--- Day changed Tue May 12 2009 02:05 < genehacker> http://www.sciencedaily.com/releases/2009/05/090510200001.htm 02:20 < fenn> how convenient 02:20 < fenn> but is it more convenient than just engineering whatever you're after to be expressed in e. coli? 02:24 < genehacker> ??? 02:24 < genehacker> dunno 02:36 -!- genehacker_ is now known as genehacker 09:02 < faceface> kanzure-: about transfection - yup and yup - both great ideas. 15:50 < kanzure-> faceface: which two were good ones 15:50 < kanzure-> Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries 15:50 < kanzure-> http://adl.serveftp.org/papers/Functional%20cross-kingdom%20conservation%20of%20mammalian%20and%20moss%20(Physcomitrella%20patens)%20transcription,%20translation%20and%20secretion%20machineries.pdf 15:55 < kanzure-> huh. apparently /tmp needs to be chmod'd for global read/write. 15:58 < kanzure-> fenn: feel like coming into the lab today? 16:07 < kanzure-> "Devil's Theory of Innovation: Competition produces stasis. Only complacency drives change. .. animals' appearance alters and their behavior changes not in conditions of scarcity, but in landscapes of plentitude. This pattern makes for 'relaxed selection'." 16:23 < genehacker> glad you saw that one 16:24 < genehacker> also heybryan was down last time I checked 17:16 < xp_prg> kanzure do you see the demonizing of do it yourself biologists? 17:42 < kanzure-> xp_prg: I see morons. 17:42 < kanzure-> genehacker: I don't have an internet connection at the apartment yet. 17:42 < kanzure-> genehacker: are you on campus? 18:50 < xp_prg> what is the best wiki to use kanzure? 19:22 < kanzure-> hahah http://common-lisp.net/project/clpython/ 19:36 < cis-action> kanzure-: http://www.vimeo.com/4614021 19:37 < kanzure-> what is it? 19:38 < cis-action> it's a video and my notes about searching across large pdf collections 19:38 < cis-action> I also am in the middle of testing out the olpc and the kindle as mobile readers for the pdf library. I have some pictures comparing them. 19:39 < kanzure-> okay 19:39 < kanzure-> on Wednesday I should be back to my normal self 19:39 < cis-action> ... is it exam time or something? 19:39 < kanzure-> yes 19:39 < kanzure-> but I also do not have an internet connection back at the apartment 19:39 < cis-action> oh. 19:39 < kanzure-> just moved. 19:41 < fenn> kanzure-: just got up. i actually was thinking about coming down to the lab today 19:42 < genehacker> check out diybio 19:42 < genehacker> http://groups.google.com/group/diybio/browse_thread/thread/7a108447506cd579?hl=en 19:43 < genehacker> http://groups.google.com/group/diybio/browse_thread/thread/7a108447506cd579?hl=en 19:44 < kanzure-> genehacker: what about it 19:45 < genehacker> oh no, biohackers are gonna STEAL YOUR DNA AND USE IT TO GROW HORRIBLE DOOMSDAY VIRUSES THAT WILL CAUSE COMMUNISM IN AMERICA 19:45 < genehacker> is pretty much what those articles said 19:45 < genehacker> That's when the phone rang. A man saying he was doing research for the U.S. government called with a few polite, pointed questions: How did she build that lab? Did she know other people creating new life forms at home? 19:45 < genehacker> hmmmm... 19:46 < genehacker> makes me want to build that DNA synth from a projector even more 19:46 < genehacker> they'd totally freak out 19:48 < kanzure-> "don't poke the bear" 19:48 < genehacker> if I got a call from the government, I'd totally troll them 19:48 < genehacker> oh yeah, we need to figure out how to extract DNA from microarrays before we can have fun 19:49 < kanzure-> what do you mean 'extract' 19:49 < kanzure-> usually you just have a bead bound to a surface via streptavidin 19:49 < kanzure-> and then you release the streptavidin bond via some enzyme or something 19:49 < genehacker> the oligos are stuck to the chip 19:49 < kanzure-> er, however that stuff works. It's been a while since I've reviewed it. 19:49 < kanzure-> not if you grow the oligos on beads, or something 19:49 < genehacker> it's bonded via a silane group 19:50 < genehacker> or something like that 19:50 < kanzure-> doesn't have to be. 19:50 < genehacker> I was thinking something like PCR 19:50 < kanzure-> ? 19:51 < genehacker> v 19:51 < genehacker> http://arep.med.harvard.edu/pdf/Tian04.pdf 19:51 < genehacker> here's how they do it currently 19:52 < kanzure-> fenn: clisp -c isn't compiling for me :( 19:52 < genehacker> is there some sort of method to induce double stranded breaks in DNA 19:52 < genehacker> IE you have AAAAAATTTT 19:52 < genehacker> and you want just the AAAAAA part 19:53 < kanzure-> "clisp is a common lisp interpreter. It is easy to use, but does not compile to binary executables." <- oh. 19:53 < genehacker> well I have to go 19:53 < kanzure-> genehacker: surely you know about endonucleases 19:53 < genehacker> no 19:53 < kanzure-> it breaks apart DNA at a specific sequence 19:53 < genehacker> what do they do? 19:53 < kanzure-> it breaks apart DNA at a specific sequence 19:53 < genehacker> with sticky ends? 19:53 < genehacker> I don't want stickyends 19:53 < kanzure-> I think so. yes. 19:53 < kanzure-> what do you want? 19:54 < fenn> why not sticky ends? 19:54 < fenn> can't see how you'd build a decent length sequence otherwise 19:54 < fenn> but anyway you're only synthesizing a single strand 19:55 < genehacker> I want (DNA Sequence I want) seperated(sequence that bonds it to the chip) 19:55 < genehacker> well I gotta go search campus for where the heck my review session is 19:57 < fenn> so, speaking of which kanzure- will you be at the lab a while? 19:58 < kanzure-> no, I'm leaving at 4:15. 19:58 < kanzure-> hrm. I should zip up my modifications to adesign.. 19:58 < fenn> did you ever get it working in interactive mode? 19:59 < kanzure-> before that happens I have to get it to run a bit faster. in the non-interactive mode it's doing something but slowly- campbell says to try to compile it into a binary. 19:59 < kanzure-> my work is largely in bryantest.lisp and any file that has been modified in 2009 (or the last 5 years for that matter) 20:01 < kanzure-> http://adl.serveftp.org/papers/adesign-edited.zip 20:01 < fenn> maybe you should try to acquire a copy of franz lisp 20:01 < kanzure-> comments are sprinkled throughout the files now, somewhat explaining wtf is going on 20:02 < kanzure-> http://www.cs.berkeley.edu/~fateman/lisp-opus38.92.tar 20:02 < kanzure-> that? 20:03 < fenn> franz is a compiler/interpreter/ide 20:03 < fenn> and what campbell used iirc 20:04 < kanzure-> oh. allegro lisp is what he said. 20:04 < kanzure-> http://www.franz.com/downloads/ 20:04 < kanzure-> aha. I see. 20:07 < kanzure-> 43.1 MB .. hrm. 20:14 < kanzure-> jerks. they meant to name the file .tar.bz2 instead of just .bz2 20:41 < kanzure-> so "compiling" apparently means 'run it as if it was being interpreted' 20:50 < fenn> after compiling it does the same thing, but faster 20:50 < fenn> you can't compile all possible interpreted expressions 20:51 < kanzure-> it doesn't "compile" at all 20:51 < kanzure-> it's just running the interpreted code.. 20:51 < kanzure-> in other words, there's no binary being generated 20:51 < kanzure-> it literally just enters the loop and runs the code. 20:52 < fenn> are you trying to compile your modified version or the original? 20:52 < fenn> because i think we removed a bunch of compile directives 20:52 < kanzure-> should I be using the compile directives? 20:53 < kanzure-> I just made a new project and imported the files into it 21:08 < kanzure-> maybe I should just go dump the software on my quadcore 21:11 < kanzure-> ok, I'm gone. 21:13 * fenn wonders what kanzure- does without internet access 21:35 < genehacker> the reason I don't want sticky is because 21:35 < genehacker> I want a sequence that doesn't have the section that is cut in between 21:38 < genehacker> so the guy that claimed to be from the government was this guy 21:38 < genehacker> http://www.european-futurists.org/wEnglisch/aktuelles/2008_08_29_Interview_Nils_Gilman_meldung.php 21:38 < genehacker> Nils Gilman 21:40 < genehacker> posted in Diybio thread too 21:43 < xp_prg> https://noisebridge.net/wiki/Hello_World_in_Synthetic_Biology#Hello_World_DNA_Cell_Based 21:44 < genehacker> invalid security certificate 21:44 < genehacker> let me guess 21:45 < genehacker> it involves GFP 21:45 < xp_prg> yup :> 21:46 < genehacker> does it turn on GFP in response to something 21:46 < xp_prg> yes the binding protein to the promoter reigion of the gene that makes hello world 21:47 < genehacker> ok 21:48 < xp_prg> so do you like the comparison? 21:52 < genehacker> it's ok 21:54 < genehacker> oh ok it looks like in that paper they remove the junk sequence 21:54 < genehacker> or generic primer sequence 22:57 < fenn> re "I want a sequence that doesn't have the section that is cut in between" 22:57 < fenn> it doesn't matter if it's a restriction site or not because you are synthesizing the two complementary strands separately, so te sticky sequence can be watever you want