2010-06-24.log

--- Day changed Thu Jun 24 2010
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fennwah wah wah.. linux isnt linux.. whatever. what i meant was it's a general purpose thing that runs on any gadget that you can make do whatever you want within the actual hardware capabilities of the gadget00:20
uniqanomaly_"Supported platformsIA-32, MIPS, x86-64, SPARC, DEC Alpha, Itanium, PowerPC, ARM, m68k, PA-RISC, s390, SuperH, M32R and more"00:27
uniqanomaly_you mean which linux00:27
uniqanomaly_lol00:31
fennthat was my point, that it's the same linux on various architectures00:54
fennsee, i started first with the idea that you should be able to do whatever you want with some piece of hardware, but it's hard to learn the specifics of the device, so we should have some kind of abstraction layer that still provides full control if you need it.. then i realized that this is basically what linux does00:57
fennbut an ASIC can't do anything but what it was intended to do00:58
fennvs say a SIMD processor00:58
uniqanomaly_i'd say 'the same linux on various architectures' is rather advantage 01:10
jrayhawkOnce again, an ASIC is like a program that you write directly to hardware. No operating system needed.01:15
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kanzureFile Formats, Compatibility, and Open Source http://forums.reprap.org/read.php?1,49824,4985906:03
kanzure`Why do I need to buy a $4,000 CAD program to read "open-source" RepRap related blueprints? `06:03
kanzure`Please also consider that in many parts of the world $4,000 is more than a yearly wage. On one hand, RepRap is advertised as being "Wealth Without Money" and on the other hand you need $4,000 in order to obtain information on how to create "Wealth Without Money." `06:03
kanzurekive: i didn't see your pm until now. sorry. i thought you'd reply in here. oops :)06:03
kanzureok. replies sent.06:05
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pmetzgermorning06:46
kanzuremorning good sir!06:48
kanzurehow goes the world domination invasion force for nyc?06:48
JayDuggerGood morning, all.06:51
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pmetzgerAh, world domination. That's so yesterday. Now we're talking about multiverse domination.07:12
kanzurefenn: did we ever figure out wtf is wrong with 'patrick anderson'?07:21
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kanzurehahah07:30
kanzureso the people on the opencascade forums have asked for release dates07:31
kanzurehttp://www.opencascade.org/org/forum/thread_18818/07:31
kanzureand so someone at opencascade responds:07:31
kanzure"Hello Community, Thank You for your timed inputs."07:31
kanzurequite telling how they think of The Community07:31
kanzure"Hello Community.."07:31
pmetzgertimed?07:32
pmetzgerthey said timed?07:32
* kanzure nods07:33
* drazak eyerolls07:33
pmetzgerhahahaha07:33
pmetzgerhow fast were the inputs if they were timing them? :)07:34
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genehackerkanzure you really shouldn't hate .stl07:51
genehackerit's not that bad after all07:51
genehackerseriously why are meshes that bad?07:51
kanzureit's like sending aroud compiled code07:53
kanzure*around07:53
genehackeryeah, so?07:54
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kanzuregenehacker: load up an STL file into solidworks and remove a chamfer08:18
genehackerok08:18
genehackerdone08:18
kanzurewtf08:18
kanzureuh, i don't think that's possible, genehacker 08:18
genehackerok good point08:19
genehackerbut really it shouldn't be too hard to do that too a mesh08:19
genehacker*to08:19
kanzurebut wouldn't it just be easier if people just gave you CAD data?08:20
genehackerwell it'd be damn nice if there was a CAD format out there that would preserve smart dimensions on export08:20
kanzureSTEP has the capability to do that08:21
genehackerit does?08:21
kanzureyes, but i don't think solidworks supports that feature :(08:21
kanzureit's really weird!08:21
genehackerhas someone found a way to generate step code08:21
genehackerfuckers08:21
kanzureyeah, i've been working on something for the past two days now08:22
kanzureit's pretty much working (almost)08:22
genehackerwith smart dimensions?08:22
genehackerREALLY?08:22
kanzurei have an "export a sphere" demo08:22
kanzureno not with smart dimensions (not yet)08:22
kanzurebut it's going to be open source, so someone else (or me) can later add it in08:22
genehacker:(08:22
pmetzgerwhat are smart dimensions?08:22
kanzureho ho ho08:22
* pmetzger is not a mech e type.08:22
kanzureyou'll like this08:22
genehackersmart dimensions are the best thing ever08:22
kanzuregenehacker: where is the carnegie mellon kinematics library thing08:22
genehackerthere dimensions that get this: you can resize!08:23
genehackercarnegie mellon don't you mean cornell?08:23
kanzurepmetzger: it's basically constraints + graph theory applied to an assembly and design elements (like fundamental primitives and CSG elements)08:23
kanzuregenehacker: yes i probably mean cornell08:23
genehackerexcept in practice it sucks08:23
genehackerit'08:23
kanzurehttp://kmoddl.library.cornell.edu/08:23
genehackerit doesn't work when you have dimensions as the function of other dimensions08:24
kanzuregenehacker: pmetzger wants some mechanical linkage, gears, cams stuff08:24
pmetzgerso the notion is that a set of parts are set up so that if one is resized the others alter to suit?08:24
genehackeror maybe I'm doing something wrong08:24
kanzuregenehacker: i think we could do sympy to do functions of other dimensions.. that's definitely possible08:24
pmetzgergenehacker: are there any intro mech e texts that explain all that stuff?08:24
genehackerno, just 5 minutes playing around with CAD software08:25
kanzureyeah :)08:25
genehackeranyway you want a linkage?08:25
kanzuredownload a copy of solidworks08:25
kanzure(or ask me)08:25
genehackerdon't pirate solidworks, that's bad, plus solidworks has super lawyers08:26
kanzurei think torrents are a part of solidworks marketing strategy08:26
genehackernope that's autocad08:26
genehackeryou're confusing them08:26
kanzurebecause when the new kids show up to a company, they'll have to purchase a license08:26
kanzureoh08:26
kanzurehrm08:26
genehackerthough if you can prove that solidworks is distributing software via torrents you will make my day08:27
pmetzgerah, solidworks does simulation of mechanical parts. as I expected...08:27
genehackeranyway pmetzger, you said you want a mechanical linkage?08:27
pmetzgerno. I want to learn about them.08:28
pmetzgerI want to learn about all such things, and I can't find textbooks.08:28
genehackerhmmm...08:28
pmetzgerI can only find books on mechanical designs from the 19th century, which really isn't what I wanted. :)08:28
genehackerlet's see here08:28
kanzuretextbooks aren't the way to learn mechanical engineering, unless you want to do math on kinematics and such :)08:28
genehackerthose are what you want08:28
kanzureyou should hang out in a machine shop for a few months08:28
genehackershoot we didn't cover linkages that much08:29
kanzuregenehacker: he wants something like campbell's class, i think08:29
kanzurewhat was the book campbell was using?08:29
genehackerit doesn't cover linkages08:29
genehackeror that much atleast08:29
kanzureyeah but it covers a lot of other things that pmetzger wants08:29
genehackerlike what?08:30
genehackerdesigning bolts to last long, figuring out how long a bearing will last, the involute gear profile?08:30
pmetzgerall sorts of things like that would be of interest.08:30
kanzuregears, linkages, cams, bolts, servos, steppers, ..08:30
genehackerlinkages are in a mechanisms book08:31
genehackerok well I'll look up my book later08:31
pmetzgermy interest is this: long term, I want to be designing mechanical nanomachines, but I have no mech e background.08:31
pmetzgerso I want to develop a mech e background.08:31
pmetzgerI've actually set myself some weird projects to try to get myself some field experience, like building a mechanical clock.08:31
genehackerok08:32
pmetzgerthough I'd prefer to learn by reading what others can tell me so I don't have to re-discover the wheel.08:32
genehackerI think I've got a book/class you might be interested in08:32
pmetzgerthis is a very long term project for me, I expect I won't need to understand this stuff for a few years.08:32
genehackerit's called the FUNdamentals of design08:32
pmetzgerchange "very" to just long term, a few years isn't that far...08:32
pmetzgerbut you get what I mean...08:32
genehackerand I'm trying to learn some of the stuff in it08:32
pmetzgerlink to book?08:33
genehackerfinding it08:33
genehackerhttp://dev.forums.reprap.org/read.php?1,3137108:34
genehackerok so nanomachines are probably going to be a bit different than macromachines08:35
genehackerI'm wondering if one can even apply the bar bending formulas reliably to nanosized diamond bars?08:36
pmetzgerthat is discussed in chapter 2 of nanosystems.08:36
pmetzger(see my mantra.)08:36
genehackerhmmm...08:37
genehackerso this mechanical engineering education of mine actually might be useful?08:38
genehacker*useful as defined as doing ground breaking stuff08:39
pmetzgerthere is a newer version of that book than the one linked there08:39
pmetzgersee: http://stellar.mit.edu/S/course/2/sp09/2.007/materials.html08:39
genehackeranyway I think you should look more into kinematics and mechanisms08:40
pmetzgerhttp://stellar.mit.edu/S/course/2/sp09/2.007/courseMaterial/topics/topic4/studyMaterial/FUNdaMENTALs_Book_zipped/FUNdaMENTALs_Book_zipped.zip08:40
pmetzgerprobably.08:40
genehackerit might be worth developing a unique approach to solving nanoscale solids problems08:40
pmetzgeranyway, a big section of nanosystems is on scaling laws at the nanoscale.08:40
pmetzgermany laws fail utterly, some continue to work.08:40
pmetzgersome unexpected things happen, like lubrication is not an issue.08:40
genehackeryeah but you still have friction which generates heat and saps away power08:41
genehackerand due to high surface area volume ratios friction can become quite troublesome08:41
genehackerdoesn't it?08:41
genehackersome of the power requirements for nanofactories I've read about were pretty high08:42
genehackeranyway as far learning ME, I'd suggest reading about some statics and dynamics08:43
pmetzgerfriction is different at this scale.08:45
pmetzgervery different.08:45
pmetzgerit is true that you don't get lossless rotation or what have you, that's impossible...08:45
pmetzgerand you do turn energy input into systems into phonons, i.e. heat in the end.08:45
genehackerthe basics of statics you can essentially learn in about an hour, much of the rest is specialized approaches to solving problems without a lot of effort(IE, designing a truss structure and not spending years doing it)08:45
pmetzgerbut it actually is rather different than at the macroscale.08:45
genehackerwhat do you mean no lossless rotation?08:46
pmetzgergot a book recommendation on that part?08:46
genehackersomeone's managed to get frictionless sliding on the nanoscale08:46
pmetzgerI mean that if you have a nanoscale gear, 100% of the energy won't be transmitted through it, just as at the macroscale.08:46
pmetzgerbut things aren't like at the macroscale.08:47
pmetzgerif you have a molecule with a sigma bond in it, you often get free rotation around the sigma bond.08:47
genehackerwell it's not but it can be arbitrarily low08:47
pmetzgernot arbitrarily low. that's a dangerous turn of phrase...08:47
pmetzgeryou can calculate the limits very preciselly.08:48
pmetzgerer precisely.08:48
pmetzgeranyway, you can get free rotation, but certain positions are lower energy than others08:48
genehackerarbitrarily low on the macroscale08:48
pmetzgerbecause the forces aren't the same at all points in the rotation....08:48
pmetzgeryou can't get arbitrarily low on the macroscale either, you can just get low enough to ignore.08:48
genehackeryeah08:49
pmetzgeranyway, there are a couple of chapters in nanosystems on how nanomechanical systems experience friction and dissipate energy.08:49
pmetzgerthey're pretty good reads.08:49
pmetzgerthe interesting part is, you can run such systems in the GHz range in many cases without them dissipating too much or overheating too much, or so the calculations say.08:49
genehackerthe thing that gets me is the higher surface area volume ratio08:49
pmetzgerwhcih is pretty amazing.08:50
pmetzgersurface area and volume aren't really meaningful here.08:50
genehackeryeah but the energy usage per unit volume is pretty high08:50
pmetzgerat the macroscale, a metal plate will dissipate energy off of its surface08:50
pmetzgerbut at the nanoscale, you are dealing with individual phonon production08:50
pmetzgerthings get weird.08:50
pmetzger(or individual photon emission but that is rarer as a dissipation mode.)08:50
genehackerno the thing I'm worried about is the energy requirements08:51
pmetzgerthere is a chapter on that. :)08:51
pmetzgerit is a really really really great book. I can't recommend it highly enough.08:51
genehackernanoscale factories require two orders of magnitude more energy than conventional manufacturing processes08:51
pmetzgerer, huh?08:51
pmetzgerwhere do you get that from?08:52
genehackerhttp://jetpress.org/volume13/Nanofactory.htm08:52
genehackerenergy requirement: 140 kwh/kg material08:53
genehackerplastic molding: 3 kwh/kg08:53
genehackermicrochip fabrication: 23 kwh/kg08:54
genehackerwant sources for the last two?08:54
pmetzgerare you paying attention to how much energy goes into the production of the silicon ingots?08:54
genehackeryes08:54
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pmetzgerSi refining is very energy intensive, followed by the purification stage, followed by the Choralski (sp is wrong there) process for forming the ingots...08:55
genehackeryeah it is08:55
genehackerbut not nearly as intensive as moving individual atoms08:55
genehackeranyway let me check to be sure it is08:56
pmetzgerlet me read Chris' document here, I haven't seen it before. Sec.08:56
genehackerwww.it-environment.org/publications/1.7%20kg%20microchip.pdf08:56
kanzureczochralski08:56
genehackeryup it was08:56
genehackerthough to be fair with nanomanufacturing you can make stuff that's impossible(with conventional manufacturing)08:57
pmetzgerthat pdf doesn't have a power estimate on it, it is one page...08:58
genehackerand you can take advantage of the awesome strength to weight ratio of diamond08:58
genehackeroh crap08:58
pmetzgerbut 1600g of fossil fuels for 2g of Si seems like a very high number as well.08:58
pmetzgerthat implies like a ton of fossil fuel for one kg of silicon chip, similar orders of magnitude to what we're talking about.08:59
genehackerhttp://web.mit.edu/preeya/MacData/afs.course.lockers/2/2.813/www/readings/WilliamsMicrochip.pdf09:00
genehackerso here's the deal09:01
pmetzgerpage 550709:02
pmetzgerhas a very different number than the one you gave09:02
pmetzger2130kwh per kilogram.09:02
pmetzgerVERY different from the number you gave09:02
pmetzgersee table 309:02
pmetzgergood that we looked for the original source material09:02
genehackerhmmm09:03
genehackerlooks like I entered the number wrong09:03
pmetzgerand this is probably not counting some of the other inputs -- what it took to get the carbon itself that is used in the SiO2 to Si step.09:04
genehackerso that's pretty awesome that nanomanufacturing could be more efficient than semiconductor production09:04
pmetzgerthat's generally from coal or what have you...09:04
genehackerso transporting stuff takes nothing in energy terms09:04
pmetzgerAlso, given nanomachines, we can make very efficient solar panels with little waste in production09:04
pmetzgerprobably 60% efficient, meaning peak generation of 600W/m^2 in ideal circumstances.09:05
pmetzgerand we'll need much less material for many purposes -- diamond is much much stronger than steel.09:05
genehackeryeah09:05
genehackerso the problem I have with nanomachines is making nanomachine computers09:05
genehackermechanical nanocomputers09:06
pmetzgerwhat's the issue you see?09:06
pmetzgerwe don't need to make mechanical ones, btw. drexler just proposed those as a proof of concept in his papers.09:06
genehackerthey're not very efficient09:06
pmetzgerstill, he has full explanations of the design in "nanosystems" and his papers09:06
genehackerthey could explode if not cooled09:07
pmetzgeroh, they are quite efficient.09:07
pmetzgerand all modern machines will explode if they aren't cooled.09:07
genehackerhow close are they to the bit flipping energy?09:07
genehackermost machines won't09:07
pmetzgerThey can get pretty close to the kT limit if you're operating in good conditions.09:07
pmetzgerbut there is a full explanation in the last third of nanosystems.09:07
pmetzger(see: mantra. :) )09:08
genehackerthere are better ways to do things than to use mechanical computers09:08
pmetzgerbut I doubt we'll make mechanical computers.09:08
pmetzgerthey're just a proof of engineering concept.09:08
genehackerok09:08
pmetzgerdrexler needed to show he could build control systems at that scale09:08
pmetzgerand he had no way to figure out how to build electronic systems at that scale.09:08
pmetzgerso he designed rod logic instead.09:09
genehackerhe hasn't considered electron fluidic logic gates?09:09
pmetzgerit was for purposes of exploratory engineering, not serious design.09:09
pmetzgerfluid would be much less efficient than rod logic.09:09
klafkamechanical computers may be useful, can't mechanical computers function at smaller distances than electrons can coherently travel in silicon?09:09
genehackernot when that fluid is electrons09:09
pmetzgeryou can probably build single electron gates.09:09
genehackerthat's sort of what electron fluidic logic gates are09:10
pmetzgerI suppose electrons can constitute a fermi liquid, but...09:10
genehackersupposedly you can build them with individual atoms too09:10
pmetzgerit probably makes more sense just to design molecular gates. people have done research on that.09:10
pmetzgeranyway, way too big a topic to cover in real detail on IRC. :)09:10
pmetzgerI'm more worried at this point about getting the first, inefficient, badly designed machines to work.09:11
pmetzgeri.e. bootstrapping.09:11
genehackerhttp://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=523389109:11
pmetzgeronce we have primitive crap, we can make better crap with the primitive crap.09:11
genehackervery true09:11
pmetzgerah, this is a plasmonics idea.09:11
klafkayeah09:12
pmetzgerI understand plasmons virtually not at all. didn't take the solid state class at columbia. probably should have.  :)09:12
klafkahow far are we from primitive crap?09:12
pmetzgerI'll have to correct that someday.09:12
genehackerneither do I09:12
klafkathe best primitive crap we have atm is biotech09:12
genehackerwe're already there if you count DNA nanotech09:12
pmetzgerwell, there are two ways of looking at it.09:12
klafkayeah09:12
klafkawell i don't particularly09:12
pmetzgerI count biochemistry as molecular manufacturing, but not my kind of molecular manufacturing.09:13
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klafkabiochemistry is a specific type that's not particularly suitable to a lot of things09:13
pmetzgerThe diamondoid stuff we have very good ideas on how to proceed, but we have too few people by far working on it...09:13
pmetzgerklafka: in particular, it can't handle high energetics, and can only handle things that can be assembled in solution phase.09:13
pmetzgerabout the highest energetics it can manage is stuff like the reaction catalyzed by cytochrome p450, whcih is impressive for natural systems, but still pretty low energy.09:14
genehackerso I assume drexler has a way to get around the brittleness of diamond for making stuff?09:14
pmetzgerDiamond isn't very brittle. It has amazing tensile strength, and a reasonable young's modulus.09:14
genehackerlike sliding joints to make things compliant?09:14
pmetzgerbut drexler isn't much in the picture at this point.09:15
klafkais he still alive?09:15
pmetzgerhe is.09:15
pmetzgerhe just is burned out.09:15
pmetzgerhe does stuff, but not a lot.09:15
klafkaaah09:15
pmetzgerand he's pretty much convinced that direct to diamondoid is a bad move and we should be doing enzyme engineering.09:15
genehackerlots of stuff has amazing tensile strengths and high youngs modulus's09:15
pmetzgerdiamond is orders of magnitude better than steel.09:15
pmetzgeron both. :)09:15
genehackersingle crystals of boron and zinc should be incredibly strong09:16
pmetzgeranyway, Merkle and Freitas are doing more research on direct-to-diamondoid. Drexler is kind of out of the research game right now, and I don't think he believes in direct-to-diamondoid09:16
pmetzgerThe other material people have talked about is saphire actually.09:16
pmetzgeror another material at least.09:16
genehackeroh wait ceramics09:16
pmetzgerpeople have written a lot on sapphire.09:17
pmetzgerI'd say the biggest obstacle right now on getting to bootstrap is a lack of people.09:17
genehackerceramics are extremely strong and have high strengths and large youngs, but because they are brittle(can't yield) their usage is limited09:17
klafkapeople and funding?09:17
pmetzgerfunding will be more important later.09:18
pmetzgerright now the amount of money that could be productively spent absent more people is small.09:18
pmetzgerJim von Ehr tried throwing money at the problem and couldn't get enough people to make the money useful.09:18
pmetzgercost him a fortune in the process.09:18
pmetzgerHuman minds are always the most important resources in creating a new technology.09:19
klafkahmm so atm the problem is in the process 09:19
pmetzgerMoney is #209:19
klafkapmetzger, totally09:19
pmetzgerThis is one of the reasons I keep trying to get people to read Nanosystems. :)09:19
kanzurei think the problem is the idea09:19
kanzurei haven't seen a bootstrapping plan yet09:19
pmetzgerI hope that some small percentage of them will get seduced. :)09:19
klafkai think i have drexler's nanosystems09:19
klafkaor a few books of his09:20
pmetzgerkanzure: you read the Merkle & Freitas toolset paper, yes?09:20
pmetzgerklafka: Engines of Creation is nontechnical.09:20
klafkait was neat and seductive but, i didn't want to go into engineering/chemistry/etc...09:20
kanzurei don't think the toolset paper explained how to build the tools09:20
pmetzgerkanzure: that paper points the way to a bootstrapping method...09:20
kanzureoh09:20
kanzureblah i should re-read it09:20
pmetzgerkanzure: if you have those tools, and they're fairly small molecules, you can build those tools.09:20
pmetzgerso presumably we look to ways to make those molecules by other means like synthesis.09:21
pmetzgerIF they will work.09:21
pmetzgerit is hardly a full bootstrap plan but it has the germ of a very good idea.09:21
klafkahmmm how about laser modulated enzymes as tools09:21
klafkathat seems like a good tool frankly09:21
pmetzgerklafka: it depends on what you're using enzymes for.09:21
klafkaand they are doing that shit w/ optogenetics09:21
pmetzgerklafka: enzymes are usually meant to run in aqueous solution.09:21
klafkai guess the problem is the energetics like you said09:22
klafkathat too09:22
kanzureklafka: andrew and i are working on a proposal for electrically modulated template independent polymerases09:22
pmetzgerklafka: with fairly low energies.09:22
kanzureklafka: but fenn (in here) had an idea a while back for embedding chromophores into polymerase and then using lasers to control which nucleotides it writes09:22
pmetzgerthat's a bizarre and cool idea. :)09:22
kanzurefenn: ping09:23
pmetzgerthis is only for synthesizing arbitrarily long DNA stretches, though.09:23
klafkakanzure interesting, how would you change the polymerase configuration to write a specific nucleotide09:23
kanzurevia the chromophore09:23
kanzureso, the laser-based one is a very complicated process09:23
kanzurei tried designing some experiments to build it09:23
kanzurefirst, we'd have to find what i call a 'retarded' polymerase09:23
klafkayeah09:23
kanzurea polymerase that only writes one of the four nucleotides09:23
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klafkafor each of the four nucleotides09:23
kanzureyes09:23
kanzureand then try to incorporate that into a chromophore switch09:24
kanzuredefinitely a feat of enzyme engineering and motif hackery09:24
pmetzgeryou need to design a modified polymerase to make this work. hard problem...09:24
klafkathat'll be challenging in itself, until MD simulations come along09:24
pmetzgeryou need more than MD simulations to do this.09:24
kanzurepmetzger: you wouldn't design it; you'd use self-compartmentalized evolution09:24
pmetzgerbecause MD only gives you the folding.09:24
klafkawell MD simulationscould do both pmetzger but in either case it's completely intractable09:24
kanzureoops09:24
pmetzgerdunno what you mean by "self-compartmentalized evolution"...09:24
kanzure"compartmentalized self-replication"09:24
kanzurehttp://www.ncbi.nlm.nih.gov/pubmed/1127435209:24
kanzureDirected evolution of polymerase function by compartmentalized self-replication.09:25
kanzurecompartmentalized09:25
pmetzgerMD simulations are pseudo-neutonian. they don't tell you what reactions happen...09:25
kanzurepdf: http://heybryan.org/~bbishop/docs/ellingtonia/polymerase/Directed%20evolution%20of%20polymerase%20function%20by%20compartmentalized%20self-replication%20-%20Ghadessy.pdf09:25
pmetzgeror how a chromophore would transfer energy...09:25
kanzureso anyway, the chromophore idea is more complicated09:25
klafkayea09:25
kanzurebut i might be getting some funding for the electrically-modulated polymerase idea09:26
kanzureand we don't even need to demonstrate writing really09:26
kanzurejust that we can tether polymerase with streptavidin and biotin09:26
pmetzgerthis paper has a neat trick in it...09:26
kanzureand that we can electrically turn it on and off09:26
kanzurethrough some mulitplexing circuit i guess09:26
pmetzgercool paper...09:27
kanzure:)09:27
kanzureCSR is usually done in emulsions (but there are other ways)09:27
pmetzgerback to work with me...09:28
klafkawhat is your goal for it past turning it on/off, how are you gonna get to template independent09:28
kanzurewasn't my idea.. i'm just seeing what i can do with it09:28
klafkaaah09:28
kanzureright now i don't think we'll be able to control which nucleotides it throws in09:28
kanzurebut we'll see.09:28
pmetzgerso whatever you do, you want it to be accurate for millions of cycles.09:29
pmetzgerbut if you could demonstrate even ten or twenty that would be huge.09:29
pmetzgerAm I mistaken or is the state of the art still solid support based synthesis? i.e. attach stuff to teeny polystyrene beads etc.09:30
pmetzgerdoing something that didn't require step after step that way would be enormous.09:30
pmetzgerrevolutionary.09:30
kanzureDMD based DNA synthesis is the new rage09:31
kanzurephotochemical-based DNA synthesis, etc.09:31
kanzurephosphoramidite is old and clunky, yes09:31
pmetzgerexpand DMD?09:32
kanzuremicromirror arrays you find in office projectors mounted on ceilings09:32
pmetzgerah, the silicon micromachined mirror arrays Texas Instruments makes, yes.09:34
pmetzgerso people have come up with a method there that works?09:34
pmetzgeror at least that works a little bit?09:35
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kanzurethere's been a few papers, yes09:36
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kanzurehi lepton 09:41
leptonhowdy09:42
leptonI've been trying to get EMC2 setup for so long, kanzure09:43
leptonsoooo so long09:43
kanzurewhat's been the roadblock?09:44
kanzurehaha matt mccabe is precious: "Actually, let me clarify.  How do you keep competitors from using your publicly available info to undercut your company?  If it is about user experience, then a larger company with more resources could easily take you out with a blink of an eye...at least if it is worth their time."09:45
kanzurere: open source hardware09:45
kanzureit strikes me as very ironic09:45
kanzurethe answer is, of course they'll undercut you! market forces, yo09:45
kanzurehttp://www.molecularist.com/lifeblog/2010/06/diybio-meet-up-report-folk-microbiology.html09:47
leptonWell, we've spent a lot of time on mundane stuff like cabling and such, but trying to get all our ducks in a row with the 5i23 and it's daughter boards has been really slow going09:47
kanzurehttp://blog.makezine.com/archive/2010/06/things_heat_up_for_openpcr_project.html09:47
kanzureoh now this just pisses me off09:47
leptonWe also had a lot of motherboard compatibility problems09:47
kanzure"09:47
kanzure"Not only are they making their plans for a key piece of DIY Bio hardware09:47
kanzureopen for everyone to use, but they're also soliciting input on its design."09:47
leptonI was reading that on OpenPCR earlier this morning09:47
kanzurenever underestimate people's ability to bullshit, raise money09:47
kanzureand then amke the community design it for you09:47
lepton:/09:47
kanzurerawr09:47
kanzurehulk smash!09:47
kanzureoh wait they do have a prototype09:48
kanzurehttp://answers.oreilly.com/topic/1641-silicone-heaters-for-openpcr/page__p__3131&#entry313109:48
kanzurethey should set up a design repository09:48
leptonAll open hardware projects09:49
leptonalmost none do :/09:49
kanzure:'(09:49
kanzurebbl09:49
leptonall open hardware projects *should09:49
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kanzureChromophore-assisted laser inactivation of proteins is mediated by the photogeneration of free radicals http://designfiles.org/papers/polymerase/Chromophore-assisted%20laser%20inactivation%20of%20proteins%20is%20mediated%20by%20the%20photogeneration%20of%20free%20radicals%20-%20Liao%20-%20Roider%20-%20D%20G%20Jay%20-%201994.pdf11:13
* kanzure is slowly uplloading "Genetically targeted chromophore-assisted light inactivation"11:17
kanzure"Selective destruction of protein function by chromophore-assisted laser inactivation"11:18
pmetzgerdestruction, or temporary inactivation?11:21
pmetzgeryou want temporary inactivation right?11:21
kanzurethere are others that do temporary inactivation11:21
pmetzgerfree radicals sound destructive. :)11:22
pmetzgerOne issue in scavanging for fun things is that photochemistry isn't the primary mechanism in most enzymes. I bet you have better luck with electrochemistry. There's a lot more of that.11:25
kanzureaggreed\11:25
pmetzgerpresumably you want to steal existing reactants and graft them on...11:26
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kanzurehm still uploading11:37
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fennpong12:33
pmetzgerping!12:34
kanzurei was pinging you about writozyme stuff12:39
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kanzurepmetzger: i'm excited about tomorrow night. it's going to be like opening presents13:12
kanzureextropic presents13:12
pmetzger:)13:12
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leptonkanzure: what comes in tomorrow?13:40
kanzurei am going over to http://maxmore.com/ and http://natasha.cc/ 's house to type up some old 1980s/1990s extropian/transhumanist philosophy13:41
kanzurethat they have had hidden in boxes forever13:41
leptonCool13:44
leptontype up? No book scanners?13:44
pmetzgerI think he should scan, too...13:45
pmetzgerthe ancient typesetting is half the fun. :)13:45
pmetzgerand there are graphs and diagrams and such.13:45
leptonI wonder if you could get google to do it for you?13:45
leptonThere are some decent open book scanner designs out there13:45
leptonlego based designs, amongst them ;)13:46
pmetzgerThere are excellent ones...13:46
pmetzgerthe diy bookscanner crowd has been taking off.13:46
leptonI wonder what a plot of the activity of that crowd would look like over time?13:48
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leptonSeems like if its successful enough it can render itself obsolete13:48
pmetzgerhave a look at book piracy online for a curve. :)13:48
leptonall books = scanned13:48
leptonOh, I already know ;)13:48
leptonI actually just got a new ebook reader and put openinkpot on it with a bunch of old scifi books on it13:48
leptonMe and Arthur C Clarke are gonna party13:49
pmetzgerI think Clarke's state of putrefaction might impede that.13:52
AJollyLifemeh, i just use an SLR to scan my books13:56
pmetzgerAn SLR isn't bad provided one has software to deskew etc. after.13:57
AJollyLifeyep13:58
AJollyLifeabby finereader is decent13:58
pmetzgerthe diy bookscanner designs are, in fact, just cameras and setups to make using the cameras fast.13:58
AJollyLifeyeah, i dont scan enough stuff to make that worthwhile13:58
AJollyLifeand i've got a better camera than most of the diybookscanner setups, so I just split the page in software13:58
pmetzgerthe software is the issue. proper deskewing etc. is hard.14:00
pmetzgergood software in the open source community to do it is only now appearing.14:01
AJollyLifei have yet to see great open source software for it14:01
pmetzgersee the diy bookscanner web site.14:01
pmetzgerthere is a big discussion of recently developed algorithms.14:01
pmetzgersome of them are pretty amazing.14:02
pmetzgerI suspect that that, combined with software that can combine data from multiple shots of the same page, will probably make the open source stuff ultimately better than what is currently done commercially.14:02
pmetzgerWhat I'd like to see at some point, for older books, is software that will take the scan and the OCR and re-typeset the book in the original font and style.14:03
pmetzgerthat would be amazingly cool.14:03
jcluckmmm diy bio yogurt14:09
leptonI've gotta say, in the FOSS ebook word, I'm really impressed with calbire, tried it out for the first time in a long while this week and it seems quite capable14:10
pmetzgercalbire?14:11
leptonIt's an ebook library managment and format converter program14:14
leptonI used it to do a batch conversion of PDF files to epub and rtf files14:14
leptonworked very well14:14
fennhttp://www.flickr.com/photos/juliancash/673891099/in/set-72157600572658621/14:15
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fenncalibre14:18
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fennsuperbaby in the technological womb14:20
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bkeroI use calibre to convert PDFs into EPUB files15:41
bkeroWorks alright, but you lose a lot of information15:41
bkeroI wish calibre had automatic chapter detection, page re-enumeration, etc15:41
kanzureah yes i remember when it was cool to have usernames like this: http://www.youtube.com/user/EricGokuInuyasha182316:07
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bkerowhat16:32
bkeroThat was cool at some point?16:32
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kanzuregrandma called me to tell me that she's "excited about the singularity"17:39
kanzure<317:40
cluckjlmao17:42
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fennwtf google uploader needs me to download and run a binary app?17:50
fenn(for uploading google videos)17:50
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fennack google video is dead? wtf!!!17:56
fenn"Major producers with a thousand or more hours of video can apply for Google's Premium Program, which continues to allow for the uploading of videos."17:57
pmetzgergoogle video is dead?17:58
fennyou can't upload anymore17:59
pmetzgernot entirely surprised, but youtube doesn't let you download which sucks.17:59
fennand youtube won't let you upload >10min, and their algorithm to determine if something is >10min sucks17:59
fennand instead of saying "this service is no longer offered" they just give you some weird login error18:01
fennug.. and vimeo only gives you 500MB/week18:02
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kanzurehaha it's funny seeing some other guy trying to namedrop on me19:15
kanzure"yo i was hanging with eric schmidt from google yesterday"19:15
kanzure"oh yeah? well MY guy was hanging with.."19:15
jrayhawkcclive can download from youtube, vimeo, and google video19:17
kanzurejrayhawk: try also youtube-dl19:17
pmetzgerI still think of Eric as one of the creators of lex19:18
jrayhawkwhy would i want to use a less functional tool?19:18
kanzurejrayhawk: i ask that of FreeBSD users every day19:18
pmetzgerit is weird to think of him as an executive...19:18
jrayhawkhaha19:18
pmetzgerthis is amazing:19:19
pmetzger"The new mision I herits the buggered code (i do not the bugger). How do debugger him?" http://is.gd/d2RiB 19:19
jrayhawkFWIW it's pretty easy to just stick ogv somewhere and have browsers play it natively nowadays19:19
jrayhawkSo I don't really know what a video host like youtube would be good for other than the social networking aspects which I assume most people in here don't particularly care about anyway.19:20
pmetzgerfree hosting.19:21
pmetzgerif someone downloads your video a million times you're not screwed by it.19:21
jrayhawkIf it's non-profit, make Bryan host it on his vserver.19:21
pmetzgerif you have it up on dreamhost you'll run out of bandwidth.19:21
pmetzgerdoes he have a virtual with *unlimited* bandwidth?19:21
jrayhawkPretty much.19:21
pmetzgereven if you're not being charged for it, youtube has the feature that it has an insane amount of connectivity via google.19:21
fenn"the hayabusa re-entry observation campaign" http://archive.seti.org/pdfs/csc-June-10.pdf19:23
pmetzgerI suppose, though, one could get a similar effect (if one was ot worried about costs) by using Amazon S319:24
pmetzgers/ot/not/19:24
* kanzure finally got around to setting up s3/ec2/sqs/etc.19:24
fennoops, bad url, sorry19:24
QuantumGfenn: http://www.spacevidcast.com/2010/06/22/the-little-spacecraft-that-could-hayabusa-spacepod-2010-06-22/19:25
fennhttp://airborne.seti.org/hayabusa/19:25
fenn19:28
kanzurefail19:28
fennoff to go learn about parallelism in python19:28
kanzurempi?19:28
fenni always hit ctrl-O because it's "save" in nano19:28
fennmpi?19:29
kanzureit's a multi processor interface thingy19:29
kanzurefor parallel programming voodoo19:29
fenni think this is just a basic introduction to the concepts, which is more my speed right now19:30
* fenn waves19:30
pmetzgerpython threads aren't real threads. :|19:31
pmetzgerof course, then again, that means they don't misbehave as much as real threads. :|19:31
bkeroThat's why god invented fork().19:32
kanzurehm do you mean the native threads stuff19:32
kanzurei thought twister(?) or something did real threading19:32
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kanzurehi lepton19:34
kanzureany progress with emc2?19:34
leptonyeah, things are moving along19:35
leptonStill no motion, I'll finish wiring tomorrow morning and then test it out19:35
bkerokanzure: twisted19:35
leptonThis ended up being an epic project, but I think it'll be worth it when it's done19:36
kanzurebkero: does it do threading?19:36
kanzureor is it a unit testing framework19:36
kanzurei forget :(19:36
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pmetzgertwister does event driven programs.19:41
pmetzgerwhich, to the extent that they do multiplexing well, are better than threads.19:41
bkerotwisted19:41
pmetzgerbut to the extent that it doesn't help using multiple CPUs, are worse.19:42
pmetzgerer, twisted.19:42
kanzurei'm surprised you haven't heard about mpi either19:42
kanzurethat's a common tool for doing simulations19:42
kanzurewell, i guess you might not write the actual simulation software19:42
kanzurejust a user :)19:43
leptonSo I've slightly over committed myself to CNC routering and 3d printing a bunch of stuff for a Burning Man camp19:45
leptonKnow of anything maker / open source / transhumanist stuff going on there this year?19:46
QuantumGwhat are you 3d printing with?19:52
leptonI'll soon have a BFB300, from the company bitsfrombytes in the UK19:52
leptonhopefully, at least19:53
leptonOn order for the first batch they send out to the US19:53
kanzuremartin just got makerbot #159519:53
kanzurethey have makerbots in stock now O_o19:53
leptonAwesome19:53
leptonI'm excited to use PLA with it19:54
lepton(polylactic acid) We're gonna try to make forms for plants to grow in19:55
QuantumGcool.. so what are you printing?19:55
leptonTrinket type things (with the camp's symbol and a location and time) that have different geometric shapes (stellated dodecahedron, etc)19:56
leptonand an internal structure that contains seeds19:57
leptonWhich, when you leave the dry environment of burning man, you can plant (or perhaps crush and plant) and it'll grow19:57
leptonThat's the idea, at least19:57
QuantumGneat. So did you buy the printer just for curiosity and this came along later or are you buying the printer to do this specifically?19:58
leptonWell, we're trying to add automated manufacturing hardware whenever we run into a situation where we'd need to do something expensivly and externally (machinging metal, injection molds, etc)19:58
leptonand we needed to make a few hundred small levers with unique geometry19:59
lepton$4000 for a cheap injection molding, then $0.02 per unit in small volumes19:59
leptonor $4000 for a 3d printer, at around $1.50 a knob (and much slower in production), but not limited to just that part19:59
QuantumGI must have missed it, who's "we"?19:59
leptonso 3d printer it was19:59
leptonOh, I started an engineering company20:00
QuantumGoh yeah?  what sort of work do you do?20:00
leptonembedded electronics, power electronics, mechanical engineering, lots of stuff, really20:02
QuantumGahh cool.20:02
leptonWe do consulting as well as internal products20:02
leptonWith the idea of over time accumulating automated manufacturing hardware and designs20:03
leptonSomewhat inline with kanzure's skdb sort of paradigm20:03
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leptonso far we've been developing scuba diving equipment, electric motor control hardware, battery mangement systems, and machine vision sensors20:04
leptonand working on CNC hardware a good bit, with some flashy arduino art projects thrown in the mix20:05
QuantumGcool stuff20:06
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