--- Day changed Sat May 02 2009
00:10 < 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
00:11 < 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
00:12 < genehacker> oops wobble generator
00:14 < genehacker> also, how I'd make my own motor shafts
00:16 < genehacker> the wobble generator is the silicone actuator thing
00:17 < genehacker> I want to build a larger version of this thing that puts out at least 200 oz in of torque
00:20 < genehacker> you in the adl?
00:21 < 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?
00:22 < 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
00:23 < genehacker> so microfluidic reactors
00:23 < genehacker> are cool
00:24 < genehacker> or are the cool thing at the moment for me
00:24 < kanzure-> did you see the microfluidic virus reactor dealy?
00:25 < genehacker> no
00:25 < kanzure-> give me a sec to dig up some links
00:25 < genehacker> I want a microfluidic desktop microchemical plant
00:26 < 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
00:27 < 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
00:28 < kanzure-> I think using them for high throughput combinatorial stuff is more interesting
00:28 < genehacker> like what sort of stuff?
00:29 < 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.
00:30 < 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
00:31 < 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
00:33 < kanzure-> directed selection/evolution stuff too
00:34 < 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
00:35 < genehacker> cuz it isn't an evolutionary advandtage to produce benzene
00:36 < kanzure-> if you did directed selection, you might be able to make it "advantageous" to produce benzene
00:38 < genehacker> argh can't find picture of disassembled lego micromotor
00:39 < 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
00:41 < genehacker> http://mindstorms.itgo.com/micro.htm
00:41 < genehacker> there we are
00:42 < 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.
00:43 < kanzure-> http://en.wikipedia.org/wiki/Directed_evolution
00:44 < 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
00:45 < 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
01:04 < 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
01:05 < kanzure-> overall evolving something that has a higher temperature range would be neat.
01:05 < kanzure-> room temperature polymerase, for instance.
01:08 < kanzure-> wow, no results for "directed evolution" + crescentin
01:29 < kanzure-> mreB, mreC, mreD, rodA, pbpB, pbp2, ftsZ, pbp3, FtsW, FtsI <- genes for shape in microbes
01:31 < drazak> hm
01:39 < ybit> http://blog.litstudios.com/index.php?/archives/14-Interactive-Mirror.html :: a touchscreen mirror
01:40 < ybit> too bad it's patent pending
01:40 < ybit> it was built "by hacking together parts easily acquired"
01:41 < 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
01:51 < ybit> i've seen similar hacks of the laser games from some hacking group in nyc
02:43 < kanzure-> neat.
02:43 < kanzure-> Formation and positioning of surface-related structures in protozoa (1980)
02:48 < ybit> fine, stay on topic
02:48 < ybit> :)
02:49 < kanzure-> don't know what to do with a touchscreen mirror
03:10 < kanzure-> fine, ignore me
03:22 < 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"
03:29 < kanzure-> "cellular topobiology"
03:44 < kanzure-> neat: http://heybryan.org/books/papers/morphogenesis_mutations.png
03:54 < kanzure-> weird: http://heybryan.org/books/papers/to-shape-a-cell_notes.txt
04:03 < kanzure-> heh. Sonneborn made a two-mouthed paramecium.
04:03 < kanzure-> with a single cytoplasm
04:07 < katsmeow-afk> why?
04:24 -!- any38956506 is now known as katsmeow
04:30 < 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
04:31 < kanzure-> read some of that. it's impressive.
04:47 -!- any71986970 is now known as katsmeow-afk
04:59 < kanzure-> hi cis-action 
05:38 < ybit> heybryan.org is down
05:39 < kanzure> maybe *you're* down
05:39 < kanzure> oh wait.
05:39 < kanzure> the page loads for me.
05:46 < ybit> heh, did you type http://localhost ? :P
05:46 < ybit> because it's been down all afternoon
05:51 < 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.
05:52 < kanzure-> I'm running on multiple IPs :)
05:54 < kanzure-> huh. S/ cerevisiae has a "bud scar" remaining on its membrane after replication
05:55 < kanzure-> membranes can be scarred?
06:05 < 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."
06:06 < ybit> ^ http://www.genomeweb.com/short-reads-76
06:14 < ybit> kanzure, i'm not sure how you are doing that, maybe someone else in here can report what they see?
10:58 < fenn> heybryan.org is up but mediawiki is fubared
17:40 < ybit> heybryan.org is working for me now
17:43 < ybit> and the wiki is like fenn said as well
17:58 < 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
17:59 < 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
18:02 < kanzure> Self-assembly and Characterization of Marangoni Microfluidic Actuators
18:02 < kanzure> hrm. this group worries me.
18:03 < kanzure> ah, Parviz was working with Whitesides
18:04 < 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..
18:05 < kanzure> there's a journal called "The Neuromorphic Engineer" ? sign me up.
18:07 < 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 
18:29 < kanzure> does anyone remember the gummy-bear micromachining papers?
18:35 < 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
18:50 < kanzure> parviz paper dump: http://heybryan.org/books/papers/parviz/
19:21 < kanzure> water-soluble polymers are fun.
20:39 < genehacker> WHO WANTS A FREE USB DRIVE!
20:39 < genehacker> http://realpartsrealstories.com/getkit/index.htm
20:39 < genehacker> hehehehehehe
22:06 < kanzure> http://heybryan.org/books/papers/bacterial_shape.png
22:09 < 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
22:34 < kanzure> http://www.youtube.com/watch?v=R0Soltmruis&feature=related rapid succession of microorganisms
23:14 < genehacker> 2 headed paramecium?
23:14 < genehacker> where is it?
23:15 < genehacker> damn those things sure do have a lot of actuators
23:22 < kanzure> it was engineered
23:22 < kanzure> http://www.youtube.com/view_play_list?p=B16E0C8E552629DE <- microorganism playlist
23:26 < kanzure> star wars: http://www.youtube.com/watch?v=fjYKhUwHhWw hehe