| --- Day changed Sat May 02 2009 | ||
| kanzure- | genehacker: can you send me a link to the gear-in-a-gear image? | 00:10 |
|---|---|---|
| genehacker | are you going to generate a gear profile for it? | 00:10 |
| kanzure- | was just going to show albert | 00:10 |
| genehacker | http://www.act.sys.okayama-u.ac.jp/kouseigaku/research/okamoto_wobble_06/english.htm | 00:11 |
| genehacker | oh cool | 00:11 |
| genehacker | I think I can generate it | 00:11 |
| genehacker | I'm more worried about the wobble motor at this point | 00:11 |
| genehacker | oops wobble generator | 00:12 |
| genehacker | also, how I'd make my own motor shafts | 00:14 |
| genehacker | the wobble generator is the silicone actuator thing | 00:16 |
| genehacker | I want to build a larger version of this thing that puts out at least 200 oz in of torque | 00:17 |
| genehacker | you in the adl? | 00:20 |
| kanzure- | not right now | 00:21 |
| genehacker | Albert Swantner | 00:21 |
| genehacker | Automated Synthesis and Optimization of Gear Train Topologies (MS Thesis) | 00:21 |
| kanzure- | yes, that's him. | 00:21 |
| genehacker | that albert? | 00:21 |
| kanzure- | do you see that somewhere? | 00:22 |
| genehacker | in my email | 00:22 |
| kanzure- | oh, I probably sent it to you | 00:22 |
| genehacker | did you show him it | 00:22 |
| genehacker | yes you did | 00:22 |
| genehacker | you must send a lot of email | 00:22 |
| genehacker | so microfluidic reactors | 00:23 |
| genehacker | are cool | 00:23 |
| genehacker | or are the cool thing at the moment for me | 00:24 |
| kanzure- | did you see the microfluidic virus reactor dealy? | 00:24 |
| genehacker | no | 00:25 |
| kanzure- | give me a sec to dig up some links | 00:25 |
| genehacker | I want a microfluidic desktop microchemical plant | 00:25 |
| genehacker | I heard about it | 00:26 |
| genehacker | didn't read it | 00:26 |
| genehacker | so the cool thing with microreactors is 1. they're tiny 2. they can do things normal reactors can't | 00:26 |
| genehacker | they have a low thermal mass and high surface area to volume ratio | 00:27 |
| genehacker | meaning you can play around with some pretty exothermic reactions | 00:27 |
| genehacker | though I'm more concerned with 1 | 00:27 |
| genehacker | I want a microfactory | 00:27 |
| kanzure- | I think using them for high throughput combinatorial stuff is more interesting | 00:28 |
| genehacker | like what sort of stuff? | 00:28 |
| genehacker | now what I really want though is a microfluidic factory that makes high purity supplies for DNA synthesis | 00:29 |
| kanzure- | viruses, antibodies, DNA synthesis, arrayers, stuff like that. | 00:29 |
| kanzure- | plant cell culture would be neat | 00:30 |
| kanzure- | single-cell-per-bubble stuff | 00:30 |
| genehacker | so here's a challenge I have for you | 00:30 |
| genehacker | make we a plant that produces significant amounts of benzene or ethylene | 00:31 |
| genehacker | they're both some useful industrial chemicals | 00:31 |
| genehacker | starting points for lots of stuff | 00:31 |
| kanzure- | directed selection/evolution stuff too | 00:33 |
| genehacker | though the problem with a plant that makes useful quantities of this stuff is that it could die | 00:34 |
| genehacker | or stop producing the stuff | 00:34 |
| genehacker | cuz it isn't an evolutionary advandtage to produce benzene | 00:35 |
| kanzure- | if you did directed selection, you might be able to make it "advantageous" to produce benzene | 00:36 |
| genehacker | argh can't find picture of disassembled lego micromotor | 00:38 |
| genehacker | it has a weird gear arrangement | 00:39 |
| genehacker | that I think works like the wobblemotor | 00:39 |
| genehacker | except it's used for reduction | 00:39 |
| genehacker | might be worth showing to albert too | 00:39 |
| genehacker | http://mindstorms.itgo.com/micro.htm | 00:41 |
| genehacker | there we are | 00:41 |
| genehacker | wonder how they made the mold for those tiny gears? | 00:42 |
| genehacker | AFK | 00:42 |
| kanzure- | there is no AFK | 00:42 |
| kanzure- | hrm, strategies for directed selection. | 00:42 |
| kanzure- | http://en.wikipedia.org/wiki/Directed_evolution | 00:43 |
| kanzure- | "The likelihood of success in a directed evolution experiment is directly related to the total library size, as evaluating more mutants increases the chances of finding one with the desired properties." | 00:44 |
| kanzure- | and the library size can be increased with microfluidics or nanofluidics stuff | 00:44 |
| kanzure- | "Furthermore, in vitro evolution experiments can generate larger libraries because the library DNA need not be inserted into cells, the currently limiting step. | 00:45 |
| kanzure- | Voigt, C. A.; Kauffman S., and Wang Z. G. (2001). "Rational evolutionary design: the theory of in vitro protein evolution". Advances in Protein Chemistry 55: 79–160. doi:10.1016/S0065-3233(01)55003-2. | 00:45 |
| kanzure- | yay for Kauffman | 00:45 |
| kanzure- | ok, so one simple idea for gradient directed evolution would be to test it on polymerase copying its own DNA | 01:04 |
| kanzure- | in particular, select for polymerase that happens to work at slightly varying temperatures | 01:04 |
| kanzure- | for instance, it would be a neat trick to select for types of polymerase that happen to work a few degrees below the thermostable temperatures for taq polymerase or something | 01:04 |
| kanzure- | overall evolving something that has a higher temperature range would be neat. | 01:05 |
| kanzure- | room temperature polymerase, for instance. | 01:05 |
| kanzure- | wow, no results for "directed evolution" + crescentin | 01:08 |
| kanzure- | mreB, mreC, mreD, rodA, pbpB, pbp2, ftsZ, pbp3, FtsW, FtsI <- genes for shape in microbes | 01:29 |
| drazak | hm | 01:31 |
| ybit | http://blog.litstudios.com/index.php?/archives/14-Interactive-Mirror.html :: a touchscreen mirror | 01:39 |
| ybit | too bad it's patent pending | 01:40 |
| ybit | it was built "by hacking together parts easily acquired" | 01:40 |
| ybit | so it and the laser games demo ( http://blog.litstudios.com/index.php?/archives/5-LaserGames.html ) can probably built by anyone willing to put a little time into figuring out how the devices might work | 01:41 |
| ybit | i've seen similar hacks of the laser games from some hacking group in nyc | 01:51 |
| kanzure- | neat. | 02:43 |
| kanzure- | Formation and positioning of surface-related structures in protozoa (1980) | 02:43 |
| ybit | fine, stay on topic | 02:48 |
| ybit | :) | 02:48 |
| kanzure- | don't know what to do with a touchscreen mirror | 02:49 |
| kanzure- | fine, ignore me | 03:10 |
| kanzure- | "The world is an edged tool, equivalent to the sculptor's chisel, for chipping form out of the obstinate material of consciousness." - Philip Glazebrook, Journey to Kars, cited in "To shape a cell: an inquiry into the causes of morphogenesis of microorganisms" | 03:22 |
| kanzure- | "cellular topobiology" | 03:29 |
| kanzure- | neat: http://heybryan.org/books/papers/morphogenesis_mutations.png | 03:44 |
| kanzure- | weird: http://heybryan.org/books/papers/to-shape-a-cell_notes.txt | 03:54 |
| kanzure- | heh. Sonneborn made a two-mouthed paramecium. | 04:03 |
| kanzure- | with a single cytoplasm | 04:03 |
| katsmeow-afk | why? | 04:07 |
| -!- any38956506 is now known as katsmeow | 04:24 | |
| genehacker | because it's there | 04:30 |
| kanzure- | this article is very insightful | 04:30 |
| genehacker | pics or it didn't happen | 04:30 |
| kanzure- | more notes: http://heybryan.org/books/papers/to-shape-a-cell_notes.txt | 04:30 |
| kanzure- | read some of that. it's impressive. | 04:31 |
| -!- any71986970 is now known as katsmeow-afk | 04:47 | |
| kanzure- | hi cis-action | 04:59 |
| ybit | heybryan.org is down | 05:38 |
| kanzure | maybe *you're* down | 05:39 |
| kanzure | oh wait. | 05:39 |
| kanzure | the page loads for me. | 05:39 |
| ybit | heh, did you type http://localhost ? :P | 05:46 |
| ybit | because it's been down all afternoon | 05:46 |
| kanzure- | oh? | 05:51 |
| kanzure- | how is it that I am uploading stuff to it though? | 05:51 |
| kanzure- | it's technically not localhost for me. | 05:51 |
| kanzure- | I'm running on multiple IPs :) | 05:52 |
| kanzure- | huh. S/ cerevisiae has a "bud scar" remaining on its membrane after replication | 05:54 |
| kanzure- | membranes can be scarred? | 05:55 |
| ybit | "Codon Devices shut down operations. The synthetic biology company, co-founded by George Church, Jay Keasling, and Drew Endy, among others, had raised $11 million in private financing last year." | 06:05 |
| ybit | ^ http://www.genomeweb.com/short-reads-76 | 06:06 |
| ybit | kanzure, i'm not sure how you are doing that, maybe someone else in here can report what they see? | 06:14 |
| fenn | heybryan.org is up but mediawiki is fubared | 10:58 |
| ybit | heybryan.org is working for me now | 17:40 |
| ybit | and the wiki is like fenn said as well | 17:43 |
| kanzure | Christopher J. Morris and Babak A. Parviz, "Micro-scale metal contacts for capillary force-driven self-assembly", Journal of Micromechanics and Microengineering,v 18, n 1, 2008, p1-10 | 17:58 |
| kanzure | Ranjana Mehta, Maryam Rahimi, John A. Lund, Babak A. Parviz, "Rapid extension of single and double stranded DNA on atomically flat conductive surfaces", IEEE Transaction on Nanotechnology, v 6, n 6, 2007, p 734-736 | 17:58 |
| kanzure | Angela J. Shum, Justin Crest, Gerold Schubiger, Babak A. Parviz, "Drosophila as a live substrate for solid-state microfabrication", Advanced Materials, v 19, 2007, p 3608-3612 | 17:58 |
| kanzure | Declan Ryan, Maryam Rahimi, John Lund, Ranjana Mehta, Babak A. Parviz, "Toward nanoscale genome sequencing", Trends in Biotechnology, v 25, n 9, 2007, p 385-389 | 17:59 |
| kanzure | Xiaorong Xiang, Mary Lidstrom, Babak A. Parviz, "Microorganisms for MEMS", ASME/IEEE Journal of Microelectromechanical Systems, v 16, n 2, 2007, p 429-444 | 17:59 |
| kanzure | Christopher J. Morris, Harvey Ho, and Babak A. Parviz, "Liquid Polymer Deposition on Free-Standing Microfabricated Parts for Self-Assembly", ASME/IEEE Journal of Microelectromechanical Systems, v 15, n 6, 2006, p 1795-1804 | 17:59 |
| kanzure | Sean A. Stauth and Babak A. Parviz, "Self-Assembled Single Crystal Silicon Circuits on Plastic", Proceedings of the National Academy of Sciences, v 103, n 38, September 2006, p 13922-13927 | 17:59 |
| kanzure | Jianchun Dong and Babak A. Parviz, "Using Noise for Controlled Disassembly of Nano-Scale Gold Wires", Nanotechnology, v 17, 2006, p 5124-5130 | 17:59 |
| kanzure | Self-assembly and Characterization of Marangoni Microfluidic Actuators | 18:02 |
| kanzure | hrm. this group worries me. | 18:02 |
| kanzure | ah, Parviz was working with Whitesides | 18:03 |
| kanzure | John A. Lund and Babak A. Parviz, "Electronic DNA sequencing", invited paper, submitted and accepted for publication in Current Pharmaceutical Analysis | 18:04 |
| kanzure | huh, I've read papers by Lund before.. | 18:04 |
| kanzure | there's a journal called "The Neuromorphic Engineer" ? sign me up. | 18:05 |
| kanzure | John Lund, Jianchun Dong, Ranjana Mehta, Maryam Rahimi, Babak A. Parviz, "Using Electron Tunneling for Direct Sequencing of DNA", proceedings of the NSTI Nanotechnology Conference, v 2, p 480-483,Santa Clara, CA, May 20-24 2007 | 18:07 |
| kanzure | does anyone remember the gummy-bear micromachining papers? | 18:29 |
| kanzure | or anything about gummy-bears. there were some particularly cool papers that I have completely forgotten, and I just found another cool one, but unfortunately I don't remember what the previous awesomesauce was | 18:35 |
| kanzure | parviz paper dump: http://heybryan.org/books/papers/parviz/ | 18:50 |
| kanzure | water-soluble polymers are fun. | 19:21 |
| genehacker | WHO WANTS A FREE USB DRIVE! | 20:39 |
| genehacker | http://realpartsrealstories.com/getkit/index.htm | 20:39 |
| genehacker | hehehehehehe | 20:39 |
| kanzure | http://heybryan.org/books/papers/bacterial_shape.png | 22:06 |
| kanzure | anyone know of a way for me to find the academic ancestry of an individual in relation to another individual (author)? there was a site that did this, but I have failed in remembering its name | 22:09 |
| kanzure | http://www.youtube.com/watch?v=R0Soltmruis&feature=related rapid succession of microorganisms | 22:34 |
| genehacker | 2 headed paramecium? | 23:14 |
| genehacker | where is it? | 23:14 |
| genehacker | damn those things sure do have a lot of actuators | 23:15 |
| kanzure | it was engineered | 23:22 |
| kanzure | http://www.youtube.com/view_play_list?p=B16E0C8E552629DE <- microorganism playlist | 23:22 |
| kanzure | star wars: http://www.youtube.com/watch?v=fjYKhUwHhWw hehe | 23:26 |
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