--- Day changed Mon May 11 2009 00:40 -!- any80603747 is now known as katsmeow-afk 03:24 -!- any39753496 is now known as katsmeow-afk 06:09 -!- fenn_ is now known as fenn 06:47 < ybit> i was spammed this site: http://academicearth.org/ 13:54 < faceface> thanks UtopiahGHML 13:54 < faceface> nice bok 13:54 < faceface> book 13:56 < UtopiahGHML> hi faceface , np if I find related material Ill forward it 13:59 < faceface> heh... 13:59 < faceface> don't have much time for this atm 13:59 < faceface> but thanks for thinking of me 13:59 < faceface> everyone seen this: http://smw.referata.com/wiki/Emergent_Neural_Network_Simulation_System 15:11 < kanzure-> genehacker: there is this device that is a semicircular cooling unit that sits on your neck. it's a mini air conditioner. 15:11 < kanzure-> xp_prg: I don't know what you mean by videos of the infrared protein .. 15:11 < kanzure-> drazak, fenn: I think the tyical Taq polymerase purification step is either chromatography or SDS-PAGE. Another good trick would be antibody-binding or aptamer-binding. 15:16 < faceface> kanzure-: seen http://smw.referata.com/wiki/Emergent_Neural_Network_Simulation_System ? 15:19 < kanzure-> No, not yet. 15:20 < kanzure-> Chaperonins govern growth of Escherichia coli at low temperatures 15:20 < kanzure-> http://adl.serveftp.org/papers/Chaperonins%20govern%20growth%20of%20Escherichia%20coli%20at%20low%20temperatures.pdf 15:21 < kanzure-> However, the recent discovery of a single protein (Cpn60) isolated from an Antarctic bacterium, Oleispira antarctica, radically expands the low temperature growth limit of ecoli. 15:21 < kanzure-> temperatures as low as 10 celsius 15:33 < kanzure-> I need someone to check my work. 15:33 < kanzure-> I've been wearing glasses for at least a decade now. Sometimes water gets on the lenses (maybe it's raining). 15:33 < kanzure-> For the longest time I would just ignore what I saw in the drop, 15:33 < kanzure-> but I've since realized that there might be something interesting going on there. 15:34 < kanzure-> The other day I was using the contours of my thumbnail with a thin layer of water to examine my eye. 15:34 < kanzure-> but now I'm not sure if I was seeing my eye in microscopic detail, or if I was just tripping on account of not having an internet connection. 15:35 < kanzure-> if it is microscopic detail that I am seeing, then it's useless anyway since I can only see the cornea- although a second finger with a second drop of water might be able to reflect the light from another object in sufficient detail? 15:36 < kanzure-> David has completed his makerbot. 15:45 < kanzure> "Another delta group, the bdellovibrios, are predators that attack other bacteria. A bdellovibrio charges its prey at a speed of 100 microns per second, which, relatively speaking, is like a human running about 600 km per hour, half the speed of sound! Then the predator turns into a bacterial drill, boring into its prey by spinning at 100 revolutions per second." 15:50 < kanzure> Translocation of an outer membrane protein into prey cytoplasmic membranes by bdellovibrios. 15:52 < kanzure-> "outer membrane proteins" (OMPs) 15:53 < kanzure-> if you can attach streptavidin or biotin to the bdellovibrio's OMPs, and in particular also attach DNA, 15:53 < kanzure-> I wonder if that would be an easy method of transfection/transformation via predation? 15:56 < kanzure-> "INtravenous infusion of coconut water" 16:08 < kanzure> so, I didn't know that "DNA guns" and "gene guns" were literally just converted .22-caliber rifles. 16:42 < kanzure-> lipofection is the most awesome thing ever. 16:43 < kanzure-> I think you could extract the lipids from cheeseburgers and combine them with DNA in order to transfect cells .. cheeseburger transfection :) 17:55 < kanzure-> fenn: did you get my messages from earlier today? 17:57 < fenn> about taq polymerase? 17:58 < kanzure-> fenn: up to and about cheeseburgers. 17:58 < fenn> yes 18:00 < fenn> NVidia released the Tesla C870 a new GPU that is designed for non-graphics processing, assuming you can write your code in terms of matrix and vector operations. It's already being used in neural network simulations by Evolved Machines . 18:00 < fenn> "We simulated neuronal components closel modeled after neurons in the brain, and synthesize arays which wire themselves by simulating neural circuit growth in 33-dimensions." 18:01 < kanzure-> 33 dimensions 18:01 < fenn> that was some weird paste error.. it's just 3 dimensions 18:01 < kanzure-> that's kind of sick 18:01 < kanzure-> oh 18:09 < fenn> how come the name 'brian mingus' sounds familiar? 18:29 < kanzure-> nimbus cloud? 18:33 < ybit> anyone have access to ieee papers? 18:33 < kanzure-> ys 18:33 < kanzure-> yes 18:33 < ybit> http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=265093 18:34 < ybit> could you please fetch that for me? 18:34 < ybit> "Driver circuit for piezoelectric motor" 18:34 < kanzure-> http://adl.serveftp.org/papers/Driver%20circuit%20for%20piezoelectric%20motor.pdf 18:34 < kanzure-> you owe me 1 cookie 18:35 < ybit> :) 18:35 < ybit> thanks 18:40 < kanzure-> has anybody confirmed my thumbnail microscope yet? 18:40 < kanzure-> spit can work if you're all too damn lazy to go to a sink 18:45 < cis-action> hey kanzure, I don't use linux, but I'm planning on bringing an OLPC with me on a three-week trip to malaysia this summer, primarily as a reading device for my pdf collection of papers and textbooks. Do you have any suggestions for pfd organization and reading applications for debian / gnome? 18:46 < cis-action> Also, I use quicksilver on the mac - can you suggest a similar accelerator for gnome? 18:52 < kanzure-> I don't know what quicksilver is. 18:52 < xp_prg> kanzure any video on the infared proteins yet? 18:52 < kanzure-> xp_prg: no. just read the paper. 18:53 < xp_prg> that is wayyyy cool 18:53 < xp_prg> can't wait to see some video using it 18:53 < kanzure-> cis-action: There are many shortcut programs built into the main editors like vim and emacs, but I don't know if that's what you want. 18:53 < kanzure-> cis-action: for PDF reading, I've lately been using zotero. 18:53 < kanzure-> pack multiple PDF readers .. otherwise you'll be sorry. xpdf, kpdf, gs, djvu, etc. 18:54 < cis-action> ok 18:54 < cis-action> all i have right now is xpdf. I hear that mendeley has a linux distro... 18:56 < kanzure-> mendeley begins to suck when you add more than 1,000 papers 18:56 < cis-action> darn 18:57 < cis-action> quicksilver / spotlight / google desktop all provide fast searching of the OS via an index, firstly for accessing applications, media, etc, and also for executing commands 19:00 < cis-action> I'm really interested in being able to search through the content of the pdf collection I bring along. Any pointers on how to get started learning about that on deb / gnome? 19:02 < kanzure-> cis-action: I don't use search mechanisms for PDFs. Most of the time search fails me because PDFs are just scanned images. 19:02 < kanzure-> anyway, you should check out 'grep' 19:03 < cis-action> oh 19:03 < kanzure-> what's harder? making an imager array or making nano-scale wires individually routed to who-knows-where 19:03 < kanzure-> cis-action: I also suggest "apt-cache search " 19:03 < kanzure-> (run that in the shell) 19:04 < cis-action> let me show you my particular search workflow on os.x 19:04 < cis-action> what is the class of protein that was being discussed earlier? IR-fluorescent? 19:04 < kanzure-> yes, an infrared fluorescent protein. 19:08 < cis-action> grep might work, but SpotLight and google desktop both precompute search indexes, so they may be faster 19:14 < fenn_> grep doesn't work on pdf's because they aren't plaintext 19:14 -!- fenn_ is now known as fenn 19:14 < kanzure-> some are. 19:14 < fenn> maybe htdig would work? 19:18 < drazak> kanzure-: did anyone relay my dna box idea to you? 19:18 < kanzure-> I saw it. 19:18 < kanzure-> I don't know whether or not you just copied what I said in the email 19:18 < drazak> (05:41:13) (drazak) so how about this 19:18 < drazak> (05:41:16) (drazak) glass chip 19:18 < drazak> (05:41:32) (drazak) with 2 areas that contain fluid 19:18 < drazak> (05:43:33) (drazak) one of which has a way to add more to it via capilary action, or whatever, the outside one has one of those dna boxes containing two compounds, one that dissolves endothermically, one that disolves exothermically, in 19:18 < drazak> the inner fluid area that can have fluid added to it, there are many of those dna boxes present, each with different reagents in it, so that you can do a multituyde of tests, depending on what kind of light it's exposed to 19:19 < drazak> (05:46:53) (drazak) the outer fluid area is to provide the proper temperature, such that if you're using something like benedicts reagent you could provide the heat easily 19:19 < drazak> (05:47:02) (drazak) it would be great for quick field tests 19:19 < drazak> oh, you said something like that? 19:19 < drazak> I didn't read all the emails, just the first one 19:19 < kanzure-> http://groups.google.com/group/diybio/browse_thread/thread/a506cb173466130b 19:20 < drazak> oh 19:20 < drazak> I saw the light bit 19:21 < drazak> but I don't think you mentioned putting different reagents in the dna boxes, instead of dna in them 19:21 < kanzure-> er, yes I did, but it doesn't matter 19:22 < drazak> yeah, guess not 19:22 < drazak> dunno, doesn't matter who had the idea, it's a collaborative process 19:23 < kanzure-> not saying it matters .. just wondering what's new about it. 19:23 < drazak> dunno 19:23 < drazak> but it might be a way to make a jack-of-all-trades laoc 19:23 < drazak> er, loac 19:25 < kanzure-> why not just use spherical particles that explode in response to different wavelengths of light? I'm pretty sure they exist 19:25 < drazak> how do you mind spherical particles to stuff like CuSO4 19:26 < drazak> s/mind/bind/ 19:26 < kanzure-> why would that matter 19:26 < drazak> well wouldn't the presence of CuSO4 mess with whatever other reagents you're using? 19:26 < kanzure-> separate chambers? 19:27 < drazak> well then it's not a jack of all trades laoc, then it's just one with many chambers, that would be better served as seperate laocs 19:27 < kanzure-> how would your DNA-box-array solve that problem? 19:28 < drazak> you could keep the reagents in the dnaboxes, assuming the molecules are close enough together 19:28 < drazak> and then use the light activated azobenzene to open the lid 19:28 < kanzure-> but they are still in the same area as all the other DNA boxes. 19:29 < kanzure-> "well wouldn't the presence of CuSO4 mess with whatever other reagents you're using?" 19:29 < drazak> you're saying the spherical particles would be able to keep something like CuSO4 from reacting with other reagents? 19:29 < kanzure-> no. 19:29 < kanzure-> I think you're the one saying that .. except for DNA boxes. 19:30 < drazak> the dna boxes would be able to, I'd think, but maybe I'm wrong 19:30 < drazak> if you're going to have seperate compartments, why have the spherical particles 19:32 < kanzure-> you can store them all in the same location and address them by light 19:32 < drazak> without them reacting with eachother? 19:32 < kanzure-> such as i.e. to disconnect from the floor 19:32 < kanzure-> and then to flow down to the reaction chamber zone 19:32 < drazak> hm 19:33 < drazak> seems to me that you're adding another level of uneeded complexity with that, why not have them in the reaction chamber? 19:38 < kanzure-> because you don't want the reactions to happen on things you didn't want to happen 19:44 < drazak> right, which is where the dna boxes would come in, they could contain the reactants in such a way that no reaction taes place 19:55 < kanzure-> but not when you open them 19:56 < drazak> no, but you could selectively open them 19:56 < drazak> your azobenzene key idea 19:58 < drazak> say you have the dna keys bound to the bottom of the reagent chamber with different reactive 'links', each link can be broken for a different reagent 20:00 < drazak> red light gives enough energy to THIS link to release the key for the benedects reagent box, THIS link releases lugols iodine key, THIS link lets you release the key for biuret reagent boxes, etc 20:01 < drazak> guess I didn't explain it well enough 20:03 < kanzure-> what do the "links" link from and to? 20:03 < drazak> from the bottom of the reagent chamber, some sort of stucture there, and to the dna keys, on the phosphate backbone perhaps 20:06 < kanzure-> I must not get it 20:06 < drazak> the dna boxes contain the reagents 20:06 < kanzure-> why wouldn't the reagents react with the DNA boxes when you open up a particular DNA box 20:06 < drazak> dunno, you'd have to test it 20:19 < ybit> concerning http://co.de i cancelled my order with domainmonger, it's actually a legit company with very helpful customer support 20:20 < ybit> i just don't like split names, e.g.: del.icio.us 20:20 < ybit> went with heath.im 20:20 < ybit> thought you guys should know this :P 20:21 < drazak> mhm 21:11 < kanzure-> ack, ubuntu isn't booting up 21:11 < kanzure-> it thought it ran out of hard drive space (it didn't) and now gdm refuses to work 21:16 < kanzure-> oh there it goes 21:16 < kanzure-> apparently it does not like /tmp being dynamically linked to /host/tmp (/host is a mounted partition) 21:22 < kanzure-> is /tmp not actually tmp stuff? 21:22 < kanzure-> because I deleted all of it 22:14 < drazak> xit is temp stuff