--- Day changed Mon May 25 2009
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00:36 < kanzure> hi mindspillage.
00:36  * mindspillage waves
00:36 < kanzure> have you considered re-attaching your skull cap so as to stop the spilling
00:37 < mindspillage> As I'm not Jewish I'm afraid it would give people the wrong idea...
00:38 < 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?
00:40 < 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
00:41 < 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?
00:42 < kanzure> whether or not I'll be shot by lawyers for having somebody that gives me funding to do dangerous, reckless self-experimentation
00:44 < mindspillage> Nah, probably not. The funder's lawyer might want to shoot him. :-)
00:47 < 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.
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00:58 < kanzure> cis-action: I just added something to your inbox.
00:59 < kanzure> maybe you know someone
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01:31 < kanzure> http://austin.craigslist.org/crs/1187421323.html
01:45 < kanzure> http://austin.craigslist.org/grp/1187427836.html
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02:11 < 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
02:46 < genehacker> kanzure bet you ten bucks the myostatin one gets you some willing test subjects
02:54 < 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
--- Log closed Mon May 25 03:06:49 2009
--- Log opened Mon May 25 03:07:00 2009
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03:09 < genehacker> ok I bet you some wuffie then
03:11 < genehacker> within a month
03:11 < genehacker> sanger sequencer looks awesome
03:11 < genehacker> it looks like it is happy
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07:41 < faceface> nurse bot?
07:41 < faceface> http://www.cs.cmu.edu/~nursebot/web/scope.html
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--- Log opened Mon May 25 08:23:30 2009
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09:14 < kanzure> cis-action: you've been reading many metagenomics-related papers.
09:15 < 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
09:16 < kanzure> the collection of mutations that this would reveal might prove interesting
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10:18 < faceface> kanzure: I want to visit the einstein museum to collect his dna
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10:28 < 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> "
11:18 < 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?
11:19 < kanzure> or do we not see that in genomes?
11:36 < kanzure> nevermind
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11:59 < 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)
12:01 < kanzure> it's common to attach DNA to beads.
12:05 < 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 :(
12:11 < cis-action> hey kanzure.
12:14 < 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
12:15 < cis-action> I think polony sequencing might get around this, but I don't know how expensive it is.
12:28 < kanzure> uh, what about electrophoresis to separate the strands?
12:37 < nsh> kanz, that seems like a painfully difficult way to sequence
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12:38 < kanzure> nsh: sequencing tends to be painfully difficult apparently
12:39 < 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
12:40 < nsh> brb, dinner
12:41 < kanzure> nsh: I don't think AFM costs as much as you think it does :)
13:01  * nsh adds it to his amazon wishlist then
13:05 < kanzure> did you see the CAD files and instructions for building one?
13:07 < nsh> nope. link?
13:16 < kanzure> server down. not right now.
13:19 < nsh> not to worry
13:25 < 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
13:26 < 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
13:29 < nsh> i take it you saw this kanz: http://www.rockefeller.edu/evolution/video.php?src=joyce_low ? 
13:30 < nsh> accelerated directed molecular-scale evolution in PCR 
13:35 < kanzure> yeah
13:35 < kanzure> was that the recent one about ribosomes?
13:36 < nsh> no, just RNA molecules in a continually-cycling [microfluidics] PCR reaction with selective pressure
13:37 < nsh> worth a watch
13:58 < 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
13:59 < genehacker> it's not working
14:00 < 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
14:01 < 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?
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14:01 < genehacker> I ALWAYS READ PDFS IN WEBBROWSER
14:01 < genehacker> and save the ones I like the best
14:02 < 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
14:04 < kanzure> um. I think it involves disabling the adobe plugin.
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14:23 < kanzure> Heloo TheMyster.
14:23 < kanzure> *Hello
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14:30 < genehacker> heh
14:30 < genehacker> somebody plays Myst
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14:36 < nsh> actually, someone set up my ircproxy secondary nickname as "TheMysteriousNsh"
14:37 < nsh> and it just cut like that
14:37 < nsh> never played myst, to my demerit
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14:37 < kanzure> you have shamed him :(
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14:38 < genehacker> FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
14:38 < genehacker> firefox crashed
14:39 < kanzure> it tends to do that a lot
14:39 < kanzure> I recommend Opera
14:44 < genehacker> how many tabs can you open in opera before it crashes
14:45 < genehacker> I think I have run 50 tabs and that's about when it crashes
14:46 < kanzure> 400
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14:59 < genehacker> wow
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17:07 < kanzure> fenn: ok. 
17:07 < kanzure> fenn: feel free to drop by.
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17:31 < fenn> ok
17:33 < kanzure> mom wants to meet you though
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17:45 < fenn> is she there now?
17:48 < 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.
17:49 < fenn> er, ok
17:56  * fenn is in the middle of a dist-upgrade
17:58 < kanzure> is there something new out
18:01 < fenn> kde3 is no longer supported, it was chapping my balls
18:05  * fenn shudders @ new konqueror icons
18:06 < drazak_> you guys know anything of pace university?
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18:21 < fenn> kanzure: you're running kde4 right? if you type 'systemsettings' does it launch the control panel thingy?
18:25 < fenn> what a mess
18:26 < kanzure> fenn: 3.5 all the way for me :)
18:27 < kanzure> 20 GB available on a disk. should I install ubuntu or not?
18:27 < fenn> if you enjoy that sort of thing
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18:33 < fenn> well this is obviously going to take a while to sort out, so i'll see you in 10 mins ok?
18:48 < kanzure> ok
18:48 < drazak_> kanzure: you have any new ideas you want to talk about?
19:01 < kanzure> drazak_: are you bored?
19:01 < drazak_> yes
19:01 < drazak_> I was going to call you
19:02 < drazak_> my uncle is growing skeletal muscle on a darpa contract at harvard
19:02 < kanzure> neat
19:03 < 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
19:04 < kanzure> food is for the weak
19:04 < drazak_> it is when you have a corded phone
19:05 < drazak_> any ones you want me to look at first?
19:08 < kanzure> nah, just look at the .png's and be amazed
19:08 < kanzure> http://adl.serveftp.org/papers/?C=M;O=D
19:16 < drazak_> waz your number?
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19:34 < drazak_> kanzure: sorry man, I was bored
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20:31 < kanzure> drazak_: was not a problem
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21:34 < genehacker> so how do I open PDF outside of browser
21:47 < kanzure> are you serious
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21:53 < kanzure> genehacker: try opening a file by clicking on it or hitting the ENTER key.
22:03 < genehacker> ok
23:02 < genehacker> tried by clicking on it and pressing enter
23:02 < genehacker> it opens in my browser
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23:58 < kanzure> genehacker: try uninstalling the adobe pdf reader plugin
23:58 < genehacker> ok
23:58 < genehacker> I'm deleting the system 32 folder
23:59 < 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