fenni got confused.. just spent half of yesterday reading about the hitchhiker's guide14:58
kanzureyou've never read it?14:59
fenni've read it, but i've never read _about_ it14:59
kanzureah14:59
fennum, nevermind14:59
fennyou shouldn't describe your dna/rna transcription circuits as using 'genes' since genes usually produce a protein and this gets confusing15:02
kanzurehrm15:02
fennthe ellington stuff on the other hand actually uses genes15:04
kanzurehere's the real Ellington stuff15:05
kanzurehttp://ellingtonlab.org/mediawiki-1.10.0/index.php/Main_Page15:05
kanzurehm15:06
kanzurehe has an amorphous computation guy15:06
fennnot a very useful webpage15:08
kanzureright15:08
fenni mean the transcription factors and gene products on this page are actually proteins http://heybryan.org/genetic-circuits.html15:09
kanzureyes15:09
fennyou will have to interface with proteins at some point in order to do sensing15:10
fennotherwise why bother running a biological computer?15:10
kanzurethat's okay15:10
kanzureinhibition of circuits is possible15:10
kanzurevia the methods that were from genetic-circuits.html15:10
kanzurei.e., a protein can prevent transcription15:10
kanzure(inihibition)15:10
kanzuredna.caltech.edu says --  15:11
kanzureSoftware packages that we actively use for research, e.g. mfold, Vienna, Namot2, Tcl, RasMol..., as well as other software installed on our cluster, e.g. VMware, MATLAB, Mathematica, ...15:11
kanzurehuh15:18
kanzurehttp://gcat.davidson.edu/GcatWiki/index.php/Logic_Gates_-_Emma_Garren15:18
kanzurethis might be good15:18
kanzurealso see Enzyme-free nucleic acid logic circuits - DNA_logic_circuits2006.pdf15:25
fennyes i'm reading that15:25
kanzureI like how they conveniently exclude DNA sequences.15:26
kanzureooh15:35
kanzurelook at the bottom right-hand corner of the last page15:35
kanzurethe materials are on sciencemag.com15:35
kanzurewhich I do not have access to.15:35
kanzurewoiah15:39
fennhttp://www.dna.caltech.edu/Papers/DNA_logic_circuits2006_supp.pdf15:39
kanzureI got it15:39
kanzureyeah, 18 pages15:39
kanzurethis is much easier to understand than the paper15:39
kanzurepage 16 for DNA.15:40
kanzureSequences were from: [S7] Lagos-Quintana, M., & Rauhut, R., & Yalcin, A., & Meyer, J., & Lendeckel, W., & Tuschl, T. (2002) Current Biology 12 735–739.15:41
kanzure[S8] Lagos-Quintana, M., & Rauhut, R., & Meyer, J., & Borkhardt, A., & Tuschl, T. (2003) RNA 9, 175–179.15:41
kanzurehm15:48
kanzureit's interesting that they were using sequence optimization techniques15:48
kanzurewhy not just generate a few megabyte file with a list of all possible sequences15:49
kanzurefor the lengths that they are working with15:49
kanzureI am pretty sure they were using only the Flamm software packages. Maybe they will tell me if I ask nicely?15:49
fenn'sequence optimization' means getting rid of things that can go wrong, right?15:51
kanzureyep15:51
kanzurewhile also making sure the sequences meet requirements15:51
fennwhat would you do with a bunch of lousy sequences that probably wont work?15:52
kanzurehuh?15:52
kanzureyou want a list of things that *will* work15:52
kanzureit's a toolset15:52
fennyes15:52
kanzureso then xxDNA will just come in and select a few for the circuit that you are encoding into DNA.15:52
fennsure, 1 2 315:52
fennor maybe 5 6 715:52
kanzureso save the effort and have a pre-generated list15:53
kanzuregenerate once, use many15:53
fennwhat are the limiting factors?15:53
kanzure minimization of secondary structures in single-stranded species 15:53
kanzureas predicted by the minimum-free-energy (MFE) structure [S3] at 25◦ C using DNA parameters [S4];15:53
kanzureminimization of cross-talk between all single-stranded species, as measured by the ∆G◦ of association between pairs of15:54
kanzurestrands (estimated as intramolecular MFE for a ‘virtual’ strand linking the two sequences via 5 unpaired nucleotides);15:54
fenni mean, you cant have a zillion different signals without paying for it somehow15:54
kanzureright, so we'd constrain the generation-list to maybe length = 1015:54
kanzurewhich would be 4^10 possibilities, and then you narrow it down from there15:54
kanzureby obviously avoiding certain sequences for testing heh'15:55
fennhow did they calculate the 'delta-g of association'15:55
kanzurefor example15:55
kanzureno clue15:55
kanzurefor example -- they say they don't want any 3 nt to be next to each other that are the same nt15:55
kanzureso15:55
kanzurethat narrows it down significant15:55
kanzure*significantly15:56
kanzureI don't remember my number theory enough to be able to recall what that might look like15:56
fennnumber theory? just do a brute force method, it's only 4^10 possibilities :)15:56
kanzurethat's quite a lot :)15:56
fennonly 1e12, and you only have to calulate the list once15:57
fennand a partial list is still useful15:57
kanzureoh15:57
kanzureonly E1215:57
kanzurethat's not bad15:57
kanzurehow much meta-information would be generated, after all?15:57
kanzureonly yes/no15:57
kanzureand the actual sequence15:58
kanzureso it's up to (number of bits required to express the strand + 1 bit for yes/no) * E12 15:58
fennnot yes/no, you'd get a binding strength and a specificity value (standard deviation?)15:58
kanzureyou'd do the evaluation at runtime15:59
kanzureand you'd just have to encode a "cut off point" for making the team or not ;)15:59
kanzure*at generationtime (so runtime, but not runtime of xxdna)15:59
fennright? am i thinking this right? (4^10 different sequences)^216:00
kanzurewhy's that?16:01
fennto compare each sequence against every other sequence16:01
kanzureoh shit16:01
kanzurethat's not good16:01
kanzureand yes, you're right16:01
fenn4^10 is about 1e616:01
kanzure4^10 is E1216:01
fennno 4^10*4^10 = e1216:01
kanzurewait16:01
kanzureokay16:01
kanzureso16:02
kanzuretechnically there would be subgroupings that can work together16:02
kanzurebut not with others16:02
kanzureso for each sequence we would have to specify which ones they work with16:02
kanzuremaybe it would be optimal to do "groupings"16:02
kanzureand then part of the "generation program" parameters would be "how many divisions do you want?"16:02
kanzureand obviously you could do up to 4^10 divisions if you wanted to16:02
kanzureor one division (making all results compatible)16:03
kanzure*compatable16:03
fenni think 'how many divisions' is the 10 base pairs16:03
kanzureI disagree16:03
kanzurethink about it: the first and last might be exclusive16:03
kanzurebut the first one and #14141 is good16:03
kanzureso just because first-and-last are mutually exclusive, does that mean #1 and #14141 is bad? not at all16:03
kanzureyou just need to have some 'rules' or 'classifications'16:04
* fenn searches desperately for an analogy16:04
kanzurekind of like ethnic stereotypes16:04
kanzureno asians and jews in the same room16:04
fennpreferably something in a computer context16:04
kanzureheh'16:04
kanzureoh16:04
kanzureeither way, this idea sucks16:05
kanzurelots of computation and simulation time is required16:05
fenni guess the sequence would have 'factors' which are the sub-sequences16:05
kanzurethat would make the task much less daunting16:06
kanzurebut I think it requires a simulation of their interaction16:06
fennlike 0110 is 0011*2 (the 11 is a factor)16:06
kanzurelike, we can't just say "No AAA and TTTA"16:06
fennso what you're really combining is the sub-sequences, not the individual bases16:07
fennbleh16:07
kanzureyeah ...16:08
kanzurehow did they do it, then?16:08
kanzuredid they just get lucky?16:08
fennsmall search space16:08
kanzureooh16:08
kanzureno16:08
fennthey only had 6 nt in the sequence16:08
kanzurethis is the inverse folding problem16:08
kanzureso if you have specifications for a number of entities to inversely fold16:09
kanzureyou provide their stats and numbers16:09
kanzureand then they come up with the sequences :)16:09
fennare we talking about the same thing?16:10
kanzureyes16:10
kanzuresee16:10
fenni'm coming up with a 10 nt toehold sequence that should have low-cross talk16:11
kanzurewe were originally talking about generating a list of usable components16:11
kanzureright16:11
kanzureif we do it by generating nt seqs, then we have lots of processing to do16:11
kanzurebut we already know what we want the finished thing to be like16:11
kanzurewe don't care what its sequence is16:11
kanzureas long as it interacts in the defined ways16:11
kanzurethis is basically why we have inverse folding =)16:11
fennok16:11
kanzuresearching bottom-up (from possible nt seqs) would be much more computationally intensive16:12
fennisn't that how inverse folding works though?16:12
kanzurethere's energy minimization algorithms at work, I think16:13
kanzureso that they constrain search space significantly16:13
fenni thought the energy minimization referred to the self-assembly of the structure, not the algorithm16:13
fennthe structure assumes the minimal energy configuration16:14
kanzurehttp://www.tbi.univie.ac.at/~ivo/RNA/RNAinverse.html16:14
kanzurecheck out the options16:14
kanzureoh16:14
kanzureRNAinverse searches for seqs bruteforce16:15
kanzurecrap16:15
kanzurehttp://freebirds.com/16:17
kanzureI'll be back later.16:17
fennif only they delivered via UAV16:18
kanzurewe can arrange that16:19
kanzurethey are ran by college students with nothing better to do16:19
kanzureEUREKA16:22
kanzurewe'll do it in solution16:22
kanzurescrew computation16:22
kanzurewe just need a way to get rid of all of the sequences that have *not* binded16:22
kanzureerm, woops16:22
kanzureget rid of the ones that have bound together16:22
kanzurei.e., maybe they are too heavy16:22
kanzureand cannot be electrically attracted 16:22
kanzureto a certain anode16:22
kanzureand then we just do DNA sequencing for all of the strands that *do* work16:22
* kanzure goes back to the shower ...16:23
fennthat's a lot of gels to run16:23
fennthis reminds me of DNA microarrays16:33
fennanyway i'd rather a computer-based method as it is more easily replicated16:36
fenneasily run on parallel clusters16:37
fennthis is really cool http://www.dna.caltech.edu/Papers/DNAorigami-nature.pdf16:46
fennalso the prospect of an FPGA from self-assembling tile sets (DNA/CNT hybrid structures)17:30
fennthat's a straightforward path to a self-replicating computer18:17
fennpresumably there would be a way to read the configuration data from some DNA into the FPGA's electronic circuitry18:18
-!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com]18:20
-!- ircname : purple18:20
-!- channels : #gcc ##electronics #biology ##neuroscience #bioinformatics @#namcub #wrongplanet @##wikipeding 18:20
-!- server : irc.freenode.net [http://freenode.net/]18:20
-!- away : Away18:20
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-!- End of WHOIS18:20
kanzureWhat would take longer? Simulation on a supercomputer, or using a solution and just mix them? Maybe we can use the DNA microarray idea, yes. DNA microarrays use mRNA probe tips to do 18:25
hybridization, so if you detect an energy change you know there's been some binding. But this would only test one probe to the other sequences that you have in all of the wells.
kanzureBut this would only test one probe to the other sequences that you have in all of the wells. 18:25
fennif you're doing gel electrophoresis, the probes would all have to be different lengths or they won't separate18:35
kanzureI prefer STM DNA sequencing.18:36
fennassuming you could detect a 1% difference in length (tough) how do you go about setting up the combinations?18:36
kanzureDNA synthesizer.18:36
kanzuregiant inkjet printer ;)18:36
kanzurethat does oligosynthesis chemistry.18:37
fenncrap STM sequencing was sci-fi last time i read anything about sequencing18:37
kanzureheh18:37
kanzurehttp://heybryan.org/mediawiki/index.php/DNA_sequencing 18:37
kanzureor sequencer or something18:37
kanzureI have lots of notes on STM-DNA sequencing.18:37
kanzureI also have a $100 STM design up there.18:37
kanzureHuh. I think they are using a genetic algorithm to come up with the optimal sequences.18:56
kanzureother side. Scores for each of these soft criteria were weighted and summed to obtain an overall score for the set of18:56
kanzuresequences being designed. Sequence optimization proceeded by random descent to minimization of the overall score:18:56
kanzuresequence mutations were made randomly (subject to satisfying the structural constraints) and accepted if the score18:56
kanzurewas reduced. If the final sequences were unsatisfactory, the scoring weights were adjusted, new initial sequences were18:56
kanzurechosen, and optimization was attempted again.18:56
kanzureSounds like a GA to me.18:56
fennagreed18:57
kanzureOkay. I got most of the requirements for the simulation. I just need to go get ref 3, 5, and 6.18:58
kanzurehttp://heybryan.org/music/Yngwie%20Malmsteen%20-%20I%20Am%20a%20Viking.mp319:35
kanzureNow just the Seeman ref.19:35
kanzurewell21:46
kanzurethat was interesting21:46
kanzureWinfree offered me a spot.21:46
Day changed to 17 Mar 2008
kanzureHey.17:52
kanzureSo Winfree replied to my email and said that I should try looking for an analytical method of coming up with the RNA sequences. I have come up with the following formalization, I want 17:52
you to take a look at it.
kanzureIn any set N with 4^N different possible combinations, there are X specific "lonely RNA"s. In set N+1, the set X of specific "lonely RNAs" is not necessarily the new X subset of set N+1. 17:54
If there's a general pattern in **which** sequences are "lonely RNAs" per each iteration, then we can do it analytically.
kanzureI just got done unfolding 24 hand-written pages of notes (on my own ideas, not school stuff) from my pocket. They are all from the last month or so.19:22
fennhands-down keyboard, keep it in your pocket20:01
fennhttp://en.wikipedia.org/wiki/Image:Septambic_key_numbering.jpg20:03
kanzureKnow anything about NMR?20:23
fenni know how it works20:25
fennwikipedia is probably a better source of info though :)20:25
fennahh motherfucking irssi silently puts server notices like 'private messages are not allowed from unregistered users' into the server tab21:33
kanzureheh21:33
fennhttp://en.wikipedia.org/wiki/Image:Septambic_key_numbering.jpg keep it in your pocket21:33
kanzureForget my NMR question. I would need E308 molecules.21:33
kanzureThere's only E77 atoms in the universe.21:33
fennd'eaux21:34
kanzureI need to magically obtain a copy of matlab. Any suggestions?23:35
Day changed to 18 Mar 2008
fenniirc the demo is free00:41
fennthen there's the pirate bay00:42
kanzureindeed00:42
kanzurehttp://www.youtube.com/watch?v=vimz7sz9Fx4&feature=related Star One - Space Metal - High Moon.00:42
fennor you could use Octave or Scilab00:42
kanzureyep00:43
kanzureI'm looking into Scilab.00:43
kanzurehttp://shiriah.net/ayreon/Disc%201/07-Ayreon%20-%20Ride%20The%20Comet.mp301:18
kanzureFind your way home, little extremophiles 01:18
kanzureFind your way home, donors of life 01:18
kanzureYou're on your own, little extremophiles 01:18
kanzureYou're on your own, cleaving the skies 01:18
kanzure[Chorus]: 01:18
kanzureCarry out our dangerous task 01:18
kanzureSail uncharted spheres 01:18
kanzureLive out our dreams, ride the comet 01:18
kanzureJourney on the Migrator trail 01:18
kanzureCross the new frontiers 01:18
kanzurePass on our genes, ride the comet01:18
kanzurerelevant.01:18
fenna panspermian hymn?02:04
-!- kanzure: No such nick/channel02:04
-!- There is no such nick kanzure17:20
kanzureThere goes Arthur C. Clarke.18:49
Day changed to 19 Mar 2008
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-!- fenn [n=pz@adsl-76-251-87-108.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap16:11
[Users #hplusroadmap]16:11
[ Enki-2] [ epitron] [ fenn] [ kanzure] 16:11
-!- Irssi: #hplusroadmap: Total of 4 nicks [0 ops, 0 halfops, 0 voices, 4 normal]16:11
-!- Channel #hplusroadmap created Sat Mar 22 15:44:12 200816:11
-!- Irssi: Join to #hplusroadmap was synced in 28 secs16:12
kanzureHey fenn.17:04
kanzureYou get my email?17:04
fennyep17:06
kanzureI don't think it's much of a problem17:06
kanzurethat it's a Hamiltonian cycle17:06
kanzurebut it just goes to show this will require lots of number crunching17:06
fenni looked it up and it didnt mean much to me17:07
kanzureOh, well, it's Traveling Salesman problem.17:07
kanzureyou have a guy that wants to go travel a path and wants to optimize his route17:07
kanzureand hit up a few clients or whatever17:07
kanzurethere's an optimal path that gets all of the points17:07
kanzurebut this can't be solved in polynomial deterministic time or something17:07
kanzurehttp://en.wikipedia.org/wiki/Traveling_Salesman17:08
kanzureNP-hard ;)17:08
fenni hope the database isnt complex enough that it will take a computer very long17:08
kanzurethis depends on what we want to do17:09
kanzuredo we want to (1) hand-code all connections between packages?17:09
kanzureor (2) let the computer figure out possible connections between packages? We can program in "matter/energy converters" - since all mechanical energy can become chemical energy, etc.17:10
kanzure#1 means we will probably know it all so that we will know if something seems stupid17:10
kanzurebut by #1 we may miss stuff17:10
kanzureby #2 we get lots of bloat, longer search time, and maybe not a 'reduced' graph (although it will give us the general idea)17:10
fenn#2 seems very difficult17:11
kanzuremaybe not -- just code in modules for each type of variable to interact with each other17:11
fennnot impossible, but crikey, it's like the holy grail of automated engineering17:11
kanzurejust like in C++ where you have to define how the + operator interacts with other classes for a certain object17:11
kanzurehaha17:11
kanzureyes, I suppose that's true.17:11
fennnow i've had people say stuff like that to me all the time, and it doesnt necessarily mean anything17:12
kanzurethe holy grail stuff?17:12
fennafter all we have gigahertz computers with gigabytes of ram and terabytes of storage17:12
kanzurethat's true17:12
kanzureand not all of it has to be 'simulated' with physics and so on17:12
kanzureit's really just testing out how to put legos together17:12
fennand still using the same software from the 1980's for most CAD/CAE stuff17:12
kanzureit's like having a giant bucket of legos17:13
kanzurebut these legos don't all connect17:13
kanzurehrm, the lego analogy doesn't work I think17:13
kanzuresince they are not functional-legos17:13
fennits like trying to use your SCSI tape reader to play video on the VCR17:13
kanzurehah17:13
kanzureI don't think so. What happened to the dependency-loop ideas and so on ?17:14
fennand then record computer backup data onto a video tape17:14
fennwell the interesting thing about a dependencey loop is it's sort of a mini exponential growth without self replication17:15
kanzureOh, Wikipedia is correcting me. It's not a Hamiltonian cycle. Just a closed path.17:16
kanzurehm?17:16
fenn"i'm fat because i eat so much, i eat because i'm depressed, i'm depressed because i'm fat. it's a vicious cycle that took years to perfect." -garfield the cat17:16
kanzureclosed cycle, actually (cycle means path, except the path ends/begins at same vertice)17:16
kanzureI remember that one :)17:16
kanzureso, the only reason why we need skdb and the solver is really just because we can't come up with a 2-module system that makes itself, really. A sand-processor that makes a 17:18
glass-processor, and the glass-processor makes the sand processor (but this doesn't make sense).
kanzureand as you fill out the requirements, it is kind of like exponential growth17:18
kanzuresince the more you need, the more components you have to add17:18
kanzurethat's why I like starting with a part already -- an arm, say17:18
kanzureand then we add components to the arm until it is able to self-replicate17:18
fennalso i was thinking about symbiosis, where you have not one single point through which the loop passes, but more like several interconnected loops in parallel17:18
kanzurelike the character '8' ? 17:19
fennmore like a knitted headband17:19
kanzurelike oooooooooo17:19
kanzurehm17:19
kanzurexxxxxxxxxx ?17:19
kanzurebut those cross17:19
fennhttp://fennetic.net/pub/irc/directed_cyclic.png17:22
kanzurethat's hard to understand17:23
kanzurecould you color the cycles?17:23
fenna b c are the replicators17:23
kanzurethe entire design?17:23
fennalone they couldnt replicate17:24
kanzurewhy is there two sets of a, b, c ? Showing the replication?17:24
fennjust to connect the top and bottom17:24
kanzureI'm sort of thinking there should be more symmetry here17:25
kanzureThe requirements:17:27
kanzureA+B = C17:27
kanzureA + C = B17:27
kanzureB + C = A17:27
fennok reload. the green are new copies of the red ABC, but their position in the graph is identical17:27
fennthe purple is a leaf node, unrelated to replication (but requires b and c)17:28
kanzureB + C looks required for replication17:28
kanzurebut not the purple one, right17:28
kanzurearen't these supposed to be directed?17:29
fennyesmeh17:29
fenndia is a pain to use17:30
kanzurethis is dia?17:30
kanzurehaha17:30
fennno, that's kolourpaint17:30
kanzurehehe17:30
fenni added numbers17:32
fennyou might say that node 6 or node 7 is "the" replicator17:32
kanzureWhat about 5?17:33
fennhmm how do you show in graph theory that you must approach a vertex from two edges at the same time?17:35
kanzurethat's interesting17:35
kanzuredraw arrows with matching colors?17:35
kanzurelemme ask #math17:35
fenn7 should depend on 5 and 6 being present17:36
fenni added 9, which depends on 5 and 817:37
fenni'm sure this could be simplified17:38
kanzurea "required vertice" is interesting17:38
kanzurerequired vertices17:38
kanzureit's a functional graph, in a sense17:38
kanzureso you just have to say that "vertice X does not exist without vertice Y"17:38
fennwell, it might exist, but you can't get to it17:38
fennlike, i might have a lathe and bar-stock, but no cutting bits17:39
fennok poor example17:41
kanzuremaybe you need two graphs17:43
kanzureone for the dependencies and then one for the vertice dependencies17:44
kanzureor something like that17:44
fennearlier i was talking about different graphs for streams and packages (run-time and build-time, respectively)17:44
fennbut you can also have a package that makes packages17:45
fennor streams that spontaneously degrade into something17:45
kanzurehm17:49
kanzureso then you have to figure out a way to specify the extra requirements for the graph then17:50
fenngosh math is really useless sometimes18:02
kanzurereading up on Wikipedia?18:02
fenn"the sum of all the vertex-degree is equal to twice the number of edges"18:03
kanzurethe vertex-degree is something like the number of connections18:04
kanzureto a certain vertice18:04
fennyep18:04
fennsince a line connecting the vertices has two end points, there are 2*lines number of endpoints18:05
fennbig deal18:05
kanzurehaha18:06
kanzure=)18:06
kanzurefenn, what exactly are you looking into at the moment?18:20
fennstrange loops and graph theory18:28
kanzuremind pasting anything you find interesting ?18:31
fennIn 1974 the Consumer Product Safety Commission recalled 80,000 of its own lapel buttons promoting toy safety. The buttons had paint with too much lead, sharp edges, and clips that could be 18:35
broken off and swallowed.
kanzurehuh? for graph theory?18:37
kanzurehehe18:37
fennapparently irony is self-referential18:38
kanzuredidn't know?18:41
fennthis looks about right: http://www.graphviz.org/Gallery/directed/fsm.html19:09
kanzureneat.19:09
fenni really want something more interactive though19:11
kanzureto what extent?19:11
fennto be able to poke at the graph and rearrange it.. as if the vertices were connected by springs19:13
kanzureyes, I have wanted an interactive interface to graphviz for a while now19:14
kanzurethere's "freemind" out there on SF, it's sort of node-based but only for concept-maps, and it's all in java19:14
kanzureso it's kind of disgusting.19:14
fennsomeone i know wrote a java app that did springy networks (FEA - he's an engineer)19:16
fennthis should be pretty easy to write from scratch in whatever language19:16
kanzurefinite element analysis?19:18
kanzurehm19:18
kanzurebut hacking graphviz is not so easy, last I checked19:19
kanzurethey had lots of literature that you have to sort through, you need to have connections to get the papers19:19
kanzuremaybe I'm wrong, it's worth investigating19:19
fenni need to write a similar application for emc2 actually19:20
fenngraphical hal configurator19:20
fennthis is neat http://www.kylescholz.com/projects/speaking/tae2006/music.fm/19:25
kanzureooh19:28
kanzureit looks pretty close19:29
fennthe neat part is the search results are actually right19:30
fennyou can drag the names around if you select them19:33
fennThe main plastic we are using is polylactic acid. Anyone can make this by fermenting starch, so if you have a few tens of square meters of land to grow a starch crop you not only have a 19:38
self-reproducing machine, you have a self-reproducing source of feedstock independent of the petrochemical industry.
kanzurereprap?19:41
fennyes19:47
kanzurefenn: so what should the next steps be? any thoughts?21:29
kanzureI think we need to formalize your graph-definition and make a program to generate expandable graphviz files that follow the format21:29
fennfile format and parser21:34
fennneeds to be text based, human and machine readable21:35
fenni'm thinking about yaml or slip-xml21:35
kanzuremaybe we can write the parser in flex/bison to convert to graphviz format for the data visualization21:41
kanzureerm, I think I am cutting a few steps in the toolchain21:42
Enki-2just use flex alone21:43
Enki-2bison isn't needed if you know flex21:43
kanzureright, but the file format would not necessarily be what we want to see a graph of21:46
Enki-2i mean, flex can do translation of formats on its own, sans bison21:46
Enki-2i've done complete compilers in flex21:47
kanzurewoah, you're not fenn21:47
kanzurejust realized this :)21:47
Enki-2:P21:47
fenni dont know flex or bison, so i'm going to do a naive straightforward implementation :)22:18
kanzurebison is extremely easy22:19
kanzurehttp://dinosaur.compilertools.net/bison/bison_6.html22:19
kanzurehttp://www.gnu.org/software/bison/22:19
kanzurehttp://cs.wwc.edu/~aabyan/464/Book/22:19
kanzureThis one is really good - http://www.garshol.priv.no/download/text/bnf.html22:20
kanzureshort and to the point22:20
fennOT: just in the shower, thinking about cost of inventory space. A package's inventory complexity has to do with the number of unique items that need to be stored, their overall shape, and 22:20
the size. Each physical object can be given metrics based on its bounding shape (i.e. cube cylinder sheet rope sphere amorphous)
kanzureinventory could be external for simple designs22:20
fennthis cost comes out of human attention (our most precious commodity) unless there is an automated inventory system22:21
kanzureUh oh. News on http://utexas.edu/ (where I'm going next year) -- `BB&T gives $2 million for Ayn Rand researchPhilosophy Department to create new chair for study of novelist’s philosophy 22:21
of Objectivism.` Oh boy.
fenni take it that's bad?22:22
kanzureObjectivisim is a word-hijack22:22
kanzureit means lots of politics and capitalism22:22
kanzuregenerally not good philosophy22:22
fennwhat does politics and capitalism have to do with philosophy?22:22
kanzureAyn Rand :(22:22
fennoh, objectivism is at least slightly different from objectivity22:23
kanzurehttp://en.wikipedia.org/wiki/Objectivism_(Ayn_Rand)22:23
fennin terms of word structure22:23
kanzure` ... that the proper moral purpose of one's life is the pursuit of one's own happiness or "rational self-interest"; that the only social system consistent with this morality is full 22:23
respect for individual rights, embodied in pure, consensual laissez-faire capitalism; `
kanzurethe Proper Moral Response22:23
kanzure*Purpose22:23
fennif they can implement capitalism through a university philosophy department, more power to them :\22:24
kanzureheh22:24
fennas i see it, capitalism was demolished by corporations and the patent system22:24
fennor at least the prospect of it becoming a reality22:25
kanzurefenn: in general, I am not communist, I am not capitalist, I am not anything like that at all -- I think that these old 'socioeconomic philosophies' need to be dismantled and replaced 22:26
with a more intense, rigorous mathematical framework where we don't have bullshit "Social Contracts" etc.
fennhow can you have patents and call it capitalism? nonsense22:26
kanzurethese old ideas are *ancient*22:26
kanzuretechnological development is accelerating22:26
kanzureperhaps when we had a constant rate of development, capitalism/communism/Objectivism/Christianity/Republicanism worked, but the world just isn't the same22:26
kanzurethese are all old, stale ideas with a massive number of people still promoting them22:27
kanzureand while there are good ideas within,22:27
kanzurethe culture is still largely one of identification and not of ... importing the good ideas ;)22:27
fennindeed22:27
fennlet it be known i'm not a sports fan22:27
kanzurehah =)22:27
fenngot any opinion on this? http://www.debian.org/social_contract22:28
kanzureoh-my-god I have access to scientific databases22:29
fennyou mean journals?22:29
kanzureyes22:30
* kanzure hugs his UT login 22:30
fenngratz. got ieee spectrum access?22:30
kanzurefenn: Not anything off the top of my head.22:30
kanzurefenn: yes22:30
fennsweet22:30
kanzurefenn: I just opened up an article on pyroelectricity22:30
kanzurePiezoelectricity and Pyroelectricity in  Polymers22:31
kanzureFirst legally accessed, paywalled scientific paper22:31
kanzurethis should go in my baby book or something22:31
fenntoday is something special.. i forget22:32
kanzurethere was chocolate today22:32
kanzureso I'd venture a guess of easter22:32
fennaha22:32
fennright, we had jehova's witnesses22:33
fenn(not for dinner)22:33
fenninternational bunny day - day of the replicator!22:33
-!- fenn changed the topic of #hplusroadmap to: happy bunny day - day of the replicator!22:34
kanzureepitron: I'll be adding a 50 MB zip file to the server later tonight.22:36
kanzurewoot, nature!22:38
kanzureAmerican Physical Society !22:39
kanzurefenn: I want to write a script to browse through Google Scholar. Any thoughts? I want the input to be a list of papers, and an output to be a nice package of PDFs.22:54
kanzureGoogle does not provide a direct interface to a PDF for a title you enter: some of the links it returns may or may not be to a PDF.22:55
kanzureso in the cases where this does not happen, you can go through whatever journal website there is and click on a link that says "PDF"22:55
fennif (grep '<a href=".*\.pdf">'): wget $1; else ... ?22:59
fennnote that was pseudo-code22:59
kanzurenah, 23:02
kanzurethe url doesn't necessarily have .PDF in it23:02
kanzurebut you can scan for PDF next to the link23:02
kanzurethere's a way to process Google pages, they have a nice systematic format with div tags and so on23:02
kanzureI need to go look at the HTTP libraries to see if there's some way to log in with cookies to a service23:02
kanzureWWW:Mechanizer might be what I want.23:03
fennyou need to get those cookies though, which might not be straightforward with a non-browser interface23:03
kanzureooh23:04
kanzureWWW::Mechanize does something interesting though23:04
fennespecially since scientific publishers arent known for their browser compatibility23:04
kanzure use WWW::Mechanize;23:04
kanzure  use HTML::TokeParser;23:04
kanzure my $agent = WWW::Mechanize->new();23:04
kanzure  $agent->get("http://www.radiotimes.beeb.com/");23:04
kanzure  $agent->follow("My Diary");23:04
kanzure  $agent->field("email", $email);23:04
kanzure  $agent->click();23:04
kanzureso in other words it's like doing the physical actions23:04
kanzureexcept there's no browser UI23:04
kanzureOkay, first part done. Neat.23:10
kanzureHm, the rest is testing my knowledge of regexps. I want to extract the first link after <b>[PDF]</b>.23:19
fenn$agent->follow("[PDF]") right?23:20
kanzureif the name of the link was [PDF], yes23:21
kanzurebut PDF is not part of the link name23:21
kanzureit's just 'near' it23:21
fennunless you want to do something like ~= <b>\[PDF\]</b>.*<a href="(.*)">23:21
kanzureso I'm thinking of splitting up the string23:21
kanzureexploding it just before [PDF]23:21
kanzureand then after the next </a>23:21
fennoh, 'follow' means click on the link23:21
kanzureright23:21
kanzurewill your regexp work?23:22
kanzure$1 would be my url, right?23:22
fenn~= '<b>\[PDF\]</b>.*<a href="(.*)">(.*)</a>'  $1 is the url $2 is the link text23:22
kanzure<td valign=top><p class=g><span class="w"><font size=-2><b>[PDF]</b></font>&nbsp;<a href="http://www.stat.yale.edu/~jtc5/GeneticNetworksGroup/GibsonAndBruck2000.pdf" onmousedown="new 23:23
Image().src='/scholar_url?sa=T&url=http://www.stat.yale.edu/~jtc5/GeneticNetworksGroup/GibsonAndBruck2000.pdf';"><b>Efficient exact stochastic simulation </b>of <b>chemical systems
</b>with <b>many species </b>and <b>many channels</b></a></span> - <a
kanzure<b>Species</b> and <b>Many</b> <b>Channels</b> Michael A. Gibson* and Jehoshua <b>...</b> 23:23
kanzureanyway, it gets nasty23:23
kanzureso you can't assume it's <a href=""> precisely23:23
kanzurehm, it's kind of smart with the "on-mouse-down" function23:24
kanzurebut that's no problem - that's what the follow() idea is, no? :)23:24
kanzureor the "click" hehe23:24
fennit gives the url in the <a href="23:25
kanzureooh23:25
kanzureyes, but 23:25
kanzurelook at what they do, they have this:23:25
kanzure<a href="http://www.stat.yale.edu/~jtc5/GeneticNetworksGroup/GibsonAndBruck2000.pdf" onmousedown="new 23:25
Image().src='/scholar_url?sa=T&url=http://www.stat.yale.edu/~jtc5/GeneticNetworksGroup/GibsonAndBruck2000.pdf';">
fennyou want to ignore that? or what?23:25
kanzure<a href="xxx" onmousedown="xxx">23:26
kanzureerm23:26
kanzure<a href="xxx" onmousedown="yyy">23:26
kanzurewhere we want the xxx, and then after the yyy"> we can get the title23:26
fenn~= '<b>\[PDF\]</b>.*<a href="(.*)" onmousedown="(.*)"'  $1 is the url $2 is the onmousedown23:26
kanzuredo I have to say $var ~= ... ?23:27
-!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has quit [Read error: 104 (Connection reset by peer)]23:27
fenn$var should be the whole document i think23:27
kanzureah, right23:27
kanzureokay23:27
fenn~= loads all that crap into special variables23:27
fenndid i mention i hate perl? :)23:27
kanzurehehe23:28
fennoh joy they use single quotes in the url23:29
kanzurehm?23:31
-!- Enki-2 [n=weechat@c-71-234-190-248.hsd1.ct.comcast.net] has joined #hplusroadmap23:34
kanzure$searchresults ~= '<b>\[PDF\].*<a href="(.*)" onmousedown="(.*)">(.*)</a>';23:35
kanzureparse error23:35
kanzurehm23:36
fennah i knew it would be something stupid23:41
fenn=~ not ~=23:41
fennhttp://fennetic.net/pub/irc/test.pl23:43
kanzurehahaha23:49
kanzurethis is awesome23:49
fenni wish they would have used a different operator23:50
kanzureepitron, fenn -- Cosmic coincidences ;) http://heybryan.org/shots/2008-03-23_autoscholar.png23:51
fennwho is eugen?23:52
kanzureI've never talked about him?23:52
kanzurehttp://eugen.leitl.org/ see for yourself23:52
kanzurehe's also mentioned here - http://heybryan.org/stats/2008-03-23-extropy-chat.html23:52
kanzurehe's also mentioned on http://heybryan.org/mediawiki/index.php/Roadmap23:52
kanzurehttp://heybryan.org/mediawiki/index.php/Getting_up_to_speed too (I think)23:53
fennmore like synthetic serendipity ;)23:53
kanzureEugen Leitl is sort of a polymath.23:54
kanzureGood guy to know. 23:54
fennmany a time i've come across chat logs of me asking the same question i was googling for23:54
kanzureI was talking on a mailing list one day about how you should just "do the transhumanism thing and be done with it, ignore politics - once you transcend, they can't stop you." He replied 23:54
within 30 seconds and said "Yes, but now that they know what you are up to, they could stop you *now*." He and I have known each other ever since.
kanzuresame here23:54
fennwell, what do you do about that?23:55
kanzurehide23:55
kanzurebut I have been a moron and am already on the net23:55
kanzurein fact, there's a very significant portion of content generated by me on the net23:55
kanzureheh23:55
fennhm.. secrecy doesn't work23:55
kanzureright23:55
kanzureit seems that the best way to go about it is to just be open as much as possible23:56
fennbetter to make yourself indispensable23:56
fennand dont get involved in shady criminal activities as a hobby23:56
fennbecause then there's a reasonable excuse for your mysterious disappearance23:56
kanzuresecretly, I was a script kiddie when I was 1123:56
fennthere werent any scripts when i was 11 :(23:57
kanzureold fart23:57
fenni'm not that old (25)23:57
kanzureokay, so the script is mostly working 23:57
kanzureit gets the wrong URL though23:57
kanzureit gets the stuff after a href=" but then doesn't stop at the first "23:58
kanzure$searchresults =~ '<b>\[PDF\]</b>.*<a href="(.*)" onmousedown="(.*)">(.*)</a>';23:58
kanzureso I need those quotation marks to match exactly23:58
fennoh, probably greedy vs non-greedy matching23:58
kanzureshould I add /g to the end?23:59
kanzureor /ig ?23:59
fenng is global?23:59
kanzureoh23:59
kanzurehrm23:59
fenn(.*?) i think23:59
kanzureoh23:59
kanzureno,23:59
kanzure=~ m/stuff/;23:59
Day changed to 24 Mar 2008
fennnot following you00:00
kanzurenope, that didn't work00:00
kanzureyou're right00:01
kanzurewget --output-file is not useful00:03
kanzureit just routes the wget output to that file00:04
kanzurenot the downloaded file00:04
fenn--output-document00:05
kanzureAlright, neat. Now I need to figure out a way to fetch a document if there is no PDF available.00:06
kanzureSo, in the case where there is not a PDF available, there's usually a link that says "All $number versions >>" and then on the following page there's a list of possible places to get 00:08
it, where we can do the PDF-search thing again, *or* click on a link that says " Get this article" which takes the user to a page where there's a Javascript "Go" button to get the
fulltext from various databases (obviously, select the first one). But
fennBut (EOL)00:09
kanzureeh00:11
kanzureat this point it takes you to Nature, or some other database, and on that page the only thing you can hope to do is search for the link with a name including "PDF" and just get that URL.00:11
kanzurethis seems pretty simple in comparison00:11
kanzureif javascript execution works00:12
fenndoes WWW::Mechanise run javascript?00:12
kanzureasking #perl atm00:12
kanzureah, shit, no00:13
kanzurehttp://search.cpan.org/dist/WWW-Mechanize/lib/WWW/Mechanize/FAQ.pod00:13
fennI don't use JavaScript myself, so I don't have an itch to scratch. <- wtf does he use WWW::Mechanize for then?00:14
kanzurehahah00:16
fennread 'So what can I do?' - is the url in the html source somewhere? (even if its not standard)00:16
kanzureyes, I figured I'd have to do that anyway00:17
kanzureand it turns out it's pretty simple in this case00:17
kanzureit's just a form call hehe00:17
fennis it the same from publisher to publisher?00:17
kanzurehttp://p9003-www.lib.utexas.edu.ezproxy.lib.utexas.edu/sfx_local/cgi/core/sfxresolver.cgi?basic1&tmp_ctx_obj_id=1&service_id=110974981369254&request_id=4760844 <-- will redirect me to 00:18
the first "full text" available option ... but not directly to the PDF. And service_id and request_id have to be extracted from the page (they are hidden form fields)
fenni think 'socialized eng kdb' should be changed, because 'socialized' actually means something rather different00:23
fennsocio-economic system in which property and the distribution of wealth are subject to control by the community00:23
fennbut you mean, distributed development and distributed knowledge right?00:24
kanzureright00:24
kanzuresocialized knowledge as in, "social knowledge"00:24
kanzuresocial as in "community-known"00:24
kanzurebut I'm good for a change00:24
fennsocietal engineering knowledge db?00:27
kanzuresure00:27
kanzurehm, it turns out I need only search for either (1) PDFs or "Get this article" links on the Google Scholar search results page00:29
kanzuremy local "should be a programmer but isn't yet" buddy just sent me this: http://www.osnews.com/images/comics/wtfm.jpg00:31
kanzureBill: so like apt-get but for science journals00:33
kanzuresmart guy too00:33
fennheh. good for ui testing at least00:34
kanzureJava.swing :(00:35
kanzureI will never again use java swing00:35
kanzureever00:35
fennbut what about the cool sketch-on-a-napkin skin?00:36
kanzurehm?00:36
kanzurexkcd ref?00:36
fennhttp://napkinlaf.sourceforge.net/00:36
fenngood for a laf at least :)00:37
kanzurehar har00:38
kanzurefenn: does .* have to match anything? 01:00
fennplease restate the question in the form of an answer01:00
kanzurehm01:00
fenn.* means any character, any number of times01:00
kanzuresee, I want to now match for <a href="(.*?)"(.*?)>.*PDF.*</a>01:01
kanzureso that I get the URL to links that have 'PDF' in their name01:01
fenn</a> might belong to a url that is later in the file01:01
kanzurehrm01:01
kanzureokay01:01
kanzureso I guess I can do (.*?) still01:02
fennso i think the second .* should be .*?01:02
kanzure<a href="(.*?)"(.*?)>.*PDF.*?</a>01:02
fennyes01:02
kanzureI don't really need the second (.*?)01:02
kanzure<a href="(.*?)".*?>.*PDF.*?</a>01:02
fenn() just changes what gets stored in special variables01:02
kanzureright01:02
kanzureso I just need the href variable01:02
fenn(in this example)01:03
fennuh, it might be a bit late to mention that there are probably lots of xml or html parsing tools01:03
kanzureI was looking into them01:03
kanzurethe perl community is obsessed with LinkExtor01:04
kanzurebut it does not return the link name01:04
kanzureand for some reason I didn't think to go more generalized with XML01:04
fenni think you need ? on all the .*'s01:05
kanzureif () { /* stuff * / } else if  ($searchresults =~ /Get this article/) { } <--- parse error at } else if () { ........ wtf?01:08
fenn / get this article/ probably has a / in it somewhere01:10
fennyou can use other characters to bound the regexp01:10
kanzureah, it was something else entirely01:11
kanzurehow ridiculous01:14
fennhow Perl01:14
kanzuremy password, I have to pass it to wget with --proxy-pass01:14
kanzureand it has a bang in it01:14
kanzurefor some reason01:14
kanzureand this messes up bash01:14
kanzureapparently I can't escape it01:14
kanzurewith \!01:14
fenn!! i think01:14
kanzureugh01:14
fennno that's no it01:15
kanzurehm01:15
kanzureecho ! works though01:15
kanzureoh01:15
fennare you doing double quotes? try single01:15
kanzureah01:16
kanzurewget still says it is ambiguous though01:17
kanzurewget --proxy-pass=hi!01:17
fennwget --proxy-pass='hi!'01:17
kanzureright01:17
kanzureeven that01:17
fennit's --proxy-password01:18
kanzurebleh01:18
kanzureoh01:19
kanzureI just realized something01:19
kanzureGoogle pulls up numerous documents that are related to the title01:19
kanzureso you have to do *exact* title searches01:19
kanzureas in, intitle:"name"01:19
kanzurewhere "name" is the name of the article01:19
kanzureelse you will get PDFs from other things01:19
kanzurefenn: 01:41
kanzurehttp://search.cpan.org/dist/WWW-Mechanize/lib/WWW/Mechanize.pm#$mech->redirect_ok()01:41
kanzureyou think there's a way to figure out the 'current URL' that it is sitting at ?01:42
kanzureah, nevermind01:42
kanzurefenn: Here's my regexp, II$r3 =~ '<a.*?href="(.*?)">.*?PDF.*?</a>';01:57
kanzureand here's what I need to match: <a title="Download PDF" class="articlenav2" target="_top" href="/nature/journal/v347/n6293/pdf/347539a0.pdf">Download PDF</a>01:57
kanzurefor some reason, I am only getting back "/nature/" ...01:57
fenndunno02:16
fenn$1 = "/nature/" ?02:17
fennalso print $r3 and make sure it's what you expect02:19
kanzureof course02:20
kanzure#perl has convinced me to switch to LinkExtractor02:20
kanzurehttp://search.cpan.org/~podmaster/HTML-LinkExtractor-0.13/LinkExtractor.pm02:20
kanzurenow I'm figuring out how to access the _TEXT variable02:20
kanzureforeach my $x ($LX->links) { $x->_TEXT; } or something ...02:21
fennhuh. linkextractor just dumps you back in the same situation02:22
fennthere's no variable containing 'I am a LINK!!!'02:23
kanzure_TEXT is it.02:23
kanzureyou just have to strip out the HTML.02:23
fennthen why bother with linkextractor :)02:24
kanzureblah, #perl is telling me to go back to the newbie tutorials02:24
kanzureI just want to get the _TEXT variable :(02:24
kanzureI thought it might be $x{_TEXT} but that wasn't it either02:24
kanzureit's a hashref, I know that much02:25
fenn$LX->links{_TEXT}?02:26
fenn for my $Link( @{ $LX->links } ) {02:26
fenn    ## new modules are linked  by /author/NAME/Dist02:26
fenn        if( $$Link{href}=~ m{^\/author\/\w+} ) {02:26
fenn            print $$Link{_TEXT}."\n";02:26
fennchange author to PDF02:26
kanzurebleh02:27
kanzurewell, not quite02:27
kanzure$$Link{href} is assuming there's a pdf in the URL02:27
fenni forget how to get an element from an array02:27
fennoh, change href to _TEXT then02:28
fennand then print the href :)02:28
kanzureyep02:29
kanzurehm, there's a few other parts of the code I have to fix02:29
kanzurebecause nature.com is a bitch and provides relative links02:29
kanzurebut that's simple enough02:29
kanzurefenn: It works.02:52
kanzurefenn: Two things to make note of. (1) If Google does not provide a link to a PDF, then the name of the PDF has to be the search string you used. This gets kind of nasty. Maybe there's a 02:52
perl-PDF library that I can use that can extract the name of the paper. That would be really useful.
kanzure(2) Doesn't yet do a list of inputs, but this is easy.02:53
fennknow anything about webs of trust?03:02
fennis it possible to 'import' a web that's already existing? for example robots.net or advogato03:02
kanzuredon't know what you are talking about03:04
fennif software doesn't work it's no big deal03:04
fennbut say you have a big dependency tree leading up to some hardware project, that costs money and time and effort03:04
fennso you'd like to know in advance the trustworthiness of the author (in the field of the invention)03:05
fennthere exist already, open systems to gauge the amount of trust an individual has acquired03:06
kanzurehttp://heybryan.org/projects/autoscholar/03:06
fenni'd like to be able to jump-start the system by finding the small-world center nodes (people) and asking them to join, but that takes a lot of work03:07
fennand they wont necessarily contribute to our project and become center nodes03:07
fennso it'd be better if we could use the whole web of trust from elsewhere that already exists03:08
fennrather than trying to build community and trust all over again for every web site03:08
fenni get annoyed about having to make new logins all the time03:09
kanzurehave you heard of OpenID?03:09
fennnope03:10
* fenn looks03:11
kanzureoh shit03:14
kanzureyeah, that's a good thing to know about03:14
kanzurehttp://claimid.com/ is what I use03:14
kanzurebut there are others out there03:14
kanzureprobably a few that are more legit03:14
fennlawdy.. forget i said anything about trust networks mmkay03:29
fenn__is it ironic that roderick long is an "ayn rand" scholar? http://en.wikipedia.org/wiki/Social_contract#Implicit_social_contract_theory_presupposes_its_conclusion04:16
-!- Irssi: Starting query in freenode2 with kanzure18:02
kanzureHey18:02
kanzureThanks for that email, it reminded me to get into gear18:02
kanzurelet's make a database/repository for these projects, for "blackboxing" whole projects18:02
kanzurewe can begin by splitting up all sorts of projects into their units18:02
kanzureand each package will include (1) some specs on what it does, (2) some variables on what can be changed, (3) an output in some "fabricator-friendly" format, and (4) a simulator to plug 18:03
in to an overall program when you want to simulate your project
kanzurejust like in APT or CPAN, you cannot specify functionality, which is unfortunate, but something that we just have to get over18:03
kanzurealso, I will be gone in 15 minutes, so think fast ;)18:03
fennuh, hi18:16
fennhello18:16
fennwhat do you mean 'blackboxing'? like depends on other packages (rather than generic functionality)18:17
fennbased on my experience with python and hasattr(), specifying generic functionality is way cooler18:17
kanzurewhat?18:28
kanzureyou'll have to tell me about that later18:28
kanzurebut basically you can't search for functionality with APT or even Google18:28
kanzureyou have to search for tags18:28
kanzureor be able to talk with somebody who can give you a package name18:28
kanzurebbl18:28
kanzureHey18:54
fennin python if you pass an object to a function, it will run it, no questions asked. you can examine the object either by type (i.e. package name) or by its attributes. by attributes is much 18:56
more flexible and powerful
fennif it's the wrong type of object, you'll get someting like 'error: "car" has no attribute "horsepower"'18:59
fennwhen it tries to access car.horsepower19:00
kanzureyes, but you can't encode the actual functionality spec19:13
kanzurebbl19:13
kanzureWhat I was basically saying is that APT works out not because it has some super-awesome way of finding software, but rather it's a very well known database of software. We just need the 22:30
same for all sorts of other projects, with ways of managing different fileformats and specifying what a module contains, but not necessarily its entire specification, just enough to
allow somebody who has already found it to find it again.
kanzureThis seems to be the same thing as the intelligence problem. You can't really select for it, but if you see it appear, you know to run with it. I think the way Andy copes with this is 23:01
via artificial biochemistries ... he has added fake nucleic acids to what he calls "uncoli" (his variant of ecoli), which boosts the bacteria from 1/2000 chance of mutation to something
much higher, like 10% chance of mutation, which allows very rapid communi
Day changed to 21 Mar 2008
kanzurehey15:29
kanzureI found another "one of us" sort of guys15:29
kanzure'epitron' on freenode15:29
kanzurehe has a favorable condition where he has this giant gaping air pocket in his skull, suitable for a brain implant15:30
fennum, how did he figure that out?16:07
kanzureMRI.16:07
kanzuredeveloped during fetal stage16:07
kanzurehttp://chris.ill-logic.com/files/my_brain.zip16:08
kanzureheh, "Chris Gahan - PROBLEM SOLVER" mentioned on his web page16:08
fennmy mom knew a girl who was apparently completely normal except that her brain was just a thin smooth balloon 16:08
kanzureinteresting16:09
kanzurethere was an article about a man like that16:09
kanzurehe recently died, they investigated his brain, it was also a thin sliver16:09
kanzurehttp://chris.ill-logic.com/wiki/CurriculumVitae16:09
kanzurehe happens to do engineering psych16:10
kanzureso he's on the "self-modification" level16:10
kanzurewhereas I'd call you more self-replication ;)16:10
fennsure16:12
fenni have no tattoos16:12
kanzurewe need to figure out a way to make a "Getting up to speed" page16:12
kanzureor at least a way to list the guys "like us". I'd list you, myself, BioMors, Superkuh, enki-2, epitron, and a few others that I may be forgetting16:13
kanzureMaybe TheWOLPRO or endos127, but they seem to be too wrapped up in school to care16:13
fennsurely there are many others, we are just the ones on freenode16:13
kanzureright16:14
kanzurebut I bet there are many others who would be interested in contributing16:14
kanzureif they had, say, a map16:14
fenn1) define the problem. 2) solve the problem16:14
kanzurehttp://heybryan.org/mediawiki/index.php/Getting_up_to_speed <-- I am going to dump some notes here.16:14
fenni think solar concentrators can provide sufficient energy to do small scale foundry work16:16
kanzuregiant mirrors?16:16
fennsteel casting.. can't do that any other way except with huge amounts of electricity16:16
fennarrays of small mirrors16:17
kanzureTesla used to use the earth for electricity and so on16:17
kanzureit would be useful if we could do the same with giant asteroids16:17
fennwell, i dont know how to do that16:17
kanzureneither do I.16:17
kanzuregiant solar cell arrays may have to be the solution16:17
kanzuremany square kilometers16:17
kanzurenot a big deal, IMO, if you have self-replication16:18
fennoh, actually i'm wrong, you can melt steel with an oxygen concentrator16:18
kanzureunless that needs steel foundry16:18
kanzureoh, good16:18
fenni was reading this and thinking about how to do it with a 'fresnel mirror' for both mirrors http://kmr.nada.kth.se/wiki/Main/PointFocus16:18
kanzure*.kth.se is good16:19
kanzurehttp://www.nada.kth.se/~asa/ <-- Anders Sandberg.16:19
fenninteresting16:19
kanzurehe used to run the Omega Point Society in Sweden.16:19
fennthe guy who wrote that paper is now head of the department(?) and doing research on "the semantic web"16:19
kanzureAnders is a good guy to get on board, he does lots of free form fabrication stuff too16:20
kanzureand used to do lots of TransVision conferences16:20
kanzuresaw him last week in Second Life.16:20
kanzurehm17:25
kanzurehttp://wiki.ill-logic.com/AugmentationNotAutomation17:25
fennagreed, but why the title "Augmentation Not Automation"?17:45
kanzureautomation is subset of augmentation17:56
fennhuh. "learning depends on social interaction" is quite true but i had never noticed18:13
kanzureyeah19:00
kanzurewhich sucks19:00
kanzureI would desperately like to prove otherwise19:00
fennperhaps you could substitute randomness (weighted with a model of your interests of course)19:01
fennbut that's television19:02
kanzurehad to bring epitron up to speed http://heybryan.org/chats/epitron-2008-03-21.html20:01
kanzurehttp://heybryan.org/shots/img_8032.jpg21:19
kanzurehm, http://knome.org/ as a 23andme/decodeme clone22:27
kanzureFound this hidden on my site -- http://heybryan.org/creating_communities.html how to make communities 23:09
fennyep that's why i mistakenly thought you were 2223:13
kanzurehm? how's that?23:13
fennscroll down to Throwaway identities23:14
kanzureooh23:14
kanzurenote the quotes23:14
fenni dont like how a lot of those are essentially advocating spamming23:15
kanzure:(23:15
kanzureit's kind of weird, though, because it kind of worked for me: I published an email announcing my biohacking kit, and I had to spread it *myself*23:16
kanzureI had to go push it on to the news websites23:16
kanzureI had to push it to Make, to hackaday, etc., 23:16
kanzurethe only way to not have to push is to go through AP and they do 'serious' stuff (supposedly)23:16
fennsure23:16
fennHypermarketer website/tool- automated emails, rss feeds with "updates" on the outbreak, spam email from botnet, multiple fake accounts on all of the popular social networking or "web 2.0" 23:17
sites, mediablitz, all within one hour, with continued postings throughout the internet to *take over* the smaller blogs if necessary. Goal: no trail to an original, single source. To
really fool anybody who might be catching on, have multiple emails across the botnet submitted at the same moment with clocks in synch.
fennis that really something you want to be associated with?23:17
kanzurenot really23:17
fennanyway it starts out good23:18
kanzureI was just doing note taking, mind you23:18
kanzureplus some brain storming ;)23:18
fenna lot of people put basically zero effort into publicizing themselves though, understandably23:18
kanzureoh, by the way23:19
kanzureI have a question23:19
fennnobody ever said 'in moderation' was easy23:19
kanzurelet's say that by some miracle I have figured out a way to hack DNA replication and can make ssDNA while inside a cell23:19
kanzureand I know that the cell will degrade it immediately23:19
kanzurehowever,23:19
kanzuredo you know of any 'molecular chaperones' that could bring it to the plasma membrane and push it through?23:19
fennnot DNA but there are lots of them for RNA23:19
fennwhy would you want to make ss DNA?23:20
kanzuressDNA does logic gates23:20
kanzureRNA logic gates are infeasible (apparently)23:20
fennuh, i thought you needed dsDNA for your scheme23:20
kanzureI have a plasma-membrane-bound SSBP 23:20
kanzureI thought it was ssDNA23:20
kanzurehttp://heybryan.org/winfree.html23:21
kanzureyeah, ssDNA23:21
kanzureanyway, I have a SSBP that I can express on the outer surface23:21
fennno, pretty sure the rna gets transcribed by regular RNA polymerase (which uses ds DNA)23:21
kanzurewhich will bind to the ssDNA23:21
kanzureoh23:22
kanzureokay, so a dsDNA template is used for the switch itself23:22
kanzureand then ssDNA for the activator for completing the promoter region or something23:22
kanzureanyway, dsDNA then.23:22
fennyou want to truck ds DNA around? probably easier in a bacterial cell23:23
fennthey do that sort of thing for 'mating'23:23
kanzureyepo23:23
kanzure*yep23:23
kanzureso that's what I am figuring.23:23
kanzureI just need a dsDNA chaperone molecule to truck it to the membrane and then bind it to it (SSBP-- this is used in bacterial transformation apparently, as part of competence)23:24
kanzureI want to encode the dsDNA logic gate strands into the genome, but that's another story -- I actually want the nucleotides to encode *which* logic to use for each gate, then have another 23:25
part come in and swap in the actual gate (AND, OR, NOR, XOR, ...) while conserving the number of used gates (for various technicalities)
kanzurethis is all so that I can evolve logic that has some 'emergent' property23:26
kanzuresince I can't come up with anything for Andy. heh'23:26
fennso this would be like 'programmable' logic gates?23:26
kanzureyes, I suppose that's true23:27
kanzureis that how an FPGA works?23:27
kanzurehaving a conserved number of gates, but you get to choose the pathways between them or something?23:27
fennan fpga has a memory element that controls the function of the gate (and, or, etc)23:27
fennyou are very limited in choosing what gate connects to what other gates23:27
fennits more like a grid than a brain23:28
kanzureah, so this is almost the same thing23:28
kanzureexcept the memory is on the genome23:29
kanzurewait, same thing23:29
kanzureI am sure of it.23:29
fenn"have another part come in and swap in the actual gate" could you elaborate on what 'another part is' and how to 'swap in' the gate function?23:29
fennlike the DNA is the compressed version of the gate, and something comes along and rewrites the DNA macro?23:30
fennexpands the macro23:30
fenndo you know about introns and exons?23:31
kanzuresomewhat, not enough23:35
kanzureas for the elaboration: Andy's lab has done this with nucleic acids. He has evolved unnatural amino acids and nucleic acids, plus the enzymes required for DNA replication with those new 23:37
units; so if you have an encoding representing AND, OR, NOT, then instead of the amino acid you have the dsDNA come up. The dsDNA can be made by replicating a portion of the DNA molecule
that specifies how to make the gates. (eof)
fennyou cant make DNA with a ribosome though?23:40
kanzuredon't know23:40
kanzurethat would be useful23:40
fennyou could do lots of splicing with mRNA using introns/exons and then reverse-transcriptase it back to DNA23:40
kanzuresplicing inside of the cell?23:41
fennyes23:41
fenndna-splicing tools are generally implements of war23:41
kanzurehrm23:41
fennnot something a cell would do in the course of everyday housekeeping23:41
fenni think it's funny that people call bacteria 'species'23:47
Day changed to 22 Mar 2008
kanzurehttp://en.wikibooks.org/wiki/Circuit_Idea/How_do_We_Create_Sinusoidal_Oscillations%3F <-- somebody has put a lot of work into this article00:22
fenni wonder who00:24
fennwiki's are cool but i dont see any reason behind doing a lot of work and not putting your name on it somewhere00:25
kanzurehttp://en.wikibooks.org/wiki/Circuit_Idea00:26
kanzurethis entire book is peculiar00:26
kanzureit's right on00:26
kanzureall about the social knowledge of electronic circuits00:26
fenni'm glad something is working. the old electronics collaborative book was festering00:28
kanzurehere's the guy's website00:28
kanzurehttp://www.circuit-fantasia.com/00:28
kanzurehttp://www.circuit-fantasia.com/circuit_stories/inventing_circuits/inventing_list_of_circuits.htm lots of content00:29
fenn*shudder*00:29
fennmake it stop!00:29
fennblack boxing = hiding : http://en.wikibooks.org/wiki/Circuit_Idea/Why_Circuit_Ideas_are_Hidden01:19
-!- kanzure: No such nick/channel01:19
-!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com]01:19
-!- was : purple01:19
-!- server : irc.freenode.net [Sat Mar 22 04:33:19 2008]01:19
-!- End of WHOWAS01:19
kanzurehttp://heybryan.org/mediawiki/index.php/Socialized_engineering_knowledge_database12:57
kanzureif you'd like to drop some notes.12:57
kanzurehuh, I think you are, in fact, the bottleneck - http://heybryan.org/mediawiki/index.php/Getting_up_to_speed13:22
kanzurealso, I noted your recent-changes on your wiki and will want to talk about amorphous fabrication + cells later, I am pretty sure cells are not the replicators that we need since they 13:23
can't specifically manufacture in "solid-state" sense
kanzurealthough ultimately since we are biological, and we have constructed these machines, we know that it should be possible to make more biological systems to produce such machines as the 13:24
ones we see before us,
kanzurebut that's pretty hard in general, since it required extensive training of the humans13:24
fennhttp://en.wikibooks.org/wiki/Circuit_Idea/Why_Circuit_Ideas_are_Hidden  <- every time you say 'blackboxing' i think of this14:17
fenni want open source hardware, and more than that, open knowledge14:17
kanzureright14:17
kanzureblackboxing just means "for now, we avoid this component and act like we know what it is"14:18
kanzureand in many cases, the ideas are hidden to make the box/circuit14:18
kanzurealthough hopefully we can change that14:18
fenncould we call it 'scrounging' or 'outsourcing' instead?14:18
kanzuresure14:18
kanzurehttp://heybryan.org/mediawiki/index.php/Blackbox14:19
kanzuredone14:19
fennhextatic is actually aimed more at empowerment of the individual than turning into a swarm of self-replicators14:21
fennit just happens that i can't think of a better starting point for a self replicator14:21
kanzurewe need to do a mega outline brain storming session for what is needed to make a self-replicator, once and for all14:23
fennmaybe it would be better to call it 'environment modification'14:23
kanzurehow's that?14:23
fennbecause the goal of having a self-replicator is to do stuff with it14:23
fennlike make a floating sky palace or whatever14:23
fennafter all, it's not me that's replicating. i can do that already, just need to find a suitable female14:24
fennand/or sheep and biotech lab :P14:25
kanzureright14:25
kanzureso I see what you mean14:26
kanzurea tool to help extend the environments in which we (as von Neumann replicators already) can work in14:26
kanzureor to help increase the number of environments in which we can setup and install ourselves14:26
fennyes14:27
kanzureit is interesting that even though we are biological, we have somehow been able to do solid state devices, even though our biology is quite 'fuzzy'14:27
kanzureso that gives hope that we can do fuzzy biological systems that will make solid state devices 14:27
kanzureunless we want to do a self-replicator without an internal dependency on biology14:27
fenni want to do a self-replicator without an internal dependence on biology14:28
fennthe dna tile thing was just a clever shortcut14:28
kanzurehrm14:28
fenni didn't anticipate it14:28
fennthe idea was 'computers are the most complex thing out there, so if we can make one of them, we can make anything'14:28
fennturns out that's not true14:28
kanzureif you do want to do it without biology, then what's with your "environment modification"-tool ?14:29
fenni'm a selfish greedy gene14:29
fennand so are the other 7 billion humans14:29
fennif i want their help, it has to be relevant for them too14:30
fennotherwise you have stuff like the artist christo - decorating islands in pink plastic14:30
fennhttp://www.christojeanneclaude.net/si.shtml14:31
fennalso i feel like using biology is cheating. you dont really truely understand how it works until you've made it from scratch14:32
kanzureso my previous method of getting started on a von neumann probe project is (in my opinion) still working pretty well: I defined what was needed and then was going to work backwards 14:32
("Humans would need these resources")
kanzureso let's do that same thing but without the biological component14:32
kanzureand since this opens up too many doors at the same time14:33
kanzurelet's add in some constraints, namely mineral constraints14:33
kanzurelet's go find out what asteroids commonly have in them, and then figure out a way to do self-replication with the processing of those materials14:33
fennlet's not add artificial constraints14:33
kanzurethen we'd have to have an "everything fabricator" and an "everything tool"14:33
fennthere will be multiple ways to do it, why start with asteroids when we are on earth?14:33
kanzurewell, I just mean to propose that scenario14:34
kanzurewhere resources are obviously limited14:34
kanzureand you don't have to make a tool to process every possible mineral14:34
fennthere are asteroids full of nickel and platinum.. the resources aren't limited they're just different14:34
fenni think we should try to make use of glass because the stuff is everywhere14:35
fennand ceramics14:35
kanzurebut didn't you just say you didn't want to constrain the possibilities? ;)14:36
fenni'm advocating their use, not saying everything else is off limits14:36
fennperhaps it's possible to make silicone rubber from raw minerals?14:38
kanzuresure, it would have to be14:38
fenni mean easily, without an army of chemists and refineries :)14:38
fennwe have to do it first by hand before programming the machine to do it14:39
kanzurecorrect14:42
kanzurewhat would silicone rubber be used for?14:42
kanzureand what other resources would you be considering for inclusion ?14:42
fenninsulation, gaskets and seals, lubrication14:42
fenni'm also thinking about aluminum14:43
kanzurewhat is the fabricator of this design?14:43
fenndo you notice a common theme? (i do)14:43
kanzuresort of, looks mechanical or vacuum-tube based14:43
fennwell, maybe. but it all comes from clay-like and sandy soil14:43
fennclay is aluminum magnesium silicate14:45
fennaluminum would be much more 'expensive' to manufacture because it requires hydrochloric acid (and where do you get the chlorine?)14:46
kanzurelet's wiki it14:46
kanzurehttp://heybryan.org/mediawiki/index.php/Clay-sand-soil_replicator14:46
kanzureI just jotted down some notes14:47
kanzurelet's do something like this14:51
kanzurehttp://en.wikipedia.org/wiki/Image:Advanced_Automation_for_Space_Missions_figure_5-29.gif14:51
kanzurethis is the one where arms pick up parts from a shelf14:51
kanzureand then assemble the parts into the replicator14:51
fennyeah looks really advanced ~~14:52
kanzurethen we can add functionality where the arms can retrieve the parts or store the parts onboard14:52
kanzurewhere the 'parts' are really just material resources14:52
fennoh, as an experimental phase? instead of actually digging dirt you just give it glass and clay?14:53
kanzureso if we have a 'number of parts' we can then go back and jot down all required machinery to make that particular part (to process the raw mineral-resources), and then if we want to do 14:53
good then we have to optimize all of that machinery to use the same resources and be made from the same arm-manipulator
kanzureyeah14:53
kanzureeventually we should just give it input such as a bucket of sand14:54
kanzureand then further down the road we make it walk outside and search for the bucket of sand14:54
kanzure(or whatever would be a good debug-test for searching for raw minerals)14:54
fenni find myself reluctant to add carbon to the list for some reason15:05
fenni think this is too complicated to do on a wiki15:05
kanzurecan it be done on paper?15:06
fennthere are lots of interconnections, and at different levels15:06
kanzurehere are my notes on the "contractionary design approach" - http://heybryan.org/mediawiki/index.php/Self-replication#The_.22contractory_phase.22_design_approach15:06
kanzureyeah15:06
fennmaybe it needs a whole namespace instead of just a page15:06
fennwhy disassembly? i dont think it's necessary for self replication, just makes for a more efficient ecology15:12
kanzureno, dissassembly for *designing* it15:12
kanzurethe actual machine need not be able to dissassemble itself15:12
fennin Hierarchy of self-reppers15:13
kanzureah, I was thinking about how cells seem to be self-destructive when they replicate15:14
kanzuresome species breed and then just die afterwards15:14
kanzurethey expend lots of energy in the process and sometimes cut their resources in half15:15
kanzurewhich is something that can't be fixed, in general, unless they go get more resources etc.15:15
fennwasteful15:15
fenni read about an alien bacterial life form (possibly fictional?) that replicated by building miniature copies inside of the cell, when then burst open15:17
fenni can see the sense in that15:17
fennbut afaik all earthian animals can lay eggs/do mitosis15:17
fennspores, seeds, rhizomes15:18
kanzureisn't there some insect that lays eggs inside her body and is eaten from the inside out for the larvae to survive?15:18
fennnot that i know of, but i'd be interested if you have a link15:18
fennping15:25
fenni've not heard of this insect15:25
fennno i've not heard of this insect15:26
kanzuregah15:27
kanzurehttp://69.180.166.50/old/_/files/operaessions_0.jpg15:27
kanzureSuperkuh gets kinda extreme.15:27
kanzureso from the look of the http://heybryan.org/mediawiki/index.php/Clay-sand-soil_replicator page it looks like you're going in the opposite direction that I was proposing (which isn't bad, 15:41
I'm just observing)
kanzureparticularly, you're starting with basic minerals and then specifying what can be made from them15:41
kanzureand then I guess you're just hoping that you started with the right mix of minerals to make machinery that can use all of them ?15:41
kanzure./join #hplusroadmap15:44
kanzureI didn't mean to pull you away from work, I thought epitron was solid16:00
fennhah16:01
fennyou thought i was solid? :)16:02
kanzurewhat?16:02
kanzurewell sure, you seem to have enough background to be able to make yourself do work16:02
-!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com]16:23
-!- ircname : purple16:23
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fenna shill?16:23
kanzurehm?16:24
fennpurple :)16:24
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-!- Topic for #hplusroadmap: happy bunny day - day of the replicator!17:50
-!- Topic set by fenn [] [Sun Mar 23 22:34:25 2008]17:50
[Users #hplusroadmap]17:50
[ Enki-2] [ epitron] [ fenn] [ kanzure] 17:50
-!- Irssi: #hplusroadmap: Total of 4 nicks [0 ops, 0 halfops, 0 voices, 4 normal]17:50
-!- Channel #hplusroadmap created Sat Mar 22 15:44:12 200817:50
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fennmeep17:51
kanzurebeep17:53
fennkanzure: have you seen n55? http://www.n55.dk/MANUALS/Manuals.html17:57
kanzureNo, hold on17:58
kanzurefenn: I just found out about this: http://wiki.workatjelly.com/Jelly-Austin-March-25-200817:58
kanzureI think I'll go.17:58
fennconstructive work in a bar? yeah, sure17:59
fennare you going to sneak in? :)18:00
kanzureoh, a bar18:09
kanzureshit18:09
kanzurefenn: I don't get n5518:10
fennit's a technology distribution18:10
kanzureis it?18:10
kanzureit looks like a recursive self-defining manual18:10
fennaimed at the functionality required for living as a human on earth18:10
kanzurehm18:11
fennit's also an art project, which helps in some ways and hurts in others18:11
fenni wish FACTORY was capable of making those damn plastic octahedron tanks18:13
fennapparently it's a lot easier to get them made in denmark18:14
-!- fenn_ [n=pz@adsl-76-251-87-49.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap20:08
-!- Topic for #hplusroadmap: happy bunny day - day of the replicator!20:08
-!- Topic set by fenn [] [Sun Mar 23 22:34:25 2008]20:08
[Users #hplusroadmap]20:08
[ Enki-2] [ epitron] [ fenn] [ fenn_] [ kanzure] 20:08
-!- Irssi: #hplusroadmap: Total of 5 nicks [0 ops, 0 halfops, 0 voices, 5 normal]20:08
-!- Channel #hplusroadmap created Sat Mar 22 15:44:12 200820:08
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