| --- Day changed Mon May 25 2009 | ||
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| kanzure | hi mindspillage. | 00:36 |
|---|---|---|
| * mindspillage waves | 00:36 | |
| kanzure | have you considered re-attaching your skull cap so as to stop the spilling | 00:36 |
| mindspillage | As I'm not Jewish I'm afraid it would give people the wrong idea... | 00:37 |
| mindspillage | Anyhow, metaphorical spillage doesn't create much mess. | 00:38 |
| kanzure | ok ok | 00:38 |
| kanzure | so, I have a legalese question for you | 00:38 |
| mindspillage | Ok... | 00:38 |
| kanzure | do you know anything about science patrons? | 00:38 |
| mindspillage | Not called by that phrase... | 00:40 |
| kanzure | what? | 00:40 |
| kanzure | is there another way to say that? | 00:40 |
| mindspillage | (I mean, I might think of foundations giving grants as "patrons" but I've never heard of someone referring to "science patrons".) | 00:40 |
| kanzure | I mean private individuals, not foundations | 00:40 |
| mindspillage | Then I think of angel investors... | 00:41 |
| kanzure | oh, that might be a neat way to do it | 00:41 |
| kanzure | ok, thanks. | 00:41 |
| mindspillage | What do you want to know about them? | 00:41 |
| kanzure | whether or not I'll be shot by lawyers for having somebody that gives me funding to do dangerous, reckless self-experimentation | 00:42 |
| mindspillage | Nah, probably not. The funder's lawyer might want to shoot him. :-) | 00:44 |
| kanzure | fenn: create-fp complains that I am passing it too many parameters when I pass it everything in the constructor's parameter list filled out. blah. | 00:47 |
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| kanzure | cis-action: I just added something to your inbox. | 00:58 |
| kanzure | maybe you know someone | 00:59 |
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| kanzure | http://austin.craigslist.org/crs/1187421323.html | 01:31 |
| kanzure | http://austin.craigslist.org/grp/1187427836.html | 01:45 |
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| kanzure | xhttp://adl.serveftp.org/papers/microfluidics_Sanger_sequencer.png | 02:11 |
| kanzure | er | 02:11 |
| kanzure | http://adl.serveftp.org/papers/microfluidics_Sanger_sequencer.png | 02:11 |
| genehacker | kanzure bet you ten bucks the myostatin one gets you some willing test subjects | 02:46 |
| kanzure | make the bet more specific and you're on | 02:54 |
| kanzure | i.e., what time frame | 02:54 |
| kanzure | do you bet that it will happen within a day? two days? | 02:54 |
| kanzure | and it can't be yourself | 02:54 |
| --- Log closed Mon May 25 03:06:49 2009 | ||
| --- Log opened Mon May 25 03:07:00 2009 | ||
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| genehacker | ok I bet you some wuffie then | 03:09 |
| genehacker | within a month | 03:11 |
| genehacker | sanger sequencer looks awesome | 03:11 |
| genehacker | it looks like it is happy | 03:11 |
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| faceface | nurse bot? | 07:41 |
| faceface | http://www.cs.cmu.edu/~nursebot/web/scope.html | 07:41 |
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| --- Log opened Mon May 25 08:23:30 2009 | ||
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| kanzure | cis-action: you've been reading many metagenomics-related papers. | 09:14 |
| kanzure | an interesting sequencing project might be to collect DNA from professors on a university campus, either through forensics or by knocking on their office door | 09:15 |
| kanzure | the collection of mutations that this would reveal might prove interesting | 09:16 |
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| faceface | kanzure: I want to visit the einstein museum to collect his dna | 10:18 |
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| kanzure | " As an example, a child that knows the manufacturing process of every | 10:28 |
| kanzure | toilet in Central Oregon may at first be interesting, but will bore others after an hour | 10:28 |
| kanzure | or two if they are even still listening and have not walked away. | 10:28 |
| kanzure | " | 10:28 |
| kanzure | Does the organization of a genome (i.e., which genes are in which location) influence viability? is there some selective advantage to pushing everything related to, say, neurons, in a stretch of the genome? | 11:18 |
| kanzure | or do we not see that in genomes? | 11:19 |
| kanzure | nevermind | 11:36 |
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| kanzure | so why haven't we seen AFM cantilever mass-based DNA sequencing? by hanging DNA from the cantilever tip, recording the force, and then selectively cleaving a single nucleotide from the strand, you should be able to detect the difference in the force of the DNA. | 11:59 |
| kanzure | (there is DNA mass spec sequencing, but not by AFM) | 11:59 |
| kanzure | it's common to attach DNA to beads. | 12:01 |
| kanzure | hm. oh. you don't necessarily have to have it hanging the entire time. you just lower it (like string/rope) and let it rest on the ground. you need a z-axis approach mechanism that has the resolution of a few angstroms though :( | 12:05 |
| cis-action | hey kanzure. | 12:11 |
| cis-action | With regards to metagenomics, I've been confounded by a a cloning step that is required to purify and segregate different amplicons from the pcr mix - if I'm going to do sanger sequencing, I can't figure out how to go from pcr on a genomic pool to pure DNA samples of identical DNAs in different tubes | 12:14 |
| cis-action | I think polony sequencing might get around this, but I don't know how expensive it is. | 12:15 |
| kanzure | uh, what about electrophoresis to separate the strands? | 12:28 |
| nsh | kanz, that seems like a painfully difficult way to sequence | 12:37 |
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| kanzure | nsh: sequencing tends to be painfully difficult apparently | 12:38 |
| nsh | yeah, but i can't imagine many techniques less amenable to parallelisation than AFM... | 12:39 |
| nsh | those things cost a lot of moneys | 12:39 |
| nsh | brb, dinner | 12:40 |
| kanzure | nsh: I don't think AFM costs as much as you think it does :) | 12:41 |
| * nsh adds it to his amazon wishlist then | 13:01 | |
| kanzure | did you see the CAD files and instructions for building one? | 13:05 |
| nsh | nope. link? | 13:07 |
| kanzure | server down. not right now. | 13:16 |
| nsh | not to worry | 13:19 |
| kanzure | quake paper dump (he's the guy that first made microfluidic valves apparently): http://adl.serveftp.org/papers/quake/ | 13:25 |
| kanzure | sorted by title: http://thebigone.stanford.edu/quake/papers.htm | 13:25 |
| kanzure | ah neat: "A synthetic Escherichia coli predator-prey ecosystem" | 13:26 |
| kanzure | that's what I've been thinking of for the accelerated evolution system device thingies | 13:26 |
| nsh | i take it you saw this kanz: http://www.rockefeller.edu/evolution/video.php?src=joyce_low ? | 13:29 |
| nsh | accelerated directed molecular-scale evolution in PCR | 13:30 |
| kanzure | yeah | 13:35 |
| kanzure | was that the recent one about ribosomes? | 13:35 |
| nsh | no, just RNA molecules in a continually-cycling [microfluidics] PCR reaction with selective pressure | 13:36 |
| nsh | worth a watch | 13:37 |
| genehacker | WTF | 13:58 |
| genehacker | adobe is still broken | 13:58 |
| kanzure | Microfabricated rubber microscope using soft solid immersion lenses | 13:58 |
| genehacker | out of PDMS? | 13:58 |
| kanzure | http://thebigone.stanford.edu/quake/publications/apl_may06.pdf | 13:58 |
| * kanzure nods | 13:58 | |
| genehacker | it's not working | 13:59 |
| nsh | friends don't let friends use adobe | 14:00 |
| genehacker | no it's not adobe | 14:00 |
| genehacker | paper isn't even download | 14:00 |
| genehacker | ing | 14:00 |
| genehacker | adobe doesn't work in the webrowser anymore | 14:01 |
| genehacker | it worked yesterday | 14:01 |
| kanzure | friends don't let friends read PDFs in web browsers | 14:01 |
| genehacker | why? | 14:01 |
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| genehacker | I ALWAYS READ PDFS IN WEBBROWSER | 14:01 |
| genehacker | and save the ones I like the best | 14:01 |
| kanzure | you could set it to open them up outside of the browser | 14:02 |
| kanzure | and then you don't have tons of multi-MB PDFs clogging up your browser memory | 14:02 |
| genehacker | oh how do i do that? | 14:02 |
| genehacker | makes sense | 14:02 |
| kanzure | um. I think it involves disabling the adobe plugin. | 14:04 |
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| kanzure | Heloo TheMyster. | 14:23 |
| kanzure | *Hello | 14:23 |
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| genehacker | heh | 14:30 |
| genehacker | somebody plays Myst | 14:30 |
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| nsh | actually, someone set up my ircproxy secondary nickname as "TheMysteriousNsh" | 14:36 |
| nsh | and it just cut like that | 14:37 |
| nsh | never played myst, to my demerit | 14:37 |
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| kanzure | you have shamed him :( | 14:37 |
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| genehacker | FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF | 14:38 |
| genehacker | firefox crashed | 14:38 |
| kanzure | it tends to do that a lot | 14:39 |
| kanzure | I recommend Opera | 14:39 |
| genehacker | how many tabs can you open in opera before it crashes | 14:44 |
| genehacker | I think I have run 50 tabs and that's about when it crashes | 14:45 |
| kanzure | 400 | 14:46 |
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| genehacker | wow | 14:59 |
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| kanzure | fenn: ok. | 17:07 |
| kanzure | fenn: feel free to drop by. | 17:07 |
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| fenn | ok | 17:31 |
| kanzure | mom wants to meet you though | 17:33 |
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| fenn | is she there now? | 17:45 |
| kanzure | no | 17:48 |
| kanzure | but she wants you to come here before she does. | 17:48 |
| kanzure | she is available on wednesday, thursday and friday evenings, but wants some advanced notice | 17:48 |
| kanzure | her schedule is almost as pliable as yours, although not quite. | 17:48 |
| fenn | er, ok | 17:49 |
| * fenn is in the middle of a dist-upgrade | 17:56 | |
| kanzure | is there something new out | 17:58 |
| fenn | kde3 is no longer supported, it was chapping my balls | 18:01 |
| * fenn shudders @ new konqueror icons | 18:05 | |
| drazak_ | you guys know anything of pace university? | 18:06 |
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| fenn | kanzure: you're running kde4 right? if you type 'systemsettings' does it launch the control panel thingy? | 18:21 |
| fenn | what a mess | 18:25 |
| kanzure | fenn: 3.5 all the way for me :) | 18:26 |
| kanzure | 20 GB available on a disk. should I install ubuntu or not? | 18:27 |
| fenn | if you enjoy that sort of thing | 18:27 |
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| fenn | well this is obviously going to take a while to sort out, so i'll see you in 10 mins ok? | 18:33 |
| kanzure | ok | 18:48 |
| drazak_ | kanzure: you have any new ideas you want to talk about? | 18:48 |
| kanzure | drazak_: are you bored? | 19:01 |
| drazak_ | yes | 19:01 |
| drazak_ | I was going to call you | 19:01 |
| drazak_ | my uncle is growing skeletal muscle on a darpa contract at harvard | 19:02 |
| kanzure | neat | 19:02 |
| kanzure | um, there are many things to talk about | 19:03 |
| drazak_ | definitely | 19:03 |
| kanzure | have you been keeping up with the papers that I have been reading and sharing? | 19:03 |
| kanzure | http://adl.serveftp.org/papers/ | 19:03 |
| drazak_ | not really, not recently atleast | 19:03 |
| kanzure | at least look at the diagrams | 19:03 |
| drazak_ | yeah, I will | 19:03 |
| drazak_ | gimme a min, fixing food | 19:03 |
| kanzure | food is for the weak | 19:04 |
| drazak_ | it is when you have a corded phone | 19:04 |
| drazak_ | any ones you want me to look at first? | 19:05 |
| kanzure | nah, just look at the .png's and be amazed | 19:08 |
| kanzure | http://adl.serveftp.org/papers/?C=M;O=D | 19:08 |
| drazak_ | waz your number? | 19:16 |
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| drazak_ | kanzure: sorry man, I was bored | 19:34 |
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| kanzure | drazak_: was not a problem | 20:31 |
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| genehacker | so how do I open PDF outside of browser | 21:34 |
| kanzure | are you serious | 21:47 |
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| kanzure | genehacker: try opening a file by clicking on it or hitting the ENTER key. | 21:53 |
| genehacker | ok | 22:03 |
| genehacker | tried by clicking on it and pressing enter | 23:02 |
| genehacker | it opens in my browser | 23:02 |
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| kanzure | genehacker: try uninstalling the adobe pdf reader plugin | 23:58 |
| genehacker | ok | 23:58 |
| genehacker | I'm deleting the system 32 folder | 23:58 |
| kanzure | um | 23:59 |
| kanzure | I don't think that's a good ideaa | 23:59 |
| genehacker | did you know that's what the government uses to prevent you from hacking? | 23:59 |
| kanzure | the law? | 23:59 |
| genehacker | no | 23:59 |
| genehacker | just kidding | 23:59 |
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