2012-07-13.log

--- Log opened Fri Jul 13 00:00:07 2012
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kanzurejrayhawk: don't leave me :(03:27
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JayDuggerGet back to sleep, kanzure.07:50
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nmz787howdy08:41
nmz787Mokbortolan_: I'm in your neck of the woods... and don't have plans while the girl is interviewing til 5pm08:42
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kanzurenmz787: go bug joe or his brother steve09:57
nmz787lol10:00
nmz787I pinged him in here10:01
nmz787dunno their info otherwise10:01
klafkahey10:01
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kanzurenmz787: ok i'll send over some data10:03
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kanzurenmz787: emailed10:06
nmz787cool10:10
nmz787gonna go to bank now to take care of something, will bug them after :D10:10
nmz787ttyl peeps10:11
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rdbow.  this is the first time that a microcontroller violently came loose from my breadboard and made a pretty deep cut in my finger11:27
rdbit's supposed to zap my brain, not cut me11:28
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kanzurehttp://beautifulmind.io/ claims to do "real-time collaborative mind mapping"11:37
kanzurehttp://beautifulmind.io/1269-kanzure11:39
rdbthat sounds interesting11:41
kanzurei usually hate mindmaps, but i know Utopiah likes them or something11:41
rdbmy connection gets lost all the time, apparently11:41
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Sankyreminds me of, uhh12:12
archelskanzure: That one seems particularly terrible.12:13
SankyI don't even know how the thing I used was named12:16
Sankyall I remember is it was in java12:16
Sankyanyway12:16
Sankyworkflowy rules12:16
kanzurewhat does workflowy do?12:18
Sankyit's a brainstorming tool/todo list of sorts12:19
Sankyit's extremely simple12:19
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kanzurehttp://blogs.plos.org/neuroanthropology/2012/07/09/roid-age-steroids-in-sport-and-the-paradox-of-pharmacological-puritanism/12:29
kanzure"timeline of performance enhancing drugs in sports" http://sportsanddrugs.procon.org/view.resource.php?resourceID=00236612:29
kanzure"His blood sample was sent to U.C.L.A.'s Olympic Analytical Laboratory, which is accredited by the World Anti-Doping Agency, and scientists there detected H.G.H. in it."12:30
kanzurehahah there's an olympic analytical lab :\12:30
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Mariuis Gregory Stock still working in U.C.L.A. ?12:34
kanzurei think he's working at http://signumbio.com/12:35
rdbI just put together what's probably the safest DIY tDCS device around.12:35
kanzureor at least.. he was12:35
Mariuoh nice12:35
rdbnow to find some sponges and fashion some electrodes12:35
Adrian_kanzure: u didnt  know?12:39
Adrian_there are a few of these labs12:40
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kanzurei know about analytics labs, just not one that is explicitly "olympic"12:40
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AdrianGi think its just a name12:41
AdrianGthere are a few labs under contract with WADA12:41
AdrianGive heard gene therapy is the hottest doping right now.12:41
kanzureheard from who12:51
kanzurei'm totally willing to make gene doping products if you can show me someone interested in paying me cash12:52
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AdrianGkanzure: rumors13:03
AdrianGkanzure: what can you make13:10
kanzurethat depends on what my motivations are13:11
kanzureright now i don't actively synthesize anything13:11
AdrianGwhat can you synthesize13:11
AdrianGthat would be useful in sports13:11
kanzurethere are many low-hanging fruit projects for sports doping13:11
kanzurehttp://diyhpl.us/wiki/germline-genetic-modifications/13:11
kanzureuh, i don't know why i named that germline-anything13:11
AdrianGyes, but can you make anything that can be used tomorrow in a real person13:14
kanzuretomorrow? gee that's a fast deadline13:15
kanzurei don't even know what you want me to synthesize yet13:15
AdrianGim asking what can you do13:16
AdrianGwell, tomorrow is flexible13:16
kanzurei have some modest lab skills, if that's what you're asking.13:16
AdrianGlondon olympics are in two weeks, you know13:16
kanzurewouldn't you want to spend more than 2 weeks checking out a drug, if you're an athlete that has to be sure he's at best performance at the event?13:17
kanzurei doubt that athletes start doping at a last minute :P13:17
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kanzureaw :(13:18
kanzuremaybe he's angry that i'm not already synthesizing something13:18
Steel2Sanky: mindmeister13:19
Steel2?13:19
Sankywhat's that?13:20
Sankyoh, no13:20
Sankysomething else, meh13:20
Steel2I like mindmeister13:20
SankyI'll try to remember it13:20
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yashterdamkanz you named it germline- because you forked it from my thing13:28
kanzurehrmmm13:28
kanzurethis makes sense13:28
yashterdamanyway gotta go, that's what I get for checking the logs before sleep13:31
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kanzurei feel that yash is misappropriating his time in amsterdamn by sleeping13:31
kanzure:P13:31
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AdrianGkanzure: im just saying we are too late for these olympics13:40
archelskanzure: what is this "gene doping"13:41
kanzurearchels: a popular example is siRNA doping13:42
kanzurewell, wait. no. there are many forms of small-molecule RNA doping, but i don't think siRNA is one of them. hrmm..13:42
archelsokay, that's roughly what I expected13:42
kanzurei also think people count adenoviral and lentiviral methods as gene doping13:43
archelsinjecting silencing RNAs?13:43
AdrianGpossibly13:43
kanzuremy /gene-therapy folder is so pathetic13:44
kanzurehttp://diyhpl.us/~bryan/papers2/gene-therapy13:44
kanzureonly 20 articles? geeze.13:44
AdrianG:<13:44
archelsindicative of the state of affairs13:44
kanzurethat i am bad at finding good articles, yes13:44
kanzurebut there's lots of stuff published13:45
kanzure(i was just observing that i seem to be slacking on that front)13:45
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archelsanything worthwhile, besides messing with silencing RNA a bit?13:45
kanzurei'm not in the right brain state right now to produce that knowledge from my brain :P13:48
kanzurei'm in javascript-and-anti-feminism-mode and very confused13:49
archelshaha, o-kay13:49
archelslike I said I doubt the problem is you; I think the problem is the state of affairs in the field13:49
archelswe're just not there yet13:49
kanzurethere have been tons of clinical trials for all sorts of interesting methods13:50
kanzureand lab studies of others; like just naked dna injection is pretty neat13:50
archelsyes, but you can't really pull that off in vivo can you13:50
archelsit's the delivery mechanism that's the crux13:50
kanzurenaked dna injection was through rat tails13:51
kanzurehow's that not in vivo :P13:51
kanzureretrograde renal vein injection http://diyhpl.us/~bryan/papers2/bio/Kidney-targeted%20naked%20DNA%20transfer%20by%20retrograde%20renal%20vein%20injection%20in%20rats.pdf13:51
kanzurealthough admittedly that's a limited method because kidneys13:52
archelsclicking13:52
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yashterdamgah fine13:54
kanzuredamn straight, boy13:54
yashterdamanyway yeah gene therapy's mostly stilted since that fucking kid died13:55
yashterdamhmm wait no it's stulted13:55
archelskanzure: I'm not following this, so the "naked DNA" plasmid is injected into the bloodstream, and then how does it find its way into the cell nuclei exactly?13:57
kanzurei don't think you need to get into the nuclei to get copied around entirely13:57
yashterdamoccasionally cells have holes in them, or there's the transient overpressure from the injection13:57
yashterdamyou do need to get into the nucleus, but in an actively dividing cell that's not a large barrier13:58
kanzurei think even ecoli is naturally competent and takes up DNA (at very very low rates)13:58
archelsah the paper they refer to has 'electroporation' in the title13:58
kanzurehttp://diyhpl.us/~bryan/papers2/bio/Genetic%20transformation%20in%20freshwater%20-%20Escherichia%20coli%20is%20able%20to%20develop%20natural%20competence.pdf13:58
kanzurehttp://diyhpl.us/~bryan/papers2/bio/Natural%20plasmid%20transformation%20in%20ecoli.pdf13:58
archelsbut e-coli sounds like in vitro13:59
kanzureoh, it's definitely not human-related, sorry14:00
archelsalthough I guess the results they describe are impressive, so they must be managing it somehow14:00
kanzurebut since we were talking about per-cell dna uptake, i thought to mention it14:00
archelsif they actually use electroporation in vivo, that's pretty nasty though14:00
yashterdamhey at least it's in a limb and not the brain14:00
kanzuredid you read the article about optical electroporation? http://diyhpl.us/~bryan/papers2/neuro/Subretinal%20injection%20and%20electroporation%20into%20adult%20mouse%20eyes.pdf14:01
kanzurei guess that's not optical electroporation14:01
kanzureelectroocularporation14:01
kanzureerm.. no that can still mean "shine lasers on to things to make them porate"14:01
yashterdamehhh eyes are a prime candidate for viral vectors, much as I dislike viral vectors14:01
archels13MB and still going14:02
archels2614:02
kanzurei apologize for how terrible science is.14:03
archelswoo pretty pictures14:03
archelsokay, so in conclusion, it seems that this intravenous DNA plasmid injection still relies on some variant of electroporation.14:05
yashterdamyou can get measurable transfection just injecting in mice, less so in larger mammals14:06
archelsyou probably need to inject unholy amounts of DNA for that, even14:08
yashterdamso what, dna is cheap14:08
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kanzureit's the one thing that we're really good at making14:08
kanzures/making/copying14:08
yashterdamyeah writing is expensive, copying much less so14:09
archelscan't be good for the animal14:10
kanzureoh yay me14:10
kanzurehttp://diyhpl.us/wiki/natural-competence14:10
archelsokay, I'm off, nice chat14:11
yashterdamok cool because I am too14:12
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gnushadiyhpluswiki.git: 914096b move germline-genetic-modifications to genetic-modifications14:12
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kanzureis there a javascript deobfuscation tool that can rename variables for me?14:34
kanzurelike if i want to rename "a" or something?14:34
kanzureit's hard to do search-and-replace on single-letter variable names14:34
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rdbkanzure, um, use \b with sed around the letter to include word boundaries?14:43
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rdblike sed -i'' 's/\ba\b/somename/g' somefile.js ?14:44
kanzurewhat does \b include though14:44
rdbnothing, just indicates word boundary14:44
kanzurewhat counts as a word boundary? parentheses? periods? whitespace?14:44
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rdb[A-Za-z0-9_] are included in the word14:45
rdbwhich means that it'll work for most variable names out there14:45
kanzurewell okay then.14:45
kanzurethanks.14:45
rdbor more fun!   for i in "abcdefghij..z"; do sed -i "s/\b$i\b/$(random /usr/share/dict/words)/g" somefile.js; done14:45
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rdbreplaces every single-letter variable name with a random english word14:45
kanzureyeah, i wanted to avoid writing regular expressions with [A-Za-z0-9_], but \b looks reasonable14:45
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kanzureoh, i guess the one exception to this that i am okay with is i, j, and k iterators in for loops14:48
kanzurehrmm14:48
rdbanyway, good luck, my brain is pretty much dead right now so I'll just head to bed14:50
kanzuregood night14:51
kanzurethanks for the regex wizardry14:51
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kanzure"nventory for Composable Elements (ICE) is being developed by the Joint Bio Energy Institute (JBEI) as an open source Registry software for biological parts. It is a web application software that can be used by laboratories to track and search their constructs."15:18
kanzurehttp://public-registry.jbei.org/15:18
kanzurehttp://code.google.com/p/gd-ice/15:18
kanzureoh boy.. soap api :(15:19
AdrianGkanzure: do you ever experience information overload15:20
kanzureno15:21
kanzureat the moment i'm writing some code in another window and i get bored waiting for the buffers to finish typing15:21
kanzureand it's javascript, so i feel terrible about it too15:21
kanzurealso i think juul or nmz787 possibly contributed to that project; hard to tell15:22
AdrianGhow do you organize information15:27
kanzurehyperlinks, git repositories, software i write15:31
kanzureAdrianG: example: http://quantifiedself.com/2011/08/bryan-bishop-on-meetlog/15:31
kanzurehttp://diyhpl.us/cgit15:33
AdrianGsometimes I suspect you are just a very convincing bot.15:36
kanzurehttp://heybryan.org/mac.html15:36
AdrianGnot because of that15:36
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kanzurerdb: apparently it is \< and \> in vim15:37
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AdrianGkanzure: r u a student15:59
kanzureno16:00
AdrianGwat u do for a living16:10
AdrianGbesides irc chatting16:10
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brownieshe types very quickly16:25
kanzureAdrianG: http://diyhpl.us/~bryan/resume.pdf16:31
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kanzurejrayhawk: why did you get kicked offline20:10
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Juulallo20:16
kanzureJuul: hi20:16
Juul:)20:16
* Juul is at HOPE20:16
JuulI was talking to some of the makerbot employees earlier20:16
Juulthey say they've talked about NURBS, but nothing has been planned20:17
JuulI didn't realize they had two-material printing20:17
Juuland when I found out I expected them to use the second material for dissolvable support20:18
Juulbut they don't have a dissolvable support material yet20:18
JuulI wonder how difficult that will prove20:18
Juulto have something that can be fed in as a somewhat bendable wire20:18
Juulwhich is dissolvable without nasty chemicals20:18
Juuland has a melting point at leas above that of PLA20:18
kanzurereprap has all sorts of printing materials, including stuff for pcb printing and tissue printing20:19
kanzuremakerbot extruders are only somewhat behind (but it's the same compatability anyway, so it's not much of a difference)20:20
Juuldo any of the cheap/home-use printers have dissolvable support yet?20:20
kanzurei can't recall at the moment.. #reprap will know20:21
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kanzurebiocurious class survey http://www.surveymonkey.com/s/W2CZJCB20:47
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joshcryerhttp://www.kurzweilai.net/hp-memristors-will-reinvent-computer-memory-by-201423:33
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--- Log closed Sat Jul 14 00:00:08 2012

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