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00:20 < fenn> wah 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 gadget
00:27 < uniqanomaly_> "Supported platforms	IA-32, MIPS, x86-64, SPARC, DEC Alpha, Itanium, PowerPC, ARM, m68k, PA-RISC, s390, SuperH, M32R and more"
00:27 < uniqanomaly_> you mean which linux
00:31 < uniqanomaly_> lol
00:54 < fenn> that was my point, that it's the same linux on various architectures
00:57 < fenn> see, 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 does
00:58 < fenn> but an ASIC can't do anything but what it was intended to do
00:58 < fenn> vs say a SIMD processor
01:10 < uniqanomaly_> i'd say 'the same linux on various architectures' is rather advantage 
01:15 < jrayhawk> Once again, an ASIC is like a program that you write directly to hardware. No operating system needed.
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06:03 < kanzure> File Formats, Compatibility, and Open Source http://forums.reprap.org/read.php?1,49824,49859
06:03 < 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 < kanzure> kive: i didn't see your pm until now. sorry. i thought you'd reply in here. oops :)
06:05 < kanzure> ok. replies sent.
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06:46 < pmetzger> morning
06:48 < kanzure> morning good sir!
06:48 < kanzure> how goes the world domination invasion force for nyc?
06:51 < JayDugger> Good morning, all.
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07:12 < pmetzger> Ah, world domination. That's so yesterday. Now we're talking about multiverse domination.
07:21 < kanzure> fenn: did we ever figure out wtf is wrong with 'patrick anderson'?
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07:30 < kanzure> hahah
07:31 < kanzure> so the people on the opencascade forums have asked for release dates
07:31 < kanzure> http://www.opencascade.org/org/forum/thread_18818/
07:31 < kanzure> and so someone at opencascade responds:
07:31 < kanzure> "Hello Community, Thank You for your timed inputs."
07:31 < kanzure> quite telling how they think of The Community
07:31 < kanzure> "Hello Community.."
07:32 < pmetzger> timed?
07:32 < pmetzger> they said timed?
07:33  * kanzure nods
07:33  * drazak eyerolls
07:33 < pmetzger> hahahaha
07:34 < pmetzger> how fast were the inputs if they were timing them? :)
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07:51 < genehacker> kanzure you really shouldn't hate .stl
07:51 < genehacker> it's not that bad after all
07:51 < genehacker> seriously why are meshes that bad?
07:53 < kanzure> it's like sending aroud compiled code
07:53 < kanzure> *around
07:54 < genehacker> yeah, so?
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08:18 < kanzure> genehacker: load up an STL file into solidworks and remove a chamfer
08:18 < genehacker> ok
08:18 < genehacker> done
08:18 < kanzure> wtf
08:18 < kanzure> uh, i don't think that's possible, genehacker 
08:19 < genehacker> ok good point
08:19 < genehacker> but really it shouldn't be too hard to do that too a mesh
08:19 < genehacker> *to
08:20 < kanzure> but wouldn't it just be easier if people just gave you CAD data?
08:20 < genehacker> well it'd be damn nice if there was a CAD format out there that would preserve smart dimensions on export
08:21 < kanzure> STEP has the capability to do that
08:21 < genehacker> it does?
08:21 < kanzure> yes, but i don't think solidworks supports that feature :(
08:21 < kanzure> it's really weird!
08:21 < genehacker> has someone found a way to generate step code
08:21 < genehacker> fuckers
08:22 < kanzure> yeah, i've been working on something for the past two days now
08:22 < kanzure> it's pretty much working (almost)
08:22 < genehacker> with smart dimensions?
08:22 < genehacker> REALLY?
08:22 < kanzure> i have an "export a sphere" demo
08:22 < kanzure> no not with smart dimensions (not yet)
08:22 < kanzure> but it's going to be open source, so someone else (or me) can later add it in
08:22 < genehacker> :(
08:22 < pmetzger> what are smart dimensions?
08:22 < kanzure> ho ho ho
08:22  * pmetzger is not a mech e type.
08:22 < kanzure> you'll like this
08:22 < genehacker> smart dimensions are the best thing ever
08:22 < kanzure> genehacker: where is the carnegie mellon kinematics library thing
08:23 < genehacker> there dimensions that get this: you can resize!
08:23 < genehacker> carnegie mellon don't you mean cornell?
08:23 < kanzure> pmetzger: it's basically constraints + graph theory applied to an assembly and design elements (like fundamental primitives and CSG elements)
08:23 < kanzure> genehacker: yes i probably mean cornell
08:23 < genehacker> except in practice it sucks
08:23 < genehacker> it'
08:23 < kanzure> http://kmoddl.library.cornell.edu/
08:24 < genehacker> it doesn't work when you have dimensions as the function of other dimensions
08:24 < kanzure> genehacker: pmetzger wants some mechanical linkage, gears, cams stuff
08:24 < pmetzger> so the notion is that a set of parts are set up so that if one is resized the others alter to suit?
08:24 < genehacker> or maybe I'm doing something wrong
08:24 < kanzure> genehacker: i think we could do sympy to do functions of other dimensions.. that's definitely possible
08:24 < pmetzger> genehacker: are there any intro mech e texts that explain all that stuff?
08:25 < genehacker> no, just 5 minutes playing around with CAD software
08:25 < kanzure> yeah :)
08:25 < genehacker> anyway you want a linkage?
08:25 < kanzure> download a copy of solidworks
08:25 < kanzure> (or ask me)
08:26 < genehacker> don't pirate solidworks, that's bad, plus solidworks has super lawyers
08:26 < kanzure> i think torrents are a part of solidworks marketing strategy
08:26 < genehacker> nope that's autocad
08:26 < genehacker> you're confusing them
08:26 < kanzure> because when the new kids show up to a company, they'll have to purchase a license
08:26 < kanzure> oh
08:26 < kanzure> hrm
08:27 < genehacker> though if you can prove that solidworks is distributing software via torrents you will make my day
08:27 < pmetzger> ah, solidworks does simulation of mechanical parts. as I expected...
08:27 < genehacker> anyway pmetzger, you said you want a mechanical linkage?
08:28 < pmetzger> no. I want to learn about them.
08:28 < pmetzger> I want to learn about all such things, and I can't find textbooks.
08:28 < genehacker> hmmm...
08:28 < pmetzger> I can only find books on mechanical designs from the 19th century, which really isn't what I wanted. :)
08:28 < genehacker> let's see here
08:28 < kanzure> textbooks aren't the way to learn mechanical engineering, unless you want to do math on kinematics and such :)
08:28 < genehacker> those are what you want
08:28 < kanzure> you should hang out in a machine shop for a few months
08:29 < genehacker> shoot we didn't cover linkages that much
08:29 < kanzure> genehacker: he wants something like campbell's class, i think
08:29 < kanzure> what was the book campbell was using?
08:29 < genehacker> it doesn't cover linkages
08:29 < genehacker> or that much atleast
08:29 < kanzure> yeah but it covers a lot of other things that pmetzger wants
08:30 < genehacker> like what?
08:30 < genehacker> designing bolts to last long, figuring out how long a bearing will last, the involute gear profile?
08:30 < pmetzger> all sorts of things like that would be of interest.
08:30 < kanzure> gears, linkages, cams, bolts, servos, steppers, ..
08:31 < genehacker> linkages are in a mechanisms book
08:31 < genehacker> ok well I'll look up my book later
08:31 < pmetzger> my interest is this: long term, I want to be designing mechanical nanomachines, but I have no mech e background.
08:31 < pmetzger> so I want to develop a mech e background.
08:31 < pmetzger> I've actually set myself some weird projects to try to get myself some field experience, like building a mechanical clock.
08:32 < genehacker> ok
08:32 < pmetzger> though I'd prefer to learn by reading what others can tell me so I don't have to re-discover the wheel.
08:32 < genehacker> I think I've got a book/class you might be interested in
08:32 < pmetzger> this is a very long term project for me, I expect I won't need to understand this stuff for a few years.
08:32 < genehacker> it's called the FUNdamentals of design
08:32 < pmetzger> change "very" to just long term, a few years isn't that far...
08:32 < pmetzger> but you get what I mean...
08:32 < genehacker> and I'm trying to learn some of the stuff in it
08:33 < pmetzger> link to book?
08:33 < genehacker> finding it
08:34 < genehacker> http://dev.forums.reprap.org/read.php?1,31371
08:35 < genehacker> ok so nanomachines are probably going to be a bit different than macromachines
08:36 < genehacker> I'm wondering if one can even apply the bar bending formulas reliably to nanosized diamond bars?
08:36 < pmetzger> that is discussed in chapter 2 of nanosystems.
08:36 < pmetzger> (see my mantra.)
08:37 < genehacker> hmmm...
08:38 < genehacker> so this mechanical engineering education of mine actually might be useful?
08:39 < genehacker> *useful as defined as doing ground breaking stuff
08:39 < pmetzger> there is a newer version of that book than the one linked there
08:39 < pmetzger> see: http://stellar.mit.edu/S/course/2/sp09/2.007/materials.html
08:40 < genehacker> anyway I think you should look more into kinematics and mechanisms
08:40 < pmetzger> http://stellar.mit.edu/S/course/2/sp09/2.007/courseMaterial/topics/topic4/studyMaterial/FUNdaMENTALs_Book_zipped/FUNdaMENTALs_Book_zipped.zip
08:40 < pmetzger> probably.
08:40 < genehacker> it might be worth developing a unique approach to solving nanoscale solids problems
08:40 < pmetzger> anyway, a big section of nanosystems is on scaling laws at the nanoscale.
08:40 < pmetzger> many laws fail utterly, some continue to work.
08:40 < pmetzger> some unexpected things happen, like lubrication is not an issue.
08:41 < genehacker> yeah but you still have friction which generates heat and saps away power
08:41 < genehacker> and due to high surface area volume ratios friction can become quite troublesome
08:41 < genehacker> doesn't it?
08:42 < genehacker> some of the power requirements for nanofactories I've read about were pretty high
08:43 < genehacker> anyway as far learning ME, I'd suggest reading about some statics and dynamics
08:45 < pmetzger> friction is different at this scale.
08:45 < pmetzger> very different.
08:45 < pmetzger> it is true that you don't get lossless rotation or what have you, that's impossible...
08:45 < pmetzger> and you do turn energy input into systems into phonons, i.e. heat in the end.
08:45 < genehacker> the 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 < pmetzger> but it actually is rather different than at the macroscale.
08:46 < genehacker> what do you mean no lossless rotation?
08:46 < pmetzger> got a book recommendation on that part?
08:46 < genehacker> someone's managed to get frictionless sliding on the nanoscale
08:46 < pmetzger> I mean that if you have a nanoscale gear, 100% of the energy won't be transmitted through it, just as at the macroscale.
08:47 < pmetzger> but things aren't like at the macroscale.
08:47 < pmetzger> if you have a molecule with a sigma bond in it, you often get free rotation around the sigma bond.
08:47 < genehacker> well it's not but it can be arbitrarily low
08:47 < pmetzger> not arbitrarily low. that's a dangerous turn of phrase...
08:48 < pmetzger> you can calculate the limits very preciselly.
08:48 < pmetzger> er precisely.
08:48 < pmetzger> anyway, you can get free rotation, but certain positions are lower energy than others
08:48 < genehacker> arbitrarily low on the macroscale
08:48 < pmetzger> because the forces aren't the same at all points in the rotation....
08:48 < pmetzger> you can't get arbitrarily low on the macroscale either, you can just get low enough to ignore.
08:49 < genehacker> yeah
08:49 < pmetzger> anyway, there are a couple of chapters in nanosystems on how nanomechanical systems experience friction and dissipate energy.
08:49 < pmetzger> they're pretty good reads.
08:49 < pmetzger> the 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 < genehacker> the thing that gets me is the higher surface area volume ratio
08:50 < pmetzger> whcih is pretty amazing.
08:50 < pmetzger> surface area and volume aren't really meaningful here.
08:50 < genehacker> yeah but the energy usage per unit volume is pretty high
08:50 < pmetzger> at the macroscale, a metal plate will dissipate energy off of its surface
08:50 < pmetzger> but at the nanoscale, you are dealing with individual phonon production
08:50 < pmetzger> things get weird.
08:50 < pmetzger> (or individual photon emission but that is rarer as a dissipation mode.)
08:51 < genehacker> no the thing I'm worried about is the energy requirements
08:51 < pmetzger> there is a chapter on that. :)
08:51 < pmetzger> it is a really really really great book. I can't recommend it highly enough.
08:51 < genehacker> nanoscale factories require two orders of magnitude more energy than conventional manufacturing processes
08:51 < pmetzger> er, huh?
08:52 < pmetzger> where do you get that from?
08:52 < genehacker> http://jetpress.org/volume13/Nanofactory.htm
08:53 < genehacker> energy requirement: 140 kwh/kg material
08:53 < genehacker> plastic molding: 3 kwh/kg
08:54 < genehacker> microchip fabrication: 23 kwh/kg
08:54 < genehacker> want sources for the last two?
08:54 < pmetzger> are you paying attention to how much energy goes into the production of the silicon ingots?
08:54 < genehacker> yes
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08:55 < pmetzger> Si 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 < genehacker> yeah it is
08:55 < genehacker> but not nearly as intensive as moving individual atoms
08:56 < genehacker> anyway let me check to be sure it is
08:56 < pmetzger> let me read Chris' document here, I haven't seen it before. Sec.
08:56 < genehacker> www.it-environment.org/publications/1.7%20kg%20microchip.pdf
08:56 < kanzure> czochralski
08:56 < genehacker> yup it was
08:57 < genehacker> though to be fair with nanomanufacturing you can make stuff that's impossible(with conventional manufacturing)
08:58 < pmetzger> that pdf doesn't have a power estimate on it, it is one page...
08:58 < genehacker> and you can take advantage of the awesome strength to weight ratio of diamond
08:58 < genehacker> oh crap
08:58 < pmetzger> but 1600g of fossil fuels for 2g of Si seems like a very high number as well.
08:59 < pmetzger> that implies like a ton of fossil fuel for one kg of silicon chip, similar orders of magnitude to what we're talking about.
09:00 < genehacker> http://web.mit.edu/preeya/MacData/afs.course.lockers/2/2.813/www/readings/WilliamsMicrochip.pdf
09:01 < genehacker> so here's the deal
09:02 < pmetzger> page 5507
09:02 < pmetzger> has a very different number than the one you gave
09:02 < pmetzger> 2130kwh per kilogram.
09:02 < pmetzger> VERY different from the number you gave
09:02 < pmetzger> see table 3
09:02 < pmetzger> good that we looked for the original source material
09:03 < genehacker> hmmm
09:03 < genehacker> looks like I entered the number wrong
09:04 < pmetzger> and 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 < genehacker> so that's pretty awesome that nanomanufacturing could be more efficient than semiconductor production
09:04 < pmetzger> that's generally from coal or what have you...
09:04 < genehacker> so transporting stuff takes nothing in energy terms
09:04 < pmetzger> Also, given nanomachines, we can make very efficient solar panels with little waste in production
09:05 < pmetzger> probably 60% efficient, meaning peak generation of 600W/m^2 in ideal circumstances.
09:05 < pmetzger> and we'll need much less material for many purposes -- diamond is much much stronger than steel.
09:05 < genehacker> yeah
09:05 < genehacker> so the problem I have with nanomachines is making nanomachine computers
09:06 < genehacker> mechanical nanocomputers
09:06 < pmetzger> what's the issue you see?
09:06 < pmetzger> we don't need to make mechanical ones, btw. drexler just proposed those as a proof of concept in his papers.
09:06 < genehacker> they're not very efficient
09:06 < pmetzger> still, he has full explanations of the design in "nanosystems" and his papers
09:07 < genehacker> they could explode if not cooled
09:07 < pmetzger> oh, they are quite efficient.
09:07 < pmetzger> and all modern machines will explode if they aren't cooled.
09:07 < genehacker> how close are they to the bit flipping energy?
09:07 < genehacker> most machines won't
09:07 < pmetzger> They can get pretty close to the kT limit if you're operating in good conditions.
09:07 < pmetzger> but there is a full explanation in the last third of nanosystems.
09:08 < pmetzger> (see: mantra. :) )
09:08 < genehacker> there are better ways to do things than to use mechanical computers
09:08 < pmetzger> but I doubt we'll make mechanical computers.
09:08 < pmetzger> they're just a proof of engineering concept.
09:08 < genehacker> ok
09:08 < pmetzger> drexler needed to show he could build control systems at that scale
09:08 < pmetzger> and he had no way to figure out how to build electronic systems at that scale.
09:09 < pmetzger> so he designed rod logic instead.
09:09 < genehacker> he hasn't considered electron fluidic logic gates?
09:09 < pmetzger> it was for purposes of exploratory engineering, not serious design.
09:09 < pmetzger> fluid would be much less efficient than rod logic.
09:09 < klafka> mechanical computers may be useful, can't mechanical computers function at smaller distances than electrons can coherently travel in silicon?
09:09 < genehacker> not when that fluid is electrons
09:09 < pmetzger> you can probably build single electron gates.
09:10 < genehacker> that's sort of what electron fluidic logic gates are
09:10 < pmetzger> I suppose electrons can constitute a fermi liquid, but...
09:10 < genehacker> supposedly you can build them with individual atoms too
09:10 < pmetzger> it probably makes more sense just to design molecular gates. people have done research on that.
09:10 < pmetzger> anyway, way too big a topic to cover in real detail on IRC. :)
09:11 < pmetzger> I'm more worried at this point about getting the first, inefficient, badly designed machines to work.
09:11 < pmetzger> i.e. bootstrapping.
09:11 < genehacker> http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5233891
09:11 < pmetzger> once we have primitive crap, we can make better crap with the primitive crap.
09:11 < genehacker> very true
09:11 < pmetzger> ah, this is a plasmonics idea.
09:12 < klafka> yeah
09:12 < pmetzger> I understand plasmons virtually not at all. didn't take the solid state class at columbia. probably should have.  :)
09:12 < klafka> how far are we from primitive crap?
09:12 < pmetzger> I'll have to correct that someday.
09:12 < genehacker> neither do I
09:12 < klafka> the best primitive crap we have atm is biotech
09:12 < genehacker> we're already there if you count DNA nanotech
09:12 < pmetzger> well, there are two ways of looking at it.
09:12 < klafka> yeah
09:12 < klafka> well i don't particularly
09:13 < pmetzger> I count biochemistry as molecular manufacturing, but not my kind of molecular manufacturing.
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09:13 < klafka> biochemistry is a specific type that's not particularly suitable to a lot of things
09:13 < pmetzger> The diamondoid stuff we have very good ideas on how to proceed, but we have too few people by far working on it...
09:13 < pmetzger> klafka: in particular, it can't handle high energetics, and can only handle things that can be assembled in solution phase.
09:14 < pmetzger> about 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 < genehacker> so I assume drexler has a way to get around the brittleness of diamond for making stuff?
09:14 < pmetzger> Diamond isn't very brittle. It has amazing tensile strength, and a reasonable young's modulus.
09:14 < genehacker> like sliding joints to make things compliant?
09:15 < pmetzger> but drexler isn't much in the picture at this point.
09:15 < klafka> is he still alive?
09:15 < pmetzger> he is.
09:15 < pmetzger> he just is burned out.
09:15 < pmetzger> he does stuff, but not a lot.
09:15 < klafka> aah
09:15 < pmetzger> and he's pretty much convinced that direct to diamondoid is a bad move and we should be doing enzyme engineering.
09:15 < genehacker> lots of stuff has amazing tensile strengths and high youngs modulus's
09:15 < pmetzger> diamond is orders of magnitude better than steel.
09:15 < pmetzger> on both. :)
09:16 < genehacker> single crystals of boron and zinc should be incredibly strong
09:16 < pmetzger> anyway, 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-diamondoid
09:16 < pmetzger> The other material people have talked about is saphire actually.
09:16 < pmetzger> or another material at least.
09:16 < genehacker> oh wait ceramics
09:17 < pmetzger> people have written a lot on sapphire.
09:17 < pmetzger> I'd say the biggest obstacle right now on getting to bootstrap is a lack of people.
09:17 < genehacker> ceramics are extremely strong and have high strengths and large youngs, but because they are brittle(can't yield) their usage is limited
09:17 < klafka> people and funding?
09:18 < pmetzger> funding will be more important later.
09:18 < pmetzger> right now the amount of money that could be productively spent absent more people is small.
09:18 < pmetzger> Jim von Ehr tried throwing money at the problem and couldn't get enough people to make the money useful.
09:18 < pmetzger> cost him a fortune in the process.
09:19 < pmetzger> Human minds are always the most important resources in creating a new technology.
09:19 < klafka> hmm so atm the problem is in the process 
09:19 < pmetzger> Money is #2
09:19 < klafka> pmetzger, totally
09:19 < pmetzger> This is one of the reasons I keep trying to get people to read Nanosystems. :)
09:19 < kanzure> i think the problem is the idea
09:19 < kanzure> i haven't seen a bootstrapping plan yet
09:19 < pmetzger> I hope that some small percentage of them will get seduced. :)
09:19 < klafka> i think i have drexler's nanosystems
09:20 < klafka> or a few books of his
09:20 < pmetzger> kanzure: you read the Merkle & Freitas toolset paper, yes?
09:20 < pmetzger> klafka: Engines of Creation is nontechnical.
09:20 < klafka> it was neat and seductive but, i didn't want to go into engineering/chemistry/etc...
09:20 < kanzure> i don't think the toolset paper explained how to build the tools
09:20 < pmetzger> kanzure: that paper points the way to a bootstrapping method...
09:20 < kanzure> oh
09:20 < kanzure> blah i should re-read it
09:20 < pmetzger> kanzure: if you have those tools, and they're fairly small molecules, you can build those tools.
09:21 < pmetzger> so presumably we look to ways to make those molecules by other means like synthesis.
09:21 < pmetzger> IF they will work.
09:21 < pmetzger> it is hardly a full bootstrap plan but it has the germ of a very good idea.
09:21 < klafka> hmmm how about laser modulated enzymes as tools
09:21 < klafka> that seems like a good tool frankly
09:21 < pmetzger> klafka: it depends on what you're using enzymes for.
09:21 < klafka> and they are doing that shit w/ optogenetics
09:21 < pmetzger> klafka: enzymes are usually meant to run in aqueous solution.
09:22 < klafka> i guess the problem is the energetics like you said
09:22 < klafka> that too
09:22 < kanzure> klafka: andrew and i are working on a proposal for electrically modulated template independent polymerases
09:22 < pmetzger> klafka: with fairly low energies.
09:22 < kanzure> klafka: but fenn (in here) had an idea a while back for embedding chromophores into polymerase and then using lasers to control which nucleotides it writes
09:22 < pmetzger> that's a bizarre and cool idea. :)
09:23 < kanzure> fenn: ping
09:23 < pmetzger> this is only for synthesizing arbitrarily long DNA stretches, though.
09:23 < klafka> kanzure interesting, how would you change the polymerase configuration to write a specific nucleotide
09:23 < kanzure> via the chromophore
09:23 < kanzure> so, the laser-based one is a very complicated process
09:23 < kanzure> i tried designing some experiments to build it
09:23 < kanzure> first, we'd have to find what i call a 'retarded' polymerase
09:23 < klafka> yeah
09:23 < kanzure> a polymerase that only writes one of the four nucleotides
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09:23 < klafka> for each of the four nucleotides
09:23 < kanzure> yes
09:24 < kanzure> and then try to incorporate that into a chromophore switch
09:24 < kanzure> definitely a feat of enzyme engineering and motif hackery
09:24 < pmetzger> you need to design a modified polymerase to make this work. hard problem...
09:24 < klafka> that'll be challenging in itself, until MD simulations come along
09:24 < pmetzger> you need more than MD simulations to do this.
09:24 < kanzure> pmetzger: you wouldn't design it; you'd use self-compartmentalized evolution
09:24 < pmetzger> because MD only gives you the folding.
09:24 < klafka> well MD simulationscould do both pmetzger but in either case it's completely intractable
09:24 < kanzure> oops
09:24 < pmetzger> dunno what you mean by "self-compartmentalized evolution"...
09:24 < kanzure> "compartmentalized self-replication"
09:24 < kanzure> http://www.ncbi.nlm.nih.gov/pubmed/11274352
09:25 < kanzure> Directed evolution of polymerase function by compartmentalized self-replication.
09:25 < kanzure> compartmentalized
09:25 < pmetzger> MD simulations are pseudo-neutonian. they don't tell you what reactions happen...
09:25 < kanzure> pdf: http://heybryan.org/~bbishop/docs/ellingtonia/polymerase/Directed%20evolution%20of%20polymerase%20function%20by%20compartmentalized%20self-replication%20-%20Ghadessy.pdf
09:25 < pmetzger> or how a chromophore would transfer energy...
09:25 < kanzure> so anyway, the chromophore idea is more complicated
09:25 < klafka> yea
09:26 < kanzure> but i might be getting some funding for the electrically-modulated polymerase idea
09:26 < kanzure> and we don't even need to demonstrate writing really
09:26 < kanzure> just that we can tether polymerase with streptavidin and biotin
09:26 < pmetzger> this paper has a neat trick in it...
09:26 < kanzure> and that we can electrically turn it on and off
09:26 < kanzure> through some mulitplexing circuit i guess
09:27 < pmetzger> cool paper...
09:27 < kanzure> :)
09:27 < kanzure> CSR is usually done in emulsions (but there are other ways)
09:28 < pmetzger> back to work with me...
09:28 < klafka> what is your goal for it past turning it on/off, how are you gonna get to template independent
09:28 < kanzure> wasn't my idea.. i'm just seeing what i can do with it
09:28 < klafka> aah
09:28 < kanzure> right now i don't think we'll be able to control which nucleotides it throws in
09:28 < kanzure> but we'll see.
09:29 < pmetzger> so whatever you do, you want it to be accurate for millions of cycles.
09:29 < pmetzger> but if you could demonstrate even ten or twenty that would be huge.
09:30 < pmetzger> Am 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 < pmetzger> doing something that didn't require step after step that way would be enormous.
09:30 < pmetzger> revolutionary.
09:31 < kanzure> DMD based DNA synthesis is the new rage
09:31 < kanzure> photochemical-based DNA synthesis, etc.
09:31 < kanzure> phosphoramidite is old and clunky, yes
09:32 < pmetzger> expand DMD?
09:32 < kanzure> micromirror arrays you find in office projectors mounted on ceilings
09:34 < pmetzger> ah, the silicon micromachined mirror arrays Texas Instruments makes, yes.
09:34 < pmetzger> so people have come up with a method there that works?
09:35 < pmetzger> or at least that works a little bit?
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09:36 < kanzure> there's been a few papers, yes
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09:41 < kanzure> hi lepton 
09:42 < lepton> howdy
09:43 < lepton> I've been trying to get EMC2 setup for so long, kanzure
09:43 < lepton> soooo so long
09:44 < kanzure> what's been the roadblock?
09:45 < kanzure> haha 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 < kanzure> re: open source hardware
09:45 < kanzure> it strikes me as very ironic
09:45 < kanzure> the answer is, of course they'll undercut you! market forces, yo
09:47 < kanzure> http://www.molecularist.com/lifeblog/2010/06/diybio-meet-up-report-folk-microbiology.html
09:47 < lepton> Well, 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 going
09:47 < kanzure> http://blog.makezine.com/archive/2010/06/things_heat_up_for_openpcr_project.html
09:47 < kanzure> oh now this just pisses me off
09:47 < lepton> We also had a lot of motherboard compatibility problems
09:47 < kanzure> "
09:47 < kanzure> "Not only are they making their plans for a key piece of DIY Bio hardware
09:47 < kanzure> open for everyone to use, but they're also soliciting input on its design."
09:47 < lepton> I was reading that on OpenPCR earlier this morning
09:47 < kanzure> never underestimate people's ability to bullshit, raise money
09:47 < kanzure> and then amke the community design it for you
09:47 < lepton> :/
09:47 < kanzure> rawr
09:47 < kanzure> hulk smash!
09:48 < kanzure> oh wait they do have a prototype
09:48 < kanzure> http://answers.oreilly.com/topic/1641-silicone-heaters-for-openpcr/page__p__3131&#entry3131
09:48 < kanzure> they should set up a design repository
09:49 < lepton> All open hardware projects
09:49 < lepton> almost none do :/
09:49 < kanzure> :'(
09:49 < kanzure> bbl
09:49 < lepton> all open hardware projects *should
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11:13 < kanzure> Chromophore-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.pdf
11:17  * kanzure is slowly uplloading "Genetically targeted chromophore-assisted light inactivation"
11:18 < kanzure> "Selective destruction of protein function by chromophore-assisted laser inactivation"
11:21 < pmetzger> destruction, or temporary inactivation?
11:21 < pmetzger> you want temporary inactivation right?
11:21 < kanzure> there are others that do temporary inactivation
11:22 < pmetzger> free radicals sound destructive. :)
11:25 < pmetzger> One 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 < kanzure> aggreed\
11:26 < pmetzger> presumably you want to steal existing reactants and graft them on...
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11:37 < kanzure> hm still uploading
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12:33 < fenn> pong
12:34 < pmetzger> ping!
12:39 < kanzure> i was pinging you about writozyme stuff
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13:12 < kanzure> pmetzger: i'm excited about tomorrow night. it's going to be like opening presents
13:12 < kanzure> extropic presents
13:12 < pmetzger> :)
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13:40 < lepton> kanzure: what comes in tomorrow?
13:41 < kanzure> i am going over to http://maxmore.com/ and http://natasha.cc/ 's house to type up some old 1980s/1990s extropian/transhumanist philosophy
13:41 < kanzure> that they have had hidden in boxes forever
13:44 < lepton> Cool
13:44 < lepton> type up? No book scanners?
13:45 < pmetzger> I think he should scan, too...
13:45 < pmetzger> the ancient typesetting is half the fun. :)
13:45 < pmetzger> and there are graphs and diagrams and such.
13:45 < lepton> I wonder if you could get google to do it for you?
13:45 < lepton> There are some decent open book scanner designs out there
13:46 < lepton> lego based designs, amongst them ;)
13:46 < pmetzger> There are excellent ones...
13:46 < pmetzger> the diy bookscanner crowd has been taking off.
13:48 < lepton> I wonder what a plot of the activity of that crowd would look like over time?
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13:48 < lepton> Seems like if its successful enough it can render itself obsolete
13:48 < pmetzger> have a look at book piracy online for a curve. :)
13:48 < lepton> all books = scanned
13:48 < lepton> Oh, I already know ;)
13:48 < lepton> I actually just got a new ebook reader and put openinkpot on it with a bunch of old scifi books on it
13:49 < lepton> Me and Arthur C Clarke are gonna party
13:52 < pmetzger> I think Clarke's state of putrefaction might impede that.
13:56 < AJollyLife> meh, i just use an SLR to scan my books
13:57 < pmetzger> An SLR isn't bad provided one has software to deskew etc. after.
13:58 < AJollyLife> yep
13:58 < AJollyLife> abby finereader is decent
13:58 < pmetzger> the diy bookscanner designs are, in fact, just cameras and setups to make using the cameras fast.
13:58 < AJollyLife> yeah, i dont scan enough stuff to make that worthwhile
13:58 < AJollyLife> and i've got a better camera than most of the diybookscanner setups, so I just split the page in software
14:00 < pmetzger> the software is the issue. proper deskewing etc. is hard.
14:01 < pmetzger> good software in the open source community to do it is only now appearing.
14:01 < AJollyLife> i have yet to see great open source software for it
14:01 < pmetzger> see the diy bookscanner web site.
14:01 < pmetzger> there is a big discussion of recently developed algorithms.
14:02 < pmetzger> some of them are pretty amazing.
14:02 < pmetzger> I 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.
14:03 < pmetzger> What 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 < pmetzger> that would be amazingly cool.
14:09 < jcluck> mmm diy bio yogurt
14:10 < lepton> I'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 capable
14:11 < pmetzger> calbire?
14:14 < lepton> It's an ebook library managment and format converter program
14:14 < lepton> I used it to do a batch conversion of PDF files to epub and rtf files
14:14 < lepton> worked very well
14:15 < fenn> http://www.flickr.com/photos/juliancash/673891099/in/set-72157600572658621/
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14:18 < fenn> calibre
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14:20 < fenn> superbaby in the technological womb
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15:41 < bkero> I use calibre to convert PDFs into EPUB files
15:41 < bkero> Works alright, but you lose a lot of information
15:41 < bkero> I wish calibre had automatic chapter detection, page re-enumeration, etc
16:07 < kanzure> ah yes i remember when it was cool to have usernames like this: http://www.youtube.com/user/EricGokuInuyasha1823
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16:32 < bkero> what
16:32 < bkero> That was cool at some point?
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17:34 < fenn_> rawr
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17:39 < kanzure> grandma called me to tell me that she's "excited about the singularity"
17:40 < kanzure> <3
17:42 < cluckj> lmao
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17:50 < fenn> wtf google uploader needs me to download and run a binary app?
17:50 < fenn> (for uploading google videos)
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17:56 < fenn> ack google video is dead? wtf!!!
17:57 < 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."
17:58 < pmetzger> google video is dead?
17:59 < fenn> you can't upload anymore
17:59 < pmetzger> not entirely surprised, but youtube doesn't let you download which sucks.
17:59 < fenn> and youtube won't let you upload >10min, and their algorithm to determine if something is >10min sucks
18:01 < fenn> and instead of saying "this service is no longer offered" they just give you some weird login error
18:02 < fenn> ug.. and vimeo only gives you 500MB/week
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19:15 < kanzure> haha it's funny seeing some other guy trying to namedrop on me
19:15 < kanzure> "yo i was hanging with eric schmidt from google yesterday"
19:15 < kanzure> "oh yeah? well MY guy was hanging with.."
19:17 < jrayhawk> cclive can download from youtube, vimeo, and google video
19:17 < kanzure> jrayhawk: try also youtube-dl
19:18 < pmetzger> I still think of Eric as one of the creators of lex
19:18 < jrayhawk> why would i want to use a less functional tool?
19:18 < kanzure> jrayhawk: i ask that of FreeBSD users every day
19:18 < pmetzger> it is weird to think of him as an executive...
19:18 < jrayhawk> haha
19:19 < pmetzger> this 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 < jrayhawk> FWIW it's pretty easy to just stick ogv somewhere and have browsers play it natively nowadays
19:20 < jrayhawk> So 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.
19:21 < pmetzger> free hosting.
19:21 < pmetzger> if someone downloads your video a million times you're not screwed by it.
19:21 < jrayhawk> If it's non-profit, make Bryan host it on his vserver.
19:21 < pmetzger> if you have it up on dreamhost you'll run out of bandwidth.
19:21 < pmetzger> does he have a virtual with *unlimited* bandwidth?
19:21 < jrayhawk> Pretty much.
19:21 < pmetzger> even if you're not being charged for it, youtube has the feature that it has an insane amount of connectivity via google.
19:23 < fenn> "the hayabusa re-entry observation campaign" http://archive.seti.org/pdfs/csc-June-10.pdf
19:24 < pmetzger> I suppose, though, one could get a similar effect (if one was ot worried about costs) by using Amazon S3
19:24 < pmetzger> s/ot/not/
19:24  * kanzure finally got around to setting up s3/ec2/sqs/etc.
19:24 < fenn> oops, bad url, sorry
19:25 < QuantumG> fenn: http://www.spacevidcast.com/2010/06/22/the-little-spacecraft-that-could-hayabusa-spacepod-2010-06-22/
19:25 < fenn> http://airborne.seti.org/hayabusa/
19:28 < fenn> 
19:28 < kanzure> fail
19:28 < fenn> off to go learn about parallelism in python
19:28 < kanzure> mpi?
19:28 < fenn> i always hit ctrl-O because it's "save" in nano
19:29 < fenn> mpi?
19:29 < kanzure> it's a multi processor interface thingy
19:29 < kanzure> for parallel programming voodoo
19:30 < fenn> i think this is just a basic introduction to the concepts, which is more my speed right now
19:30  * fenn waves
19:31 < pmetzger> python threads aren't real threads. :|
19:31 < pmetzger> of course, then again, that means they don't misbehave as much as real threads. :|
19:32 < bkero> That's why god invented fork().
19:32 < kanzure> hm do you mean the native threads stuff
19:32 < kanzure> i thought twister(?) or something did real threading
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19:34 < kanzure> hi lepton
19:34 < kanzure> any progress with emc2?
19:35 < lepton> yeah, things are moving along
19:35 < lepton> Still no motion, I'll finish wiring tomorrow morning and then test it out
19:35 < bkero> kanzure: twisted
19:36 < lepton> This ended up being an epic project, but I think it'll be worth it when it's done
19:36 < kanzure> bkero: does it do threading?
19:36 < kanzure> or is it a unit testing framework
19:36 < kanzure> i forget :(
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19:41 < pmetzger> twister does event driven programs.
19:41 < pmetzger> which, to the extent that they do multiplexing well, are better than threads.
19:41 < bkero> twisted
19:42 < pmetzger> but to the extent that it doesn't help using multiple CPUs, are worse.
19:42 < pmetzger> er, twisted.
19:42 < kanzure> i'm surprised you haven't heard about mpi either
19:42 < kanzure> that's a common tool for doing simulations
19:42 < kanzure> well, i guess you might not write the actual simulation software
19:43 < kanzure> just a user :)
19:45 < lepton> So I've slightly over committed myself to CNC routering and 3d printing a bunch of stuff for a Burning Man camp
19:46 < lepton> Know of anything maker / open source / transhumanist stuff going on there this year?
19:52 < QuantumG> what are you 3d printing with?
19:52 < lepton> I'll soon have a BFB300, from the company bitsfrombytes in the UK
19:53 < lepton> hopefully, at least
19:53 < lepton> On order for the first batch they send out to the US
19:53 < kanzure> martin just got makerbot #1595
19:53 < kanzure> they have makerbots in stock now O_o
19:53 < lepton> Awesome
19:54 < lepton> I'm excited to use PLA with it
19:55 < lepton> (polylactic acid) We're gonna try to make forms for plants to grow in
19:55 < QuantumG> cool.. so what are you printing?
19:56 < lepton> Trinket type things (with the camp's symbol and a location and time) that have different geometric shapes (stellated dodecahedron, etc)
19:57 < lepton> and an internal structure that contains seeds
19:57 < lepton> Which, when you leave the dry environment of burning man, you can plant (or perhaps crush and plant) and it'll grow
19:57 < lepton> That's the idea, at least
19:58 < QuantumG> neat. 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 < lepton> Well, 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)
19:59 < lepton> and we needed to make a few hundred small levers with unique geometry
19:59 < lepton> $4000 for a cheap injection molding, then $0.02 per unit in small volumes
19:59 < lepton> or $4000 for a 3d printer, at around $1.50 a knob (and much slower in production), but not limited to just that part
19:59 < QuantumG> I must have missed it, who's "we"?
19:59 < lepton> so 3d printer it was
20:00 < lepton> Oh, I started an engineering company
20:00 < QuantumG> oh yeah?  what sort of work do you do?
20:02 < lepton> embedded electronics, power electronics, mechanical engineering, lots of stuff, really
20:02 < QuantumG> ahh cool.
20:02 < lepton> We do consulting as well as internal products
20:03 < lepton> With the idea of over time accumulating automated manufacturing hardware and designs
20:03 < lepton> Somewhat inline with kanzure's skdb sort of paradigm
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20:04 < lepton> so far we've been developing scuba diving equipment, electric motor control hardware, battery mangement systems, and machine vision sensors
20:05 < lepton> and working on CNC hardware a good bit, with some flashy arduino art projects thrown in the mix
20:06 < QuantumG> cool stuff
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