| --- Day changed Thu Apr 16 2009 | ||
| DrTread | my bed time. zzzz | 00:06 |
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| kanzure | DrTread sleeps early :) | 00:12 |
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| kanzure | ways to not feel stupid | 07:57 |
| kanzure | I think it's about time I wrote a bot to take papers referenced in this channel and automatically download them | 07:57 |
| kanzure | http://www.commandlinefu.com/commands/browse | 08:00 |
| kanzure | still like this :) | 08:00 |
| kanzure | wait, no I don't. these should be programs. not something I have to remember.. | 08:14 |
| kanzure | nsh: did you once say you have experience with infiltrating and deconstructing cults? | 08:40 |
| kanzure | nsh: if so, could you infiltrate the group calling itself the "neurohackers"? | 08:40 |
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| kanzure | cis-action: there has been a lot of awesome discussion on diybio recently. neat. | 12:37 |
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| kanzure | Hey anthonyl. | 12:46 |
| cis-action | kanzure: yeah, for instance the OWW handle discussion | 13:06 |
| kanzure | woah wtf is this crap | 13:07 |
| kanzure | "Anyone wanting to do wetwork in our space will have to provide evidence of training (such as a degree in bioscience) or undergo training by members who possess these skills. " | 13:07 |
| kanzure | http://diybionyc.blogspot.com/ | 13:07 |
| kanzure | this is getting out of hand | 13:07 |
| kanzure | at what point can we tell them that they are not "diybio" ? | 13:08 |
| kanzure | requirements about degrees are *not* amateur friendly at all | 13:09 |
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| kanzure | http://science.slashdot.org/article.pl?sid=09/04/16/141211 "Quantum theory may explain wishful thinking!" | 14:33 |
| kanzure | "In other news: a recent study by the American Wave Mechanics Society suggests wishful thinking may explain quantum mechanics." | 14:33 |
| UtopiahGHML | so "The Secret" is true after all... | 14:34 |
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| splicer_ | ... I had my money on Deepak Chopra | 15:41 |
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| fenn | two computer programmers named meredith in diybio.. this is going to be annoying | 16:35 |
| splicer | it'll be ok.. one is a polite nerd | 16:36 |
| splicer | (not misoginy btw.. it's was what patterson said on her homepage I think) | 16:40 |
| kanzure | fenn: two female programmers is never terrible. | 16:45 |
| kanzure | I think some of the people there are actually posting from the googlegroups.com website interface | 16:46 |
| kanzure | it's scary. | 16:46 |
| splicer | I know I am | 16:47 |
| kanzure | why? | 16:48 |
| splicer | as opposed to reading it as mails? | 16:48 |
| kanzure | huh? | 16:48 |
| fenn | i just mean the name conflict | 16:48 |
| fenn | like bryan on pythonOCC list | 16:48 |
| kanzure | heh namespace conflicts. | 16:49 |
| fenn | or nasa's orion rocket | 16:49 |
| kanzure | jelle was mean to me today | 16:49 |
| kanzure | from pythonocc. | 16:49 |
| splicer | i thought we were taling about the interface | 16:49 |
| kanzure | just something that I remembered to complain about | 16:49 |
| fenn | he wasn't trying to be mean | 16:50 |
| kanzure | true, but still. he keeps trying to show that I'm wrong or something .. when I'm not. | 16:52 |
| splicer | remember the time when you wrote that the way to survive biology gone terribly wrong was brainuploading... and I tried to convince you for 20min that that was what you actually wrote? | 16:55 |
| splicer | (kopimi is a brainchild of 'the piracy bureau' btw: http://en.wikipedia.org/wiki/Piratbyr%C3%A5n ) | 16:58 |
| kanzure | http://biobricks.org/pipermail/legal_biobricks.org/2008-September/000021.html | 17:08 |
| kanzure | what be this? hrm.. | 17:08 |
| kanzure | wtf.. | 17:11 |
| kanzure | http://heybryan.org/~bbishop/docs/gears/CADgears2/wtf.png | 17:12 |
| kanzure | what's up with pythonocc? | 17:12 |
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| kanzure | http://openwetware.org/wiki/DIYbio/FAQ#BioBricks_.28legal_stuff.29 | 17:31 |
| kanzure | the third video has janet hope | 17:32 |
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| kanzure | 'standards of conduct' | 17:36 |
| kanzure | 7:58 | 17:37 |
| kanzure | 24:34? and 23:20. eh. "hide the experience that you gain about your parts" | 17:41 |
| kanzure | blah | 17:41 |
| kanzure | blah, he talks about niche markets. "it's not valuable, so therefore it's ok to .. " stupid. informing open source legal stuff by economics? | 17:42 |
| kanzure | how is that a big database of parts? it's only 4000 elements | 17:45 |
| fenn | god what a clusterfuck | 17:52 |
| fenn | the construction of DNA sequences using base pairs that do not exist in nature might allow significant room for expressive choice. Such DNA sequences might be protected by copyright, at least against verbatim copying. However, most synthetic biologists working today, including those at MIT, are working within the confines of the existing genetic code. This code constrains the expressive choices that they make, making copyright protect | 17:52 |
| fenn | that probably cut off the end eh | 17:53 |
| fenn | so, arbitrary chemistry is subject to copyright but DNA code is not, because you're constrained to using the alphabet?? | 17:53 |
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| fenn | bleh. i hope bbf finishes their clickwrap thingy some time soon so we can all stop arguing about this | 18:07 |
| kanzure | clickwrap? | 18:07 |
| kanzure | so apparently you're not constrained to using the alphabet of chemistry (elements) | 18:08 |
| kanzure | or something? | 18:08 |
| splicer | ( i didn't understand it either) | 18:08 |
| fenn | clickwrap = electronic legal contract enforcing the equivalent of copyleft; it can apply to hardware or whatnot that isn't covered by copyright, with the downside that everyone has to sign a contract (well, clicking a checkbox) | 18:09 |
| fenn | and i'm not clear about what happens in the case of 'stolen' information | 18:10 |
| fenn | i.e. "i received this info without any legal agreement, so there!" | 18:10 |
| splicer | i guess what they're saying is that if it exists in nature it's 'prior art'... if it doesn't then it's copyrightable? | 18:10 |
| fenn | splicer no, it's nothing like that | 18:10 |
| kanzure | I'm afraid I've become the Paul Fernhout of DIYbio | 18:10 |
| kanzure | what do I do :( | 18:10 |
| fenn | haha | 18:10 |
| fenn | add a 30 minute timer to every message that makes you look at what you wrote | 18:11 |
| kanzure | I hardly spend 30 minutes on a message .. | 18:11 |
| * kanzure flexes his finger muscles | 18:11 | |
| fenn | see http://bikeshed.com/ | 18:11 |
| * splicer nods enthusiastically | 18:11 | |
| fenn | kanzure: yes, it's apparent | 18:11 |
| kanzure | fenn: I still don't understand that | 18:12 |
| fenn | with a list like diybio though.. i mean, the signal to noise ratio is all over the place | 18:12 |
| kanzure | the bikeshed site I mean | 18:12 |
| kanzure | it's weird | 18:12 |
| fenn | scroll down to the warning boxes | 18:12 |
| kanzure | sometimes it's like the biologists want to stop stuff from happening | 18:12 |
| kanzure | then jonathan cline insults the biologists (wtf?) | 18:12 |
| kanzure | and then weird stuff happens | 18:12 |
| fenn | weird stuff? | 18:12 |
| fenn | he wasn't insulting anyone.. it was a joke | 18:13 |
| fenn | have you ever noticed that biologists all use macintosh? | 18:13 |
| fenn | (for the record, cline uses a mac too) | 18:13 |
| kanzure | really? they do? | 18:13 |
| fenn | um, the ones i've seen | 18:14 |
| fenn | i dont know anyone that works at big evil corporations though | 18:14 |
| splicer | aren't most of them asian women btw? | 18:15 |
| fenn | biologists? | 18:15 |
| splicer | yeah, it's like asian boys go into computer science.. and the girls into biology | 18:15 |
| fenn | relatively speaking, yes | 18:15 |
| fenn | but not on an absolute scale | 18:15 |
| kanzure | cis-action: did you get the gene engineering protocols thread into the FAQ? | 18:16 |
| cis-action | no not yet | 18:16 |
| kanzure | I'll do it. | 18:16 |
| kanzure | was just not wanting to duplicate work | 18:16 |
| cis-action | maybe we should actually start talking in the diybio room? | 18:16 |
| kanzure | why? we're all in here. | 18:16 |
| cis-action | right; no, no need to worry about that | 18:16 |
| cis-action | ha ha true | 18:16 |
| cis-action | well, some people are in the diybio room. lurkers. | 18:17 |
| splicer | invite them | 18:17 |
| kanzure | I once looked at #diybio and everyone there was already in here or something | 18:17 |
| kanzure | it was sad | 18:17 |
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| fenn | you know it would be great if it were possible to go back and change the subject line of an email thread | 18:18 |
| fenn | or at least annotate it | 18:18 |
| kanzure | so, in the google groups interface, that's how it works when your reply changes the subject line | 18:18 |
| kanzure | it displays in the thread list as the changed subject line | 18:18 |
| kanzure | even though initially it was something different | 18:18 |
| fenn | yes but in practice nobody ever changes the subject line | 18:19 |
| kanzure | right. | 18:19 |
| kanzure | oh, I see | 18:19 |
| kanzure | well good luck getting mail servers to accept that standard | 18:19 |
| fenn | wait you mean you can go back and change the subject line of a posted message? | 18:19 |
| kanzure | submit a patch to one of them :p | 18:19 |
| kanzure | no | 18:19 |
| kanzure | so look here: | 18:19 |
| kanzure | http://groups.google.com/group/diybio/topics | 18:19 |
| kanzure | if you replied to one of those threads and changed the subject, and went back to that link, | 18:20 |
| kanzure | that new subject would be displayed | 18:20 |
| kanzure | instead of the original | 18:20 |
| kanzure | it's weird functionality on behalf of Google.. | 18:20 |
| splicer | it's something a moderator can usually do... not sure google groups have moderators, maybe they just have group owners. | 18:23 |
| splicer | (the feature seems to work well though) | 18:24 |
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| kanzure | cis-action: ok, I added it | 18:27 |
| kanzure | http://openwetware.org/wiki/DIYbio/FAQ#Genetic_engineering | 18:27 |
| cis-action | good enough | 18:31 |
| cis-action | back later | 18:31 |
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| -!- help is now known as cis-action_ | 18:31 | |
| cis-action_ | is the underscore suffix an indication that I'm away? | 18:32 |
| fenn | no | 18:34 |
| fenn | it's what your irc client does if the nick you want is already taken | 18:34 |
| splicer | I noticed an anomaly with the nicks today. It seems if I'm logged in on two servers with my client one server gets the primary nick and the other gets the secondary. | 18:45 |
| -!- kanzure- [n=bryan@66.112.232.230] has joined #hplusroadmap | 18:47 | |
| splicer | ...and I can't change my nick to the primary one on the first server cause 'that nick is in use'. | 18:47 |
| fenn | what client? | 18:47 |
| splicer | xchat-gnome... It's sort of true too ... it's in use by me... on another server | 18:48 |
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| kanzure | ooh | 19:27 |
| kanzure | genehacker: reverse DNA translocation. | 19:27 |
| kanzure | remember nanopore sequencing? recently there was a paper complaining about how to draw a DNA strand through the pore | 19:27 |
| genehacker | define translocation | 19:27 |
| kanzure | or something- it was actually complaining about how dropping nucleotides won't really work | 19:27 |
| genehacker | teleportation? | 19:27 |
| kanzure | anyway, one method is to pull the strand through | 19:27 |
| kanzure | no | 19:27 |
| kanzure | http://heybryan.org/books/papers/Reverse%20DNA%20translocation%20through%20a%20solid-state%20nanopore%20by%20magnetic%20tweezers.pdf | 19:27 |
| kanzure | attach the DNA to a magnetic bead | 19:27 |
| kanzure | with strepavidin | 19:27 |
| kanzure | or biotin | 19:28 |
| kanzure | and then use electrophoresis to get the DNA straightened out, or whatever | 19:28 |
| kanzure | then use a magnet to move the bead closer to the magnet | 19:28 |
| kanzure | at some slow rate | 19:28 |
| kanzure | slow enough to detect the current that passes through whatever nucleotide is in the pore | 19:28 |
| fenn | i think you'd have to thread the strand through the pore first, then attach the bead | 19:28 |
| kanzure | right | 19:29 |
| fenn | or forget about the bead entirely and just pull the strand through with some kind of gradient | 19:29 |
| fenn | department of physics eh | 19:30 |
| genehacker | hmmm... | 19:30 |
| fenn | "nanotechnology" | 19:30 |
| genehacker | http://www.youtube.com/watch?v=PSuvFCPgwE8 | 19:31 |
| genehacker | check this out | 19:31 |
| genehacker | also my sound isn't working? | 19:32 |
| fenn | i think it'll be funny if nanotech ends up using DNA | 19:33 |
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| kanzure | fenn: winfree. | 19:33 |
| * kanzure waits for laughter | 19:33 | |
| fenn | i mean as information storage medium | 19:33 |
| fenn | gene wat was the point of that video | 19:34 |
| genehacker | it's a robot assembling a camera | 19:35 |
| fenn | so? | 19:36 |
| genehacker | it looks like it's getting visual feedback | 19:36 |
| fenn | i'm all for robot porn but that just wasn't very impressive | 19:37 |
| genehacker | so me something impressive then | 19:37 |
| fenn | festo air manta ray was cool http://www.youtube.com/watch?v=UxPzodKQays | 19:38 |
| fenn | there's a water version too http://www.youtube.com/watch?v=Nzd9KA8heXE | 19:38 |
| genehacker | I've seen that | 19:39 |
| genehacker | http://www.youtube.com/watch?v=VxiGp4R4Dsc | 19:41 |
| kanzure | http://en.wikipedia.org/wiki/Vores_Øl | 19:41 |
| kanzure | blah. | 19:41 |
| genehacker | it's ionically driven | 19:42 |
| kanzure | http://freebeer.org/ | 19:42 |
| kanzure | http://en.wikipedia.org/wiki/OpenCola | 19:42 |
| kanzure | recipes are not copyrightable? | 19:42 |
| genehacker | http://www.youtube.com/watch?v=YL6yB8-dgsI check this out too | 19:43 |
| genehacker | http://www-robotics.jpl.nasa.gov/systems/system.cfm?System=5 | 19:44 |
| fenn | airfish kind of reminds me of 'flight of the navigator" but really slow and boring | 19:44 |
| kanzure | http://www.copyright.gov/fls/fl122.html re: copyright about recipes | 19:44 |
| kanzure | I fear I'm morphing into RMS | 19:45 |
| kanzure | what do I do? | 19:45 |
| kanzure | "roar you can't call this open source" | 19:45 |
| fenn | wow lemur kinda sucks | 19:46 |
| kanzure | lemur is a monkey? | 19:46 |
| genehacker | a robot | 19:46 |
| fenn | it's slow, jerky, and poor positioning | 19:46 |
| genehacker | it's doing it autonomously | 19:46 |
| kanzure | odd. "freebeer.org" says it's CC-licensed | 19:46 |
| fenn | well, ok, that makes up for some of it | 19:47 |
| kanzure | I don't think CC is equivalent to "open source" | 19:47 |
| kanzure | I mean, people are getting all of these words mixed up | 19:47 |
| genehacker | http://www.youtube.com/watch?v=oAnB9mmCZE4 | 19:47 |
| kanzure | and just trying to be funny social-actvists | 19:47 |
| kanzure | when in truth they are just bullshit artists | 19:47 |
| genehacker | anyway, it has a fuckton of degrees of freedom | 19:47 |
| genehacker | it's legs are it's arms | 19:47 |
| genehacker | it has tools on it's legs | 19:48 |
| fenn | reminds me of one of those skull-eating slugs from the new king kong movie | 19:49 |
| genehacker | http://www-robotics.jpl.nasa.gov/systems/systemImage.cfm?System=5&Image=96 | 19:50 |
| genehacker | I wish I could find where they documented these thigns | 19:51 |
| fenn | ok so that bead+nanopore setup looks like it would actually work | 19:52 |
| genehacker | could we build one though? | 19:52 |
| fenn | does it have to be a hole or just a slit? because you could just etch a slit by etching two triangles on a piece of silicon | 19:53 |
| fenn | the triangles would be touching at the corner, and then slow dissolve away until they don't conduct anymore | 19:53 |
| fenn | i spose a piece of metal foil would work too | 19:54 |
| genehacker | hmmm | 19:54 |
| fenn | score foil, electroplate away | 19:54 |
| fenn | hard to get it even across the length though | 19:54 |
| fenn | down to a zillimeter | 19:55 |
| kanzure- | fenn: I think I actually have some papers on this | 19:55 |
| kanzure- | because I was spazzing out on nanopores a while back | 19:55 |
| kanzure- | http://heybryan.org/books/papers/Cheap%20third-generation%20sequencing%20-%20nanopores%20-%20cyclodextrin%20-%20hemolysin%20-%202009.pdf | 19:56 |
| kanzure- | http://heybryan.org/books/Biology/Nanopore%20Unzipping%20of%20Individual%20DNA%20Hairpin%20Molecules%20-%202004.pdf | 19:56 |
| kanzure- | http://heybryan.org/books/Biology/Sequence-specific%20detection%20of%20individual%20DNA%20strands%20using%20engineered%20nanopores%20-%20Howorka%20-%202001.pdf | 19:56 |
| kanzure- | http://heybryan.org/books/Biology/The%20potential%20and%20challenges%20of%20nanopore%20sequencing%20-%20Schloss.pdf | 19:56 |
| kanzure- | I also have some notes on the wiki:http://heybryan.org/mediawiki/index.php/DNA_sequencing#Nanopores | 19:57 |
| kanzure- | including a youtube video | 19:57 |
| kanzure- | cyclodextrin + alpha-hemolysin nanopore. but this is for "dropping" nucleotides through- don't know if this same type of (biological) nanopore works for running the strand through it | 19:58 |
| fenn | genehacker: also i spose you could do something with radiation or particle accelerators, to punch holes in the foil | 19:58 |
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| fenn | i think the hemolysin pore would work, its just more finicky because it's held together with duct tape, like all biological parts | 19:59 |
| fenn | "scanning tunneling microscopy technique which relies on quantum tunneling of electrons that pass through the nucleotide within the nanopore" is what i keep thinking about | 20:00 |
| kanzure- | there's also some people who have done it with AFMs | 20:00 |
| kanzure- | (instead of STMs) | 20:00 |
| fenn | how many base pairs? | 20:00 |
| kanzure- | blah. /me looks it up | 20:01 |
| fenn | i'm not talking about just scanning the dna with a STM microscope | 20:01 |
| kanzure- | wow I have no paper | 20:01 |
| fenn | i mean 'feeling' the dna go by, by measuring conductance between the two sides of the slit | 20:01 |
| kanzure- | Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps http://heybryan.org/books/Biology/Rapid%20Sequencing%20of%20Individual%20DNA%20Molecules%20in%20Graphene%20Nanogaps%20-%202008.pdf | 20:02 |
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| kanzure- | fenn: oh, I thought that's what they usually do with these nanopore methods? | 20:02 |
| kanzure- | by measuring conductance or current flow through the pore when 'clogged' | 20:02 |
| fenn | no, they measure the amount of ions flowing through the pore | 20:02 |
| fenn | i'm talking about measuring current between two electrodes | 20:02 |
| genehacker | ugh | 20:02 |
| kanzure- | they do that though .. | 20:02 |
| kanzure- | I could have sworn. | 20:02 |
| fenn | no they dont | 20:02 |
| fenn | one goes up/down, the other goes left/right | 20:02 |
| kanzure- | what goes up/down etc.? | 20:03 |
| fenn | well, assuming your pore is pointed up/down, the ion flow through the pore would be up/down | 20:03 |
| kanzure- | blah, there's a paper. I know they've done this. (and the STM paper too) | 20:06 |
| fenn | http://imagebin.org/45831 | 20:06 |
| kanzure- | right | 20:08 |
| kanzure- | if I find the paper, will I get a cookie? | 20:09 |
| kanzure- | 1991: Can STM sequence DNA? http://www.ncbi.nlm.nih.gov/pubmed/2043383 | 20:09 |
| kanzure- | way too old.. | 20:09 |
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| kanzure- | Direct Electronic Identification of Oligonucleotides with Inelastic Electron Tunneling Spectroscopy | 20:16 |
| kanzure- | http://www.cpac.washington.edu/Activities/satellite_meetings/Rome%202007/CPAC%20Rome%202007%20presentations/Wednesday/John%20Lund%20-%20Identification%20of%20Oligonucleotides.ppt | 20:16 |
| fenn | the graphene paper is almost exactly what i was thinking | 20:17 |
| kanzure- | neat: "Images of the DNA double helix in water" | 20:18 |
| kanzure- | 1990: Atomic-scale imaging of DNA using scanning tunnelling microscopy | 20:21 |
| kanzure- | well this is disappointing. I thought there were more papers on STM/AFM DNA sequencing. | 20:29 |
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| * fenn thinks about how to make a machine to quantify avocado hardness | 20:48 | |
| kanzure- | avocado hardness? | 20:49 |
| fenn | oho | 20:49 |
| kanzure- | oh, the vegetable? | 20:49 |
| fenn | gene get this for me when you find access to the journal http://www.actahort.org/members/showpdf?booknrarnr=517_52 | 20:50 |
| kanzure- | I don't have access | 20:50 |
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| kanzure- | 5-mC is a natural DNA base? | 21:03 |
| kanzure- | paper: http://heybryan.org/books/papers/The%20nuclear%20DNA%20base%205-hydroxymethylcytosine%20is%20present%20in%20purkinje%20neurons%20and%20the%20brain.pdf | 21:04 |
| fenn | methylization | 21:04 |
| fenn | er, methylation | 21:04 |
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| kanzure- | oh. I guess I still have yet to think about some timeline of skdb work if I am to be paid for it | 21:20 |
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| kanzure | hm, articles of incorporation for diybio-nyc | 22:24 |
| kanzure | yay, sudo !! works. | 22:26 |
| splicer | apparently they are planning for iGEM too | 22:50 |
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| kanzure- | even though igem said no. | 22:59 |
| kanzure- | hrm. | 22:59 |
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| splicer | maybe the team is made up of students | 23:07 |
| splicer | (...and they found a supervisor somewhere) | 23:08 |
| kanzure- | fenn: did you find the OCC 5.2 docs in some linux-friendly format? or was it only the CHM stuff | 23:14 |
| fenn | there's a .chm and a .HLP and some .pdf's | 23:26 |
| fenn | the .HLP is by far the largest file, at about 90MB (but somehow all this compresses to 11MB) | 23:26 |
| fenn | i'm not sure what to do with it, it uses "RoboHelp" functions from RoboEx32.dll | 23:28 |
| fenn | (which is included) | 23:28 |
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