| --- Day changed Mon May 11 2009 | ||
| -!- any80603747 is now known as katsmeow-afk | 00:40 | |
| -!- any39753496 is now known as katsmeow-afk | 03:24 | |
| -!- fenn_ is now known as fenn | 06:09 | |
| ybit | i was spammed this site: http://academicearth.org/ | 06:47 |
|---|---|---|
| faceface | thanks UtopiahGHML | 13:54 |
| faceface | nice bok | 13:54 |
| faceface | book | 13:54 |
| UtopiahGHML | hi faceface , np if I find related material Ill forward it | 13:56 |
| 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 | 13:59 |
| 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. | 15:11 |
| faceface | kanzure-: seen http://smw.referata.com/wiki/Emergent_Neural_Network_Simulation_System ? | 15:16 |
| kanzure- | No, not yet. | 15:19 |
| 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 | 15:20 |
| 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 | 15:21 |
| 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. | 15:33 |
| 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. | 15:34 |
| 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? | 15:35 |
| kanzure- | David has completed his makerbot. | 15:36 |
| 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." | 15:45 |
| kanzure | Translocation of an outer membrane protein into prey cytoplasmic membranes by bdellovibrios. | 15:50 |
| kanzure- | "outer membrane proteins" (OMPs) | 15:52 |
| 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? | 15:53 |
| kanzure- | "INtravenous infusion of coconut water" | 15:56 |
| kanzure | so, I didn't know that "DNA guns" and "gene guns" were literally just converted .22-caliber rifles. | 16:08 |
| kanzure- | lipofection is the most awesome thing ever. | 16:42 |
| kanzure- | I think you could extract the lipids from cheeseburgers and combine them with DNA in order to transfect cells .. cheeseburger transfection :) | 16:43 |
| kanzure- | fenn: did you get my messages from earlier today? | 17:55 |
| fenn | about taq polymerase? | 17:57 |
| kanzure- | fenn: up to and about cheeseburgers. | 17:58 |
| fenn | yes | 17:58 |
| 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." | 18:00 |
| 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 | 18:01 |
| fenn | how come the name 'brian mingus' sounds familiar? | 18:09 |
| kanzure- | nimbus cloud? | 18:29 |
| 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 | 18:33 |
| 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 | 18:34 |
| ybit | :) | 18:35 |
| ybit | thanks | 18:35 |
| 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 | 18:40 |
| 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? | 18:45 |
| cis-action | Also, I use quicksilver on the mac - can you suggest a similar accelerator for gnome? | 18:46 |
| 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. | 18:52 |
| 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. | 18:53 |
| cis-action | ok | 18:54 |
| cis-action | all i have right now is xpdf. I hear that mendeley has a linux distro... | 18:54 |
| kanzure- | mendeley begins to suck when you add more than 1,000 papers | 18:56 |
| cis-action | darn | 18:56 |
| 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 | 18:57 |
| 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? | 19:00 |
| 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' | 19:02 |
| 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 <blah>" | 19:03 |
| kanzure- | (run that in the shell) | 19:03 |
| 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. | 19:04 |
| cis-action | grep might work, but SpotLight and google desktop both precompute search indexes, so they may be faster | 19:08 |
| 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? | 19:14 |
| 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 | 19:18 |
| 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 | 19:19 |
| drazak | oh | 19:20 |
| drazak | I saw the light bit | 19:20 |
| 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 | 19:21 |
| drazak | yeah, guess not | 19:22 |
| drazak | dunno, doesn't matter who had the idea, it's a collaborative process | 19:22 |
| 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 | 19:23 |
| 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 | 19:25 |
| 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? | 19:26 |
| 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? | 19:27 |
| 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. | 19:28 |
| 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. | 19:29 |
| 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 | 19:30 |
| 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 | 19:32 |
| drazak | seems to me that you're adding another level of uneeded complexity with that, why not have them in the reaction chamber? | 19:33 |
| kanzure- | because you don't want the reactions to happen on things you didn't want to happen | 19:38 |
| 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 | 19:44 |
| kanzure- | but not when you open them | 19:55 |
| drazak | no, but you could selectively open them | 19:56 |
| drazak | your azobenzene key idea | 19:56 |
| 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 | 19:58 |
| 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 | 20:00 |
| drazak | guess I didn't explain it well enough | 20:01 |
| 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 | 20:03 |
| 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 | 20:06 |
| ybit | concerning http://co.de i cancelled my order with domainmonger, it's actually a legit company with very helpful customer support | 20:19 |
| 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 | 20:20 |
| drazak | mhm | 20:21 |
| 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 | 21:11 |
| 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) | 21:16 |
| kanzure- | is /tmp not actually tmp stuff? | 21:22 |
| kanzure- | because I deleted all of it | 21:22 |
| drazak | xit is temp stuff | 22:14 |
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