--- Day changed Sat Mar 07 2009 00:52 < kanzure> http://scholar.google.com/scholar?q=micromolding+in+capillaries 01:13 -!- ybit [n=heath@unaffiliated/ybit] has quit [Remote closed the connection] 01:18 -!- ybit [n=heath@unaffiliated/ybit] has joined #hplusroadmap 01:18 -!- ybit [n=heath@unaffiliated/ybit] has quit [Remote closed the connection] 01:20 -!- ybit [n=heath@unaffiliated/ybit] has joined #hplusroadmap 01:36 < kanzure> http://heybryan.org/books/papers/microfluidics/Micromolding%20of%20Polymers%20in%20Capillaries%20-%20Saran%20wrap.pdf 01:36 < kanzure> Micromolding of Polymers in Capillaries - Saran wrap 01:45 < kanzure> hm, I should pour some nail polish down my microchannels 01:49 < kanzure> http://heybryan.org/books/papers/microfluidics/Capillary%20Force%20Lithography.pdf 01:49 < kanzure> capillary force lithography :) 02:03 < kanzure> someone should go stalk Kahp Y Suh, a Korean researcher at Seoul National University. 02:13 < kanzure> http://scholar.google.com/scholar?q=%22Kahp+Y.+Suh%22&hl=en&lr=&btnG=Search] 02:13 < kanzure> http://scholar.google.com/scholar?q=%22Kahp+Y.+Suh%22&hl=en&lr=&btnG=Search 02:14 < kanzure> On the role of oxygen in fabricating microfluidic channels with ultraviolet curable materials 02:47 < kanzure> why: http://heybryan.org/books/papers/microfluidics/suh/ 05:20 -!- jm [n=jm@p57B9D6D1.dip.t-dialin.net] has joined #hplusroadmap 08:52 -!- nsh [n=nsh@dsl-trebrasgw1-fe56fa00-65.dhcp.inet.fi] has joined #hplusroadmap 08:58 -!- wrldpc [n=worldpea@c-98-217-197-162.hsd1.ma.comcast.net] has joined #hplusroadmap 09:01 -!- any05627821 [n=someone@75-120-7-38.dyn.centurytel.net] has joined #hplusroadmap 09:19 -!- katsmeow-afk [n=someone@99.194.251.41] has quit [Read error: 110 (Connection timed out)] 09:30 < kanzure> "Programmed assembly of 3-dimensional microtissues 09:30 < kanzure> with defined cellular connectivity," by Zev J. Gartner and Carolyn R. 09:30 < kanzure> Bertozzi, appears in PNAS Early Edition, week of March 2, 2009. 09:30 < kanzure> http://www.pnas.org/content/early/recent 09:31 < kanzure> but it's not listed in the early edition of PNAS. wtf? 09:32 < wrldpc> Anybody got Keith Henson's wiki for space power satellites? 09:32 < wrldpc> google is producing nothing :\ 09:48 < fenn> wrldpc: http://htyp.org/dollar_a_gallon_gasoline 09:48 < wrldpc> tyvm 09:48 < wrldpc> http://htyp.org/Hundred_dollars_a_kg 10:02 -!- nsh [n=nsh@dsl-trebrasgw1-fe56fa00-65.dhcp.inet.fi] has quit [Connection timed out] 10:02 -!- Netsplit verne.freenode.net <-> irc.freenode.net quits: elias`, kanzure-, willPow3r 10:03 -!- Netsplit over, joins: elias`, willPow3r, kanzure- 10:09 -!- wrldpc [n=worldpea@c-98-217-197-162.hsd1.ma.comcast.net] has quit [] 10:13 < kanzure> wrldpc, Keith has been ranting about that on the extropy list for a few months now. 10:17 -!- wrldpc [n=worldpea@c-67-189-243-111.hsd1.ma.comcast.net] has joined #hplusroadmap 10:17 < kanzure> wrldpc, Keith has been ranting about that on the extropy list for a few months now. 10:18 < wrldpc> yeah ... I just got out of a "space initiative" skype conference put on by "the space renaissance" http://www.spacerenaissance.org/work/4009.pdf 10:18 < wrldpc> chat was postponed to next week 10:29 < kanzure> oh, that was probably Charles Radley in that chat? 10:35 -!- wrldpc [n=worldpea@c-67-189-243-111.hsd1.ma.comcast.net] has quit [] 11:18 -!- wrldpc [n=worldpea@173.48.207.37] has joined #hplusroadmap 11:53 -!- splicer_ [n=patrik@h22n2c1o261.bredband.skanova.com] has joined #hplusroadmap 12:43 < fenn> hey this should be useful for something, complete street map of the US: http://perens.com/FreeSoftware/ 12:43 < fenn> wish he had linked to the actual file on the census website 12:59 -!- willPow3r [n=will@cpe-66-75-6-181.san.res.rr.com] has quit ["Leaving"] 13:07 < wrldpc> Yeah Radley 13:16 -!- gene [n=chatzill@wireless-128-62-96-13.public.utexas.edu] has joined #hplusroadmap 13:17 < gene> kanzure do you know what pyradean solar cells are? 13:19 < gene> oops pyradian 13:19 < gene> http://www.nlv-solar.com/what_we_do/products/ 13:19 < gene> damn they don't provide much information on it 13:26 < gene> http://psychology.uwo.ca/fmri4newbies/ScanningTooMuch.html 13:31 < fenn> "Not only can you recognize the brains of your frequently-scanned co-workers, but also their teeth from the bite bar impressions." hmmm.. 13:32 < fenn> 50% efficient solar eh? 13:33 < fenn> pretty sweet car too 13:35 < gene> well it looks like it has a quality of about 100% which means it's all vaporware 13:35 < fenn> naturally 13:35 < gene> plus it uses flow batteries 13:35 < fenn> whatever that means 13:35 < fenn> is that like a vanadium redox battery? 13:35 < gene> instead of gas you refill with battery electrolytes 13:36 < gene> oh wait it looks like it might be reversible 13:36 < fenn> right but with 100% efficient solar panels you can recharge it 13:36 < fenn> er 50%, whatever 13:36 < gene> http://en.wikipedia.org/wiki/Flow_battery 13:36 < gene> 50% how? 13:37 < gene> they say 38% conversion efficiency 13:37 < gene> hmmm... uranium redox flow battery 13:38 < gene> yes vanadium is one of them 13:38 < gene> http://www.imr-oarai.jp/en/research/research4-5.html 13:39 < gene> URANIUM BATTERY BEATS ALKALINE BATTERY HANDS DOWN 13:50 -!- ybit [n=heath@unaffiliated/ybit] has quit [Read error: 104 (Connection reset by peer)] 13:52 < fenn> i can just see a new clusterfuck brewing 13:53 < fenn> it has nothing to do with uranium being fissionable but it's being studied at the center for nuclear materials science 13:53 < gene> yeah 13:53 < gene> I know 13:54 < gene> depleted uranium can easily be turned into plutonium if you bombard it with neutrons you know? 13:57 < fenn> uranium is a common heavy metal which we just happen to have craploads of lying around in purified form 13:57 < fenn> oh well 13:59 < gene> really uranium is that common? 13:59 < gene> can I get acouple nuclear bombs of the stuff for escaping the universe? 14:00 < fenn> i can think of easier ways to commit suicide 14:00 < fenn> and you're missing the point 14:00 < gene> no 14:00 < gene> not to commit suicide 14:00 < fenn> they use uranium in bullets because it's heavy and cheap 14:01 < gene> really? 14:01 < fenn> well, cheap by military standards 14:01 < fenn> but if you dissolve one bullet to make an electric car go indefinitely.. that's cheap 14:02 < gene> by military standards.... 14:03 < fenn> the A-10 shoots 4200 30mm depleted uranium rounds per minute 14:03 < gene> dang can't find my link about using a micro blackhole created by nuclear bomb powered lasers to send nanobots to another universe to essentially escape from this one 14:04 < gene> well I guess that must be cheap 14:04 < fenn> that's 16000 lb of uranium? 14:04 < fenn> per mission 14:05 < fenn> now, someone has to clean up that mess afterward 14:27 -!- wrldpc [n=worldpea@173.48.207.37] has quit [] 14:30 -!- wrldpc [n=worldpea@173.48.207.37] has joined #hplusroadmap 14:46 -!- jm|earth [n=jm@p57B9D6D1.dip.t-dialin.net] has joined #hplusroadmap 15:03 -!- jm [n=jm@p57B9D6D1.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] 15:05 -!- wrldpc [n=worldpea@173.48.207.37] has quit [] 15:48 < kanzure> gene: that might have been Lee Smolin, but he doesn't talk about nuclear bombs, lasers, or nanobots, but he does talk about black holes and seeding other universes 15:49 < kanzure> 05:59:42 omg/user: i want to do stochastic reaction network modeling on the history of the debian package repository 15:59 < kanzure> fenn: did you see my notes/links last night about capillary force lithography? 15:59 < fenn> yeah but what about it 16:00 < kanzure> ever come across it before? what's your take on it? other generic questions here 16:01 < fenn> i'm surprised it works at such small scales but i dont see what it's good for 16:02 < fenn> isnt it basically the same as PDMS imprinting? 16:02 < fenn> with a thinner layer 16:03 < kanzure> it's my understanding that in PDMS, you throw plastic at some mold, and then you let it cure, then you "peel it off" and you have a plastic-gel-thingy that has your circuit in it 16:04 < fenn> oh? 16:04 < kanzure> wait, am I wrong? 16:04 < fenn> i thought you just stamped the mold onto the substrate and it cured 16:04 < fenn> then you peel the mold off 16:04 < fenn> but more likely this would be a continuous rolling stamp 16:05 < kanzure> it sounds like we're saying the same thing. in your case, you're stamping, whereas I was thinking it was where you pour the liquid on to the mold 16:05 < fenn> anyway 100nm is plenty small for all sorts of electronics 16:05 < kanzure> is there a big difference? 16:05 < kanzure> so as for that anyway, 16:05 < kanzure> capillary force lithography seems to be useful for "fabricating inside of a microchannel" 16:05 < kanzure> but I'm not sure there are many uses for that at this point 16:06 < kanzure> for instance, Whitesides' work on gradients now kinda makes sense: the interface between two flows of two different things is the site of a chemical reaction related to 'fabrication' 16:06 < kanzure> (apparently it's also considered 'ECM in a tunnel'?) 16:06 < kanzure> but if you wanted precision, you'd just go with conventional lithography 16:06 < kanzure> and get some precision 16:07 < kanzure> on the other hand, capillary force lithography is easily doable as long as you're able to fabricate your tunnels with human hair 16:07 < kanzure> so that's somewhat the appeal. Although it might not allow for the fabrication of much, making it useless. Hrm. 16:08 < fenn> sure just order me up a 6 billion fab, instant precision 16:08 < kanzure> I was thinking of trying to see if I can get the nail polish to do capillary force lithography, i.e. draw out an inverse circuit with sharpie, make my patterns, and have the nail polish crawl up and down the circuit and then cure it in place, wash off the sharpie (or peel back tape if that's possible?), and get a polymer device. 16:08 < kanzure> are you being sarcastic? 16:08 < kanzure> I don't think I could fit a 6 billion dollar fab on my debit cards. 16:08 < fenn> "you'd just go with conventional lithography" is what we're trying to get away from 16:09 < fenn> i want to know how they made the stamp 16:09 < kanzure> "they"? 16:09 < kanzure> the PDMS stuff is the conventional method found in almost every microfluidics paper 16:09 < fenn> eh, suh et al 16:09 < kanzure> in the "methods" section 16:09 < fenn> "prepared by electron beam lithography" 16:09 < fenn> i guess that could be done on an amateur scale 16:09 < kanzure> oh, let me go find which of suh's paper that was 16:10 < fenn> http://heybryan.org/books/papers/microfluidics/Capillary%20Force%20Lithography.pdf 16:11 < fenn> search for 'we used' 16:12 < kanzure> aw, prepared by electron beam method or photolithography 16:12 < fenn> you know you could rapidly fabricate 3d structures with the pdms stamp by running the same tape through at different offsets, and imprinting different slices of the structure around your roller 16:12 < fenn> so each time the loop of tape goes around it advances one slice 16:12 < kanzure> one of his other paper was about growing nanospikes kinda like that 16:12 < kanzure> except without that mechanical roller. 16:14 < kanzure> so I don't get it- if sharpie microfluidics lets you make those capillaries, what's the big deal? so what if most people use an electron beam or photolithography? 16:14 < kanzure> (the nanospikes paper was "Stretched Polymer Nanohairs by Nanodrawing", btw) 17:05 < gene> No it wasn't Lee Smolin, it was scientific american or Michau Kaku 17:07 < kanzure> Kaku? I'd be surprised. He does more pop-sci stuff these days, mroe than anything. 17:17 -!- wrldpc [n=worldpea@173.48.207.37] has joined #hplusroadmap 17:20 -!- jm|earth [n=jm@p57B9D6D1.dip.t-dialin.net] has quit [] 17:35 < gene> yeah 17:36 < gene> this was a while back I don't really know 17:36 < gene> It was probably kaku 18:12 < gene> http://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/19670018173_1967018173.pdf 18:12 < gene> woo nasa archive 18:12 < gene> I think I found a pneumatic stepper 18:13 < gene> from long ago 18:13 < gene> which might moot a patent 18:15 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has joined #hplusroadmap 18:38 -!- any05627821 is now known as katsmeow 18:42 < kanzure> where can I find a list of obscure forces and phenomena categorized by material? 18:44 < bkero> The united nations charter 18:44 < bkero> *rimshot* 18:57 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has quit [Read error: 110 (Connection timed out)] 19:03 < kanzure> aha 19:04 < kanzure> Forces of significant magnitude in the micron-to-millimeter size regime 19:04 < kanzure> gravitational [31], electrostatic [35], magnetic [41], capillary [58], fluid shear [60], hydrodynamic [41], hydrophobic [64], van der Waals [55], biospecific (protein:ligand, DNA:DNA) [56], centrifugal [57], osmotic [59], entropic [61], light [62,63], casimir [65] 19:04 < kanzure> with references from a Whitesides paper. 19:13 < kanzure> "The modeling program was written in Visual Basic C and it was used in Excel (Microsoft) to generate bar graphs." 19:13 * kanzure twitches 19:20 < gene> are you trying to simulate materials? 19:20 < gene> a company that developed a new super efficient solar cell did that 19:20 -!- ferrouswheel [n=jp@121-73-144-159.cable.telstraclear.net] has left #hplusroadmap ["Leaving"] 19:21 < gene> http://www.nlv-solar.com/what_we_do/ 19:21 < gene> kanzure 19:21 < gene> I scanned me some more books today 19:21 < gene> guess what? 19:22 < gene> they made a fluidic memory device using a bead of water 19:26 < kanzure> what's the flip state? 19:27 < fenn> no bead of water? :) 19:27 * fenn mumbles about abaci (abacuses?) 19:30 < gene> bead of water in different place 19:31 < gene> what's tunneling and could I use it to securely transfer data to you 19:31 < gene> fast 19:35 < gene> or would usb drive delivery via rocket be faster? 19:39 < fenn> depends how secure you want it 19:39 < fenn> do you really not know what quantum tunneling is? 19:40 < fenn> btw here's a fun thing to try to make http://en.wikipedia.org/wiki/Quantum_Tunneling_Composite 19:40 < fenn> it's metal powder in some kind of synthetic rubber 19:41 < gene> oh yeah 19:41 < fenn> i saw you had mutr bookmarked 19:41 < gene> yup 19:41 < gene> great place to get the stuff 19:43 < kanzure> gene: "tunneling" is SSH. 19:43 < kanzure> or at least, that's what I mean when I say tunneling 19:43 < gene> ok 19:44 < gene> what I really want to make is shear thicking fluid 19:44 < gene> thickening 19:44 < gene> http://www.mutr.co.uk/product_info.php?cPath=418_468&products_id=1304 19:44 < gene> hahahaha 19:44 < kanzure> http://heybryan.org/mediawiki/index.php/Microarray 19:44 < fenn> uh, cornstarch and water? 19:44 < kanzure> yay for forgetting content you previously found. 19:44 < gene> they could very well be selling cornstarch 19:45 < gene> well basically, but I want to make the better kind with colloidal silica 19:45 < fenn> are you rabid about this/ http://www.technovelgy.com/ct/Science-Fiction-News.asp?NewsNum=108 19:45 < gene> the kind you can impregnate kevlar vests with to make them stab proof 19:45 -!- elias` [n=me@unaffiliated/elias/x-342423] has quit [Read error: 145 (Connection timed out)] 19:46 < fenn> thought so 19:46 < gene> http://www.technovelgy.com/ct/Science-Fiction-News.asp?NewsNum=2169 19:46 < gene> fenn, every evil genius needs to have a high-tech supersuit 19:46 < fenn> 500nm silica spheres in PEG 19:46 < gene> yeah 19:47 < gene> surprisingly quack medicine people sell the stuff 19:47 < fenn> they're surprisingly open about this given its military potential 19:47 < gene> but cab-o-sil is better 19:47 < gene> speaking of which 19:47 < gene> did you see my gryscope bookmark? 19:47 < fenn> no 19:48 < fenn> FEM simulator? 19:49 < fenn> meh 19:49 < gene> http://www.abominablefirebug.com/AuthorFiles/r9006.pdf 19:49 < gene> read science fairs 19:50 < gene> http://www.abominablefirebug.com/AcousticGyro.html 19:50 < gene> better 19:51 < fenn> yeah, why bother when you can buy a chip that does the same thing 19:51 < gene> so this kid makes a superaccurate gyroscope using sound, so sensitive it measure the rotation of the earth 19:52 < gene> this is during the cold war, so he gets a cease and desist letter from a Federal Court 19:52 < gene> well how sensitive are current chips? 19:54 < fenn> no idea :P 19:54 < gene> sensitive enough to sense the rotation of the earth? 19:54 < fenn> actually that looks pretty simple 19:56 < fenn> vacuum tubes :) 19:57 < fenn> you learn something every day: http://en.wikipedia.org/wiki/Halteres 19:59 < fenn> now i think that acoustic gyro is actually worth looking into 19:59 < fenn> it'd certainly be cheaper than the MEMS gyro chips 20:00 < gene> pah vacuum tubes? why use vaccuum tubes, when you can use fluidics! 20:00 < fenn> uh, yeah. 20:01 < fenn> who needs transducers anyway 20:02 < gene> yeah it would be 50% more impractical than vacuum tubes, but it'd be able to deliver things to the amish 20:07 -!- katsmeow is now known as katsmeow-afk 20:09 < gene> now I wonder, how did punched tape n/c machines work? 20:10 < kanzure> fenn, gene, you two up for a movie tonight? 20:10 < kanzure> Emil and I are planning on seeing Watchmen at 10:20 at Dobie. 20:10 < gene> let me guess watchmen? 20:11 < gene> hmmm... that prospect sounds like it might be worthwhile 20:11 < gene> kanzure 20:11 < gene> could you bring a usb drive? 20:11 < gene> I got some delicious datar 20:11 < gene> data 20:11 < kanzure> okay. 20:11 < kanzure> do you have two USB ports? 20:12 < gene> yeah 20:12 < gene> but that doesn't matter 20:12 < gene> hmmm... 20:12 < gene> I can't take backpacks into a movie theater 20:12 < kanzure> the USB device I have needs two USB ports. 20:12 < gene> what is it? 20:12 < kanzure> a brick. 20:12 < gene> is it a 1 tb brick 20:13 < fenn> i think i'll pass on the movie 20:13 < kanzure> fenn: okay. 20:13 < gene> if it is then you might want to talk to the anime club 20:13 < kanzure> gene: what's the g/L ratio that we've been getting for neochloris? 20:13 < gene> ask sata, not me 20:13 < gene> wait 20:13 < kanzure> wasn't it like 1 g/L ? 20:14 < gene> something like that 20:14 < gene> no don't have it 20:14 < kanzure> I just came across a paper that did some genetic engineering to get 20 g/L butanol. 20:14 < kanzure> "Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels." 20:15 < gene> I just met some people who worked with making a reactor to grow stuff that makes butanol 20:15 < gene> a now obsolete design 20:15 < gene> I mean a now obsolete process 20:17 < gene> haha they have standards for punched tape NC systems 20:17 < gene> kanzure, now find a way to convert it to Acrylonitrile butadiene styrene 20:17 < fenn> bah 20:18 < fenn> why dont you work on extruding PLA which is already manufacturable from bio-stuffs 20:18 < gene> http://en.wikipedia.org/wiki/1,3-butadiene 20:19 < gene> because PLA isn't a good plastic for Texas 20:19 < fenn> you're thinking PCL 20:19 < fenn> hmm what was the corn rubber? 20:20 < gene> cars get hot 20:20 < fenn> poly beta hydroxy butyric acid 20:22 < gene> PLA can melt at texas temperatures 20:22 < fenn> so can ABS? 20:22 -!- jm [n=jm@p57B9D6D1.dip.t-dialin.net] has joined #hplusroadmap 20:22 < fenn> what are dashboards made of? some kind of vinyl (probably PVC with plasticizers) 20:22 < gene> or at least it becomes soft 20:23 < gene> at 122 degrees 20:23 < fenn> mutr has so much cool stuff 20:23 < fenn> i just want to order one of each 20:23 < gene> yeah me too 20:24 < gene> order it for the fablab 20:24 < gene> ;) 20:24 < fenn> well, the materials at least 20:24 < fenn> the kits are lame 20:24 < gene> yeah 20:24 < gene> kits lets dupe the kits 20:25 < gene> we could sell mutr materials 20:25 < gene> http://www.mutr.co.uk/product_info.php?cPath=418_556&products_id=1009544 20:25 < gene> wonder if they've been purified 20:25 < fenn> yeah i got a laugh from that 20:26 < fenn> check out their prices on gears 20:26 < fenn> you can't get gears that cheap anywhere 20:27 < fenn> http://www.mutr.co.uk/product_info.php?products_id=136 20:27 < gene> what about china? 20:27 < fenn> well sure, but you have to order 10 zillion at a time 20:28 < gene> http://www.mutr.co.uk/product_info.php?products_id=299 20:29 < gene> you know I think they used to make microchips like this 20:29 < gene> looked so pretty 20:29 < gene> you know the fablab should definately have ferrofluid 20:29 < fenn> lots of programmable chips had glass windows for UV erasing 20:30 < fenn> quartz actually 20:30 < gene> http://www.mutr.co.uk/product_info.php?products_id=1089 20:30 < gene> carbon fiber 20:31 < gene> http://www.mutr.co.uk/product_info.php?products_id=1009547 20:31 < gene> that's an awesome price 20:32 < kanzure> does PCR-based gene synthesis make sense? 20:32 < kanzure> apparently some people have been taking a set of 40 oligos and just PCR amplifying them and ligating them together to make longer sequences 20:32 < gene> yeah 20:32 < kanzure> and thus skipping the nucleotide-by-nucleotide process 20:32 < gene> that's called OEPCR 20:32 < gene> overlap extension 20:33 < gene> that's what the synners here on campus are doing 20:33 < kanzure> you haven't given me evidence that they exist yet. 20:33 < gene> what, really? 20:33 < kanzure> oh wait 20:33 < kanzure> yes you did 20:33 < kanzure> I even edited their wiki 20:34 < kanzure> okay, nevermind 20:34 < fenn> you still have to synthesize the oligos 20:34 < gene> they're the people who heard you like eukaryotes so they put eukaryotic genes in your prokaryotes so your prokaryotes can express genes like prokaryotes 20:34 < kanzure> fenn: but just once. 20:34 < fenn> and then PCR isnt that great re: typos 20:34 < kanzure> fenn: then you PCR amplify them and give them to your friends 20:35 < kanzure> and they draw their PCR circuits with sharpie or some bullshit like that 20:35 < fenn> huh? 20:35 < kanzure> what? 20:35 < fenn> PCR circuits? 20:35 < kanzure> blah, didn't I linkdump you the PCR-microfluidics papers? 20:35 < fenn> i saw the $10 thermocycler 20:35 < fenn> and i can imagine an equivalent microfluidic device 20:35 < kanzure> http://heybryan.org/books/papers/microfluidics/pcr/ 20:36 < fenn> but you still have to make the 40-oligo 20:36 < kanzure> http://heybryan.org/books/papers/microfluidics/synthesis/ 20:36 < fenn> which is the limiting step 20:36 < kanzure> yes, but that's more of a one-time deal 20:36 < fenn> it's not a one-time deal 20:36 < gene> 40 oligos can be done with maskless array gene synthesis 20:36 < kanzure> why not? 20:36 < kanzure> my DNA was a one-time deal from when I was embryo .. so neigh! 20:36 < fenn> your complete library of 40-oligos would be 2560000 tubes 20:36 < gene> and very fast 20:37 < gene> yeah, I don't think that it will work out 20:37 < kanzure> fenn: shouldn't we choose a number smaller than 40 20:37 < fenn> 10-oligo would still be 10000 tubes and probably wouldnt even work 20:39 < fenn> hmm this sounds interesting 20:39 < fenn> Nanodroplet real-time PCR system with laser assisted heating 20:39 < gene> with LASERS 20:39 < gene> AWESOME 20:40 < gene> guess what just happens to be cheap? 20:40 -!- splicer_ [n=patrik@h22n2c1o261.bredband.skanova.com] has quit [Remote closed the connection] 20:40 < gene> 200 mw lasers 20:40 < gene> that's what 20:41 < gene> use black substrate 20:41 < fenn> dye in solution 20:41 < gene> that contaminates things 20:41 < gene> hmm... I guess graphite might work 20:41 < fenn> aww it's still slow 20:41 < fenn> 370 seconds 20:41 < kanzure> 370 seconds? 20:41 < kanzure> slow! blah. 20:42 < gene> that's VERY SLOW 20:42 < fenn> 20 seconds per cycle 20:42 < kanzure> 6 minutes is too long? 20:42 < kanzure> I remember using thermocyclers for 30 to 40 minutes 20:42 < kanzure> on certain protocols. 20:43 < fenn> because they used those stupid plastic tubes 20:43 < gene> wait, 370 seconds for a whole cycle 20:43 < kanzure> as opposed to what? 20:43 < fenn> 370 seconds for an amplification reaction, 10 sec melt, 2 sec anneal, 7 sec recombine (sth like that) 20:43 < gene> link to pcb heater droplet manipulation? 20:44 < kanzure> http://heybryan.org/books/papers/microfluidics/Microthermal%20Devices%20for%20Fluidic%20Actuation%20by%20Modulation%20of%20Surface%20Tension%20-%20Basu%20-%20awesome.pdf 20:44 < fenn> gene: http://heybryan.org/books/papers/microfluidics/128-pixel digitally programmable microfluidic platform for non-contact droplet actuation using Marangoni flows - Basu.pdf 20:44 < kanzure> fenn's link is more succint. 20:44 < kanzure> the link I gave is the friggin' phd thesis 20:45 < gene> fenn's link is dead 20:45 * fenn beats gene about the head with a %20 20:46 < fenn> just download anything with 'marangoni' in the title 20:46 < kanzure> in this directory: http://heybryan.org/books/papers/microfluidics/ 20:46 < fenn> why is it people are blind to the text in URL's? 20:47 < gene> I put http://heybryan.org/books/papers/microfluidics/ in my bookmarks toolbar 20:47 < gene> cheap gene synth's are scary though 20:48 < gene> Ebola happens to have a nice small genome 20:48 < fenn> why don't you push for restrictive legislation that will hamper research 20:48 < kanzure> if you're so scared, why not work on space habitats 20:49 < gene> however it's potential for a biological weapon is severly limited by the by it's fast kill rate 20:49 < fenn> the reason ebola is so deadly is because the stupid africans roll around with the dead bodies 20:49 < gene> Scared, I like scary things, scary is more fun 20:50 < gene> so can we make our own nucleotides? 20:50 < gene> if we can't then we are screwed 20:50 < kanzure> have you memorized phosphoramidite synthesis yet? 20:50 < fenn> <- not an organic chemist 20:50 < gene> cuz the governent's gonna take them away if gene synthesizer become ez to make 20:50 < gene> <- isn't either 20:51 < fenn> that's why you want an in-vivo writozyme 20:51 * kanzure wants another way to do oligonucleotide synthesis than phosphoramidite methods. 20:51 < fenn> bypass all this silly chemistry stuff 20:51 < gene> perhaps Miller urey style? 20:51 < kanzure> hah 20:51 < kanzure> yes, I'll create a micro black hole and evolve my damn sequence 20:51 < kanzure> and then extract it through the quantum foam 20:51 < kanzure> or some other bullshit like that. 20:51 < fenn> cat /dev/random | sequencer 20:52 < gene> might cause methlab style explosions at biohackers houses though... 20:52 < gene> passing a spark through methane and what not? 20:52 < kanzure> how much calibration is done on current synthesis methods though? 20:52 < kanzure> is each run sequenced or checked or anything? 20:52 < kanzure> or do you "get what you get"? 20:53 < fenn> hah you saved my crappy inkscape drawing 20:53 < kanzure> rabid archiving. 20:54 < gene> well gene synthesis can be a bit inaccurate 20:56 < gene> so how can we use that m-effect to make a synth 20:56 < gene> or whats 20:56 < gene> the photosensitive capping chemical? 20:57 < kanzure> http://heybryan.org/mediawiki/index.php/DNA_synthesizer 20:57 < kanzure> ^ I outlined the oligonucleotide synthesis method there 20:57 < kanzure> although hopefully a better explanation exists somewhere else on the internet 20:57 < gene> ok, how do we do that using droplets? 20:58 < kanzure> what are you asking? 20:59 < kanzure> are you asking me to write the resistor-activation/deactivation program for Basu's system? 20:59 < kanzure> a good first step in that case would be to write a basic library for common fluidic operations or something, involving a sequence of activation and inactivation 21:00 < gene> no, how should we move the droplets of chemicals, IE in which pattern should we move them around 21:00 < kanzure> sounds like an optimization problem. 21:00 < fenn> yucko 21:00 < fenn> i like the DLP mirror array methods 21:01 < fenn> you could even use a LCD i bet 21:01 < gene> who needs DLP mirrors when LCDs are cheap 21:01 < gene> I mean really, why? 21:02 < fenn> they're way faster and higher contrast 21:02 < fenn> contrast = less errors 21:02 < gene> they're good enough for maskless array synthesis 21:02 < fenn> er, yes that's what i'm saying? 21:03 < gene> so what's the photo sensitive capping chemical? 21:03 < fenn> kanzure: did you say you made a marangoni flow actuator? 21:04 < kanzure> I thought that's what the 16x16 resistor microheater array was for? 21:04 -!- jm [n=jm@p57B9D6D1.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] 21:04 < kanzure> but if you just press your hand to a glass surface compressing liquid, you can see liquid move, it's sometimes called 'superspreading' 21:04 < gene> well I'm about to buy tickets for watchmen 21:04 < fenn> calixarine? 21:04 < kanzure> gene: why right now? 21:04 < gene> yeah 21:05 < gene> what, should I buy them later? 21:05 < kanzure> the movie is at 10:20. 21:06 < gene> it came out yesterday, there is a high likelihood that they will sellout relatively quickly 21:06 < fenn> gosh i wish they'd write these patent claims in python or something 21:07 < kanzure> gene: oh. 21:07 < kanzure> um, how quickly is relatively? 21:07 < gene> unknown 21:09 < kanzure> http://en.wikipedia.org/wiki/Gene_synthesis#3.29_Limitations 21:09 < kanzure> I think confining the oligo in a channel would be a method of preventing some of this from happening 21:11 < fenn> is there some way using biobrick-like restriction enzyme methods would help? 21:11 < fenn> one ligation reaction per oligo, that way you're sure to get them in the right order 21:12 < fenn> am i making sense? 21:12 < kanzure> I was trying to find a paper that describes what precisely the errors *are* 21:12 < kanzure> is it because it gets a ligation step incorrectly or something? 21:12 < fenn> in oligo synthesis? 21:12 < kanzure> yes 21:12 < kanzure> or is it a chemical effect because of phosphoramidite chem? 21:13 < fenn> hey this was my idea - bastards! 21:13 < fenn> http://www.freshpatents.com/Error-reduction-in-automated-gene-synthesis-dt20060622ptan20060134638.php 21:14 < kanzure> was this the automated overlap but plus re-synthesis of the erroneous parts paper? 21:15 < fenn> no it just precipitates the sequences with errors out of solution 21:15 < kanzure> how do they know the cause of these errors- maybe it's their incompetence versus machine limitations etc.? 21:16 < fenn> it's just chemistry i think 21:16 < kanzure> isn't that hand-waving? 21:16 < fenn> not really 21:16 < fenn> there are all sorts of side reactions that happen in any reaction 21:16 < fenn> usually they get purified out to some extent 21:16 < kanzure> pfft so let's not characterize them 21:17 < fenn> well its not my fault the literature is not revealing itself 21:17 < kanzure> it's because we don't know the right words to rape google with :/ 21:17 < fenn> "Random chemical side reactions create base errors in these single-stranded oligos." 21:18 < fenn> "oligo side reaction" gets this http://www.informaworld.com/smpp/content~content=a713643565~db=all~order=page 21:18 < fenn> which has a lot of chemistry gobbledygook 21:18 < kanzure> aha 21:18 < kanzure> "DNA synthesis errors associated with double-strand-break repair" 21:18 < kanzure> cited by 106. so that's my toehold into the literature. 21:18 < fenn> no, that's not what you want 21:19 < kanzure> oh, it might be about biosynthesis 21:19 < fenn> double-strand-break repair is some kind of natural enzyme mechanism 21:19 < kanzure> blah 21:19 < kanzure> "Genetic diversity contribution to errors in short oligonucleotide microarray analysis " 21:19 < fenn> hmm nope 21:20 < fenn> dude search for oligo side reaction 21:20 < kanzure> I've never seen any confirmation or hint from you, so please excuse this blunt question, 21:20 < kanzure> but do you use google scholar? 21:21 < fenn> no 21:21 < kanzure> I ask because you rarely ask me to get you a paper, either because your ezproxy-fu is strong enough, or because you're ignorant 21:21 < kanzure> or because you just don't care enough :) 21:21 < fenn> usually i just dont care enough to go hunting down the actual full text 21:21 < fenn> abstract is enough 21:21 < fenn> it's too much effort without university access 21:22 < kanzure> ssh access on my box would let you http to get pdfs. 21:22 < fenn> 95% of papers are pure shite anyway 21:22 < fenn> i'd like that 21:23 < fenn> "Using phosphoramidite chemistry, the main side reaction is the formation of n-x products." there you have it 21:23 < fenn> presumably "n" is purine and "x" is "something" 21:23 < kanzure> I'm trying to figure out if I want to secure down some of the more private directories or not 21:23 < kanzure> wasn't there an alternative to purine bases? 21:24 < kanzure> my chmod's are all over the place on all of my boxen :) 21:24 < fenn> uh, pyrimidine? 21:24 < kanzure> no no 21:24 < fenn> uracil? 21:24 < kanzure> I mean, synthetic nucleotides 21:24 < kanzure> unnatural nucleotides. 21:24 < fenn> oh sure, anything can be a nucleotide if you look at it the wrong way 21:24 < fenn> but WHY 21:24 < kanzure> maybe their chemistries are more stable? 21:24 < fenn> DNA is such an awesomely perfect storage mechanism already 21:25 < kanzure> and then you go steal the hacked DNA polymerases 21:25 < fenn> now synthetic amino acids on the other hand.. 21:25 < kanzure> from the labs that were working with unnatural nucleotides 21:27 < kanzure> oh. 21:28 < kanzure> fenn: fenn@dhcp-84-113.me.utexas.edu 21:28 < kanzure> have fun. I'm off to go get a ticket. 21:29 < gene> well 21:29 < gene> hope they allow me to take my backpack 22:34 -!- ybit [n=mint@unaffiliated/ybit] has joined #hplusroadmap 23:03 < katsmeow-afk> fenn, odd way to install the pistons for a diesel engine : http://www.angellabsllc.com/Piston.html 23:05 < katsmeow-afk> the pistons move in groups of 4 around the circle, and whichever pistons are moving the desired output shaft direction, turn the output shaft 23:06 < katsmeow-afk> no piston group goes backwards 23:09 < katsmeow-afk> animation at http://www.angellabsllc.com/video/mytengine3d.wmv