| --- Day changed Sat Mar 07 2009 | ||
| kanzure | http://scholar.google.com/scholar?q=micromolding+in+capillaries | 00:52 |
|---|---|---|
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| 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 | 01:36 |
| kanzure | hm, I should pour some nail polish down my microchannels | 01:45 |
| kanzure | http://heybryan.org/books/papers/microfluidics/Capillary%20Force%20Lithography.pdf | 01:49 |
| kanzure | capillary force lithography :) | 01:49 |
| kanzure | someone should go stalk Kahp Y Suh, a Korean researcher at Seoul National University. | 02:03 |
| 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 | 02:13 |
| kanzure | On the role of oxygen in fabricating microfluidic channels with ultraviolet curable materials | 02:14 |
| kanzure | why: http://heybryan.org/books/papers/microfluidics/suh/ | 02:47 |
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| 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 | 09:30 |
| kanzure | but it's not listed in the early edition of PNAS. wtf? | 09:31 |
| wrldpc | Anybody got Keith Henson's wiki for space power satellites? | 09:32 |
| wrldpc | google is producing nothing :\ | 09:32 |
| fenn | wrldpc: http://htyp.org/dollar_a_gallon_gasoline | 09:48 |
| wrldpc | tyvm | 09:48 |
| wrldpc | http://htyp.org/Hundred_dollars_a_kg | 09:48 |
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| kanzure | wrldpc, Keith has been ranting about that on the extropy list for a few months now. | 10:13 |
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| kanzure | wrldpc, Keith has been ranting about that on the extropy list for a few months now. | 10:17 |
| 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 | 10:18 |
| kanzure | oh, that was probably Charles Radley in that chat? | 10:29 |
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| 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 | 12:43 |
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| wrldpc | Yeah Radley | 13:07 |
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| gene | kanzure do you know what pyradean solar cells are? | 13:17 |
| 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 | 13:19 |
| gene | http://psychology.uwo.ca/fmri4newbies/ScanningTooMuch.html | 13:26 |
| fenn | "Not only can you recognize the brains of your frequently-scanned co-workers, but also their teeth from the bite bar impressions." hmmm.. | 13:31 |
| fenn | 50% efficient solar eh? | 13:32 |
| fenn | pretty sweet car too | 13:33 |
| 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 | 13:35 |
| 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? | 13:36 |
| gene | they say 38% conversion efficiency | 13:37 |
| gene | hmmm... uranium redox flow battery | 13:37 |
| gene | yes vanadium is one of them | 13:38 |
| gene | http://www.imr-oarai.jp/en/research/research4-5.html | 13:38 |
| gene | URANIUM BATTERY BEATS ALKALINE BATTERY HANDS DOWN | 13:39 |
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| fenn | i can just see a new clusterfuck brewing | 13:52 |
| 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 | 13:53 |
| gene | depleted uranium can easily be turned into plutonium if you bombard it with neutrons you know? | 13:54 |
| 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 | 13:57 |
| gene | really uranium is that common? | 13:59 |
| gene | can I get acouple nuclear bombs of the stuff for escaping the universe? | 13:59 |
| 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 | 14:00 |
| 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 | 14:01 |
| gene | by military standards.... | 14:02 |
| 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 | 14:03 |
| gene | well I guess that must be cheap | 14:04 |
| fenn | that's 16000 lb of uranium? | 14:04 |
| fenn | per mission | 14:04 |
| fenn | now, someone has to clean up that mess afterward | 14:05 |
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| 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 | 15:48 |
| kanzure | 05:59:42 omg/user: i want to do stochastic reaction network modeling on the history of the debian package repository | 15:49 |
| kanzure | fenn: did you see my notes/links last night about capillary force lithography? | 15:59 |
| fenn | yeah but what about it | 15:59 |
| kanzure | ever come across it before? what's your take on it? other generic questions here | 16:00 |
| fenn | i'm surprised it works at such small scales but i dont see what it's good for | 16:01 |
| fenn | isnt it basically the same as PDMS imprinting? | 16:02 |
| fenn | with a thinner layer | 16:02 |
| 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 | 16:03 |
| 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 | 16:04 |
| 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 | 16:05 |
| 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 | 16:06 |
| 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. | 16:07 |
| 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 | 16:08 |
| 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 | 16:09 |
| fenn | http://heybryan.org/books/papers/microfluidics/Capillary%20Force%20Lithography.pdf | 16:10 |
| fenn | search for 'we used' | 16:11 |
| 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. | 16:12 |
| 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) | 16:14 |
| gene | No it wasn't Lee Smolin, it was scientific american or Michau Kaku | 17:05 |
| kanzure | Kaku? I'd be surprised. He does more pop-sci stuff these days, mroe than anything. | 17:07 |
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| gene | yeah | 17:35 |
| gene | this was a while back I don't really know | 17:36 |
| gene | It was probably kaku | 17:36 |
| 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 | 18:12 |
| gene | from long ago | 18:13 |
| gene | which might moot a patent | 18:13 |
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| kanzure | where can I find a list of obscure forces and phenomena categorized by material? | 18:42 |
| bkero | The united nations charter | 18:44 |
| bkero | *rimshot* | 18:44 |
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| kanzure | aha | 19:03 |
| 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. | 19:04 |
| 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 | 19:13 | |
| gene | are you trying to simulate materials? | 19:20 |
| gene | a company that developed a new super efficient solar cell did that | 19:20 |
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| 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? | 19:21 |
| gene | they made a fluidic memory device using a bead of water | 19:22 |
| kanzure | what's the flip state? | 19:26 |
| fenn | no bead of water? :) | 19:27 |
| * fenn mumbles about abaci (abacuses?) | 19:27 | |
| gene | bead of water in different place | 19:30 |
| gene | what's tunneling and could I use it to securely transfer data to you | 19:31 |
| gene | fast | 19:31 |
| gene | or would usb drive delivery via rocket be faster? | 19:35 |
| fenn | depends how secure you want it | 19:39 |
| fenn | do you really not know what quantum tunneling is? | 19:39 |
| 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 | 19:40 |
| 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 | 19:41 |
| kanzure | gene: "tunneling" is SSH. | 19:43 |
| kanzure | or at least, that's what I mean when I say tunneling | 19:43 |
| gene | ok | 19:43 |
| 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 | 19:44 |
| 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 |
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| 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 | 19:46 |
| 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 | 19:47 |
| fenn | FEM simulator? | 19:48 |
| fenn | meh | 19:49 |
| gene | http://www.abominablefirebug.com/AuthorFiles/r9006.pdf | 19:49 |
| gene | read science fairs | 19:49 |
| gene | http://www.abominablefirebug.com/AcousticGyro.html | 19:50 |
| gene | better | 19:50 |
| 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 | 19:51 |
| 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? | 19:52 |
| fenn | no idea :P | 19:54 |
| gene | sensitive enough to sense the rotation of the earth? | 19:54 |
| fenn | actually that looks pretty simple | 19:54 |
| fenn | vacuum tubes :) | 19:56 |
| fenn | you learn something every day: http://en.wikipedia.org/wiki/Halteres | 19:57 |
| 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 | 19:59 |
| gene | pah vacuum tubes? why use vaccuum tubes, when you can use fluidics! | 20:00 |
| fenn | uh, yeah. | 20:00 |
| fenn | who needs transducers anyway | 20:01 |
| gene | yeah it would be 50% more impractical than vacuum tubes, but it'd be able to deliver things to the amish | 20:02 |
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| gene | now I wonder, how did punched tape n/c machines work? | 20:09 |
| 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? | 20:10 |
| 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? | 20:11 |
| 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 | 20:12 |
| 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 ? | 20:13 |
| 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." | 20:14 |
| 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 | 20:15 |
| 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 | 20:17 |
| 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 | 20:18 |
| 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? | 20:19 |
| gene | cars get hot | 20:20 |
| fenn | poly beta hydroxy butyric acid | 20:20 |
| gene | PLA can melt at texas temperatures | 20:22 |
| fenn | so can ABS? | 20:22 |
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| fenn | what are dashboards made of? some kind of vinyl (probably PVC with plasticizers) | 20:22 |
| gene | or at least it becomes soft | 20:22 |
| 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 | 20:23 |
| 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 | 20:24 |
| 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 | 20:25 |
| fenn | check out their prices on gears | 20:26 |
| fenn | you can't get gears that cheap anywhere | 20:26 |
| 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 | 20:27 |
| gene | http://www.mutr.co.uk/product_info.php?products_id=299 | 20:28 |
| 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 | 20:29 |
| fenn | quartz actually | 20:30 |
| gene | http://www.mutr.co.uk/product_info.php?products_id=1089 | 20:30 |
| gene | carbon fiber | 20:30 |
| gene | http://www.mutr.co.uk/product_info.php?products_id=1009547 | 20:31 |
| gene | that's an awesome price | 20:31 |
| 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 | 20:32 |
| 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 | 20:33 |
| 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 | 20:34 |
| 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/ | 20:35 |
| 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 | 20:36 |
| 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 | 20:37 |
| 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 | 20:39 |
| gene | guess what just happens to be cheap? | 20:40 |
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| gene | 200 mw lasers | 20:40 |
| gene | that's what | 20:40 |
| 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. | 20:41 |
| 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. | 20:42 |
| 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? | 20:43 |
| 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 | 20:44 |
| gene | fenn's link is dead | 20:45 |
| * fenn beats gene about the head with a %20 | 20:45 | |
| 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? | 20:46 |
| gene | I put http://heybryan.org/books/papers/microfluidics/ in my bookmarks toolbar | 20:47 |
| gene | cheap gene synth's are scary though | 20:47 |
| 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 | 20:48 |
| 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 | 20:49 |
| 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 | 20:50 |
| 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 | 20:51 |
| 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"? | 20:52 |
| fenn | hah you saved my crappy inkscape drawing | 20:53 |
| kanzure | rabid archiving. | 20:53 |
| gene | well gene synthesis can be a bit inaccurate | 20:54 |
| 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? | 20:56 |
| 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? | 20:57 |
| kanzure | what are you asking? | 20:58 |
| 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 | 20:59 |
| 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 | 21:00 |
| 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? | 21:01 |
| 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? | 21:02 |
| gene | so what's the photo sensitive capping chemical? | 21:03 |
| fenn | kanzure: did you say you made a marangoni flow actuator? | 21:03 |
| kanzure | I thought that's what the 16x16 resistor microheater array was for? | 21:04 |
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| 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 | 21:04 |
| gene | what, should I buy them later? | 21:05 |
| kanzure | the movie is at 10:20. | 21:05 |
| 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 | 21:06 |
| kanzure | gene: oh. | 21:07 |
| kanzure | um, how quickly is relatively? | 21:07 |
| gene | unknown | 21:07 |
| 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 | 21:09 |
| 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 | 21:11 |
| 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? | 21:12 |
| fenn | hey this was my idea - bastards! | 21:13 |
| fenn | http://www.freshpatents.com/Error-reduction-in-automated-gene-synthesis-dt20060622ptan20060134638.php | 21:13 |
| kanzure | was this the automated overlap but plus re-synthesis of the erroneous parts paper? | 21:14 |
| 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.? | 21:15 |
| 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 | 21:16 |
| 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." | 21:17 |
| 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 | 21:18 |
| 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 | 21:19 |
| 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? | 21:20 |
| 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 | 21:21 |
| 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 | 21:22 |
| 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? | 21:23 |
| 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 | 21:24 |
| 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 | 21:25 |
| kanzure | oh. | 21:27 |
| kanzure | fenn: fenn@dhcp-84-113.me.utexas.edu | 21:28 |
| kanzure | have fun. I'm off to go get a ticket. | 21:28 |
| gene | well | 21:29 |
| gene | hope they allow me to take my backpack | 21:29 |
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| katsmeow-afk | fenn, odd way to install the pistons for a diesel engine : http://www.angellabsllc.com/Piston.html | 23:03 |
| 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 | 23:05 |
| katsmeow-afk | no piston group goes backwards | 23:06 |
| katsmeow-afk | animation at http://www.angellabsllc.com/video/mytengine3d.wmv | 23:09 |
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