--- Day changed Sat Jun 07 2008
00:04 < kanzure> fenn_: re: getting DNA out of neurons, see DNA single-stranded binding protein (SSB)
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01:01 < parodyoflanguage> !help
01:03 < kanzure> Hey parodyoflanguage.
01:15 < kanzure> fenn_: What about writing a hacky DNA strand out of rNTPs and dNTPs and others, then using repair mechanisms to correlate each of those *types* back to the original four ddNTPs ?
02:53 < ybit> http://www.youtube.com/watch?v=ihVaL-FHUyk
02:58 < ybit> and this one if you need something watch while chowing www.youtube.com/watch?v=V026kSw4XCs
03:21 < ybit> and this is quite interesting as well: http://www.youtube.com/watch?v=sudmW97FZA0&feature=related
04:41 < ybit> perhaps i should sleep :P
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06:33 -!- Topic for #hplusroadmap: http://heybryan.org/ http://heybryan.org/mediawiki/ http://heybryan.org/exp.html | krebs is now servicing the channel. try !help
06:33 -!- Topic set by kanzure [] [Tue Apr 29 18:54:31 2008]
06:33 [Users #hplusroadmap]
06:33 [ faceface] [ fenn_  ] [ nsh             ] [ Phreedom] [ Splicer ] [ wrldpc] 
06:33 [ fenn    ] [ kanzure] [ parodyoflanguage] [ shogunx ] [ Vedestin] [ ybit  ] 
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06:33 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
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11:56 < kanzure> Hi all.
11:56 < kanzure> Hrm. We actually /lost/ people.
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11:56 < kanzure> Hey.
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11:56 < kanzure> Fine, be that way.
11:58 -!- kanzure changed the topic of #hplusroadmap to: http://diybio.org/ http://openwetware.org/ | diy bio toolkit: http://biohack.sf.net/ | Automated societal knowledge (put it to work): http://heybryan.org/exp.html | Channel blog: http://heybryan.org/mediawiki/
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12:00 < kanzure> Hey cis-action. 
12:00 < cis-action> finally got my nick changed.
12:00 < cis-action> hey bryan
12:02 < kanzure> So, the email is a success. :) At least one person.
12:02 < kanzure> I was surprised that the biobarcamp group was going ahead with book planning without wider community proliferation.
12:02 < kanzure> There's literally tons of content out there that we can do better re: organizing it.
12:03 < kanzure> So I sent out the email. :)
12:03 < cis-action> I'm surprised you didn't propose an ebook.  I don't agree that a bunch of content on a mediawiki server, or a bunch or mediawiki servers, is sufficient
12:04 < kanzure> Right.
12:04 < kanzure> an ebook would be fine, IMHO
12:04 < kanzure> What do you consider to be an ebook? PDF?
12:04 < cis-action> the whole value in an instructional book is in presenting the otherwise-torrential amount of information in a manageable and efficient manner
12:04 < kanzure> :) And links to more information.
12:04 < cis-action> I don't know what I consider an ebook
12:05 < cis-action> I don't think anyone is doing a good job solving that
12:05 < kanzure> well, let me get a bit less 'in the moment' -- what I really, really want one day
12:05 < kanzure> is to be able to download information packages
12:05 < kanzure> like apt-get install <biotech kit>
12:05 < kanzure> so, a wiki does that (sort of) because it has a database, but as you point out there are obvious limitations
12:06 < kanzure> I'm thinking of setting up a git repository with the biotech information I assembled at http://biohack.sf.net/ 
12:06 < cis-action> I think the main aspect of bookness are the careful sectioning and modularizing of the information into chapters and the intense amount of editing and fact-checking that (theoretically) goes into the book
12:06 < kanzure> sure, but I think that we can also have a backend community to generate content too
12:06 < kanzure> and then somebody can select parts of it and feed it to O'Rielly or whatever
12:06 < cis-action> yeah but bryan, that's exactly my point, there's almost more work in organizing and relating all the package and subcomponents to one another in a meaningful way than in actually building them individually
12:07 < cis-action> (concretely speaking, I think drupal has an interesting book module)
12:07 < kanzure> heh' that's why I keep linking over to my biohacking toolkit -- that's where I did tons of working on the individual building of the components, and threw all of the information together
12:07 < cis-action> *threw* is the operating verb there
12:07 < kanzure> yeah :)
12:07 < cis-action> it can't just be thrown together
12:07 < kanzure> so we can do better
12:07 < cis-action> that's not what a book is.  yeah.
12:08 < cis-action> Show me a good crowdsourced book
12:08 < kanzure> I think a git repository is a good idea in this case, actually
12:08 < kanzure> we can have multiple branches for the chapters / topics
12:08 < kanzure> and then the root branch would be the entire book
12:08 < kanzure> let me go set that up
12:08 < cis-action> what's the interface?
12:08 < cis-action> wait wait
12:08 < kanzure> there are many interfaces
12:08 < kanzure> lemme get a screenshot
12:08 < kanzure> there are web interfaces, shell interfaces, wiki interfaces, so many :)
12:08 < kanzure> it's decentralized too
12:08 < cis-action> most people have no idea what git is, much less than what the best practice is for adding text to it
12:09 < kanzure> best practice is to just write
12:09 < kanzure> then you save the file
12:09 < kanzure> then you have a program that 'commits' it
12:09 < kanzure> you tell somebody about your changes, and then they can "pull" the changes into their own working copy
12:09 < kanzure> 'working' as in, draft :)
12:09 < kanzure> main GIT website: http://git.or.cz/
12:10 < kanzure> 'Git is an open source version control system designed to handle very large projects with speed and efficiency, but just as well suited for small personal repositories; it is especially popular in the open source community, serving as a development platform for projects like the Linux Kernel, WINE or X.org.'
12:10 < kanzure> 'Every Git working directory is a full-fledged repository with complete history and full revision tracking capabilities, not dependent on network access or a central server. Still, Git stays extremely fast and space efficient.'
12:10 < cis-action> ok, you put together the first collection of 10 diybio protocols, or stubs at least, and a screencast on how to contribute to them, and I'll work on them and evangelize the idea
12:11 < kanzure> alright
12:11 < kanzure> hrm
12:11 < kanzure> yeah, give me a few minutes, this shouldn't take more than 10
12:11 < kanzure> although the screencast might take longer.
12:11  * kanzure wonders where his microphone went :)
12:11 < cis-action> no more than like 5 minutes for the screencast
12:11 < kanzure> Slides on what git is all about: http://www.slideshare.net/anildigital/git-introduction/
12:11 < kanzure> yeah, bandwidth and so on
12:11 < kanzure> it's pretty quick anyway
12:12 < kanzure> it's not meant to be a bottleneck
12:14 < cis-action> ok, I'm professor john q. coral, expert in fluorescent proteins, and I want to add a little bit from a recent study guide I wrote about how to do mutagenesis on a particular jellyfish fluorescent protein, using my vista box that the school gave me.  Thank god bryan bishop demonstrated how this new-fangled git works with his handy 4 minute screencast!
12:15 < kanzure> yep :)
12:16 < kanzure> basically that prof will dump his research into the git repo
12:16 < kanzure> by just copying + pasting the file
12:16 < cis-action> p.s. if this works and we actually end up with a community of contributors we coould consider writing it or building a web interface for http://elseviergrandchallenge.com/
12:16 < kanzure> and then it gets diffused automatically to the community
12:16 < kanzure> cis-action: I haven't seen that one before. What's it about?
12:16 < cis-action> are your legs broken?
12:17 < kanzure> hold on
12:17 < kanzure> okay, yeah I see it
12:17 < cis-action> it's elsevier's dubious science 2.0 / publishing 2.0 / collaboration 2.0 "grand challenge"
12:17 < kanzure> crap, I need to submit an abstract
12:17 < kanzure> see here: http://heybryan.org/exp.html
12:17 < kanzure> it's a bit of a broader plan, but it's not well written quite yet
12:18 < kanzure> fenn: git doesn't require ssh natively, does it?
12:19 < cis-action> caution: one of elsevier's 4 judging criteria is pragmatism
12:19 < cis-action> "The project’s potential for realization in practice: The project's potential benefits for the publishing industry as a whole, in terms of user needs fulfilled and advantages proposed, will be evaluated in terms of the possibility and ease of implementing the project within a publishing workflow."
12:20 < kanzure> hehe :)
12:20 < kanzure> it's a semantic web deal
12:20 < kanzure> wherein published papers become more 'functional' by attaching their models and BibTeX and so on
12:21 < kanzure> however, the hard part is that most people don't know about git or ikiwiki and so on
12:21 < kanzure> the tools are already out there and are well known in the progrmamer communities
12:22 < kanzure> *programmer
12:29 < fenn> ugh fuck elsevier
12:30 < kanzure> :)
12:32 < cis-action> ha
12:33 < kanzure> I think they want to implement the project themselves
12:33 < kanzure> however, there's a few communities out on the net that would not want that at all
12:33 < kanzure> open standards development, all that stuff
12:34 < fenn> one of elsevier's unstated judging criteria is "will this fuck everyone else over and make elsevier a lot of money?"
12:34 < kanzure> the answer is always 'yes'
12:34 < fenn> since that's their business model
12:36 < fenn> git 'recommends' ssh and curl, but its not a dependency
12:36 < fenn> but without them you're stuck on the same machine, and that's sorta silly
12:37 < kanzure> hrm
12:37 < kanzure> how does it use ssh anyway
12:37 < kanzure> do I need to create a new user for people to pull from heybryan.org ?
12:39 < fenn> oh, i forgot about the git protocol
12:39 < kanzure> ?
12:39 < fenn> git://
12:40 < fenn> i dont know much about it really
12:40 < kanzure> so it has its own port and everything
12:40 < kanzure> hrm
12:41 < fenn> i think http is the most convenient/least problematic
12:41 < fenn> you just compiled it without http support
12:41 < kanzure> I did?
12:41 < fenn> yep
12:41 < fenn> didnt get curl-dev or whatever
12:43  * kanzure is creating the git repo at the moment
12:43 < kanzure> it's loading up a few hundred megabytes of raw content. good thing we can download only subsets and so on :)
13:08 < kanzure> cis-action: Ok. 'Pushing' at the moment. This means that the content is being uploaded to my server. Then others will be able to "pull" it very easily. 
13:09 < cis-action> ok...
13:09 < cis-action> but no one will use it without someone like you making it uber-easy to figure out
13:09 < kanzure> right right
13:09 < kanzure> I'm working on the screencast too
13:09 < kanzure> can it just be an mpeg?
13:10 < kanzure> I don't know what youtube/dnatube/etc. wants
13:13 < fenn> did you dump the diybio stuff into it?
13:13 < kanzure> yep
13:13 < kanzure> pushing at the moment
13:14 < kanzure> "Compressing objects: 0% (23/10839)"
13:14 < kanzure> oh boy
13:14 < cis-action> h264 is the current web standard
13:14 < cis-action> or flv
13:14 < fenn> flv is just a container format anyway
13:14 < cis-action> oh really?
13:14 < cis-action> oh
13:16 < fenn> kanzure: do you know what a "mess" is?
13:17 < kanzure> fenn: the kit? :)
13:17 < kanzure> the idea is to improve it 
13:17 < kanzure> a few biotechers want to make a book
13:17 < kanzure> so I'm finally throwing up the content into something better
13:17 < fenn> i'm just wondering why you're dumping the whole thing into a git repo
13:17 < kanzure> because people want to make changes and so on?
13:19 < kanzure> writing objects :)
13:20 < fenn> ah that was pretty quick
13:20 < kanzure> 2 MB/sec. Awesome. 
13:21 < fenn> if you 'check out' a partial repo and make changes and then push back, does it actually work?
13:21 < kanzure> still uploading
13:21 < kanzure> hrm, it must be percentages based off of the number of objects, not their relative size
13:22 < kanzure> yep, 10 seconds ago it was 3%, it just shot up to 99%.
13:23 < fenn> most source code is tiny files
13:23 < kanzure> when I get more hdd space, maybe I'll do a public service and put Wikipedia into a git repo :)
13:24 < kanzure> alright, neat
13:24 < kanzure> http://heybryan.org/biotech.git
13:24 < fenn> i kinda like the fact that there's only one wikipedia
13:25 < kanzure> there's not, think of all the spam content wholes
13:25 < kanzure> that downloaded Wikipedia and threw up adds
13:25 < fenn> maybe you could have a 'metapedia' which layers all the MPOV from around the net 
13:26 < fenn> so everyone gets their say
13:26 < kanzure> an internetpedia?
13:26 < kanzure> netpedia
13:26 < fenn> i'm thinking like metacrawler
13:26 < fenn> a wiki aggregator
13:26 < kanzure> I've definitely wanted a place where I can point out weird trends on the internet
13:26 < fenn> aggropedia :P
13:26 < kanzure> re: wiki aggregator, see Wiki index
13:26 < kanzure> http://heybryan.org/mediawiki/index.php/Wiki_index
13:26 < kanzure> http://heybryan.org/mediawiki/index.php/Wikis_index
13:26 < kanzure> I dunno which one it is.
13:27 < fenn> that's just a list of wikis
13:27 < kanzure> what more?
13:27 < kanzure> oh, right
13:27 < kanzure> not just a list
13:27 < fenn> i'm talking about, one article with different perspectives on the subject from around the internet
13:27 < kanzure> with citations back to the people that are arguing that perspective?
13:28 < kanzure> how would you make sure that they don't say "well, he's not a part of our community, so we don't want him editing this article" BS?
13:28 < fenn> yes, i think.. citation has the wrong connotation
13:28 < fenn> just to solve the whole edit war thing
13:28 < fenn> if you dont like foopedia, fork it and make barpedia
13:28 < fenn> then do a diff to see what barpedia thinks differently
13:28 < kanzure> how would we make sure that we select good admins though
13:28 < kanzure> do we need admins for that?
13:29 < fenn> no, that's the point
13:29 < fenn> the problem with iwwikipedia is the admins
13:29 < kanzure> but what about banning troublemakers?
13:29 < kanzure> oh, 
13:29 < kanzure> right, just fork it
13:29 < fenn> or the self-proclaimed admins or whatever they call themselves
13:29 < kanzure> and then we'll import content that we like
13:29 < kanzure> (pull)
13:29 < fenn> yes, there's too much focus on banning misbehavior rather than searching for good content
13:30 < fenn> if you vandalize your own wiki, nobody gives a shit
13:30 < fenn> if someone publicizes you by saying 'hey this is good stuff' then you tend to work harder to making good content
13:32 < fenn> do you have any clues on the incantation to import part of a git repo?
13:32 < fenn> btw you should install gitweb because i cant even tell what's in biohack.git
13:33 < kanzure> I already have it installed
13:33 < cis-action> kanzure: are you still going to make a prospectus screencast?
13:33 < kanzure> cis-action: yeah, I have my mic working and am now installing a screencasting package
13:33 < kanzure> it'll take a few more minutes, also I want to install gitweb like fenn suggests
13:33 < cis-action> cool
13:33 < kanzure> so that I can show a web output
13:35 < kanzure> fenn: http://heybryan.org/gitweb.cgi
13:35 < kanzure> what do you think is going wrong?
13:35 < kanzure> it only shows skdb
13:36 < fenn> i think gitweb has to be in the same folder as biohack.git
13:36 < fenn> or maybe a ln -s
13:37 < kanzure> something about /etc/gitweb.conf or rather
13:37 < kanzure> fenn: it doesn't actually have a local git repository
13:37 < kanzure> I mean, it has the server one
13:37 < kanzure> but it doesn't have a local copy for editing
13:38 < kanzure> does this make a difference?
13:38 < fenn> no
13:38 < fenn> bare repo should work
13:38 < fenn> maybe you need to do 'git-update-server-info'
13:38 < kanzure> aha 
13:38 < kanzure> http://heybryan.org/gitweb.cgi
13:39 < fenn> where'd skdb.git go?
13:39 < kanzure> http://heybryan.org/gitweb.cgi?p=biotech.git;a=tree;h=0532022269e7dce28521ca9a8ac026a6d34f9f9f;hb=0532022269e7dce28521ca9a8ac026a6d34f9f9f
13:39 < kanzure> bleh, different places
13:39 < kanzure> one is in /home/bbishop/.git/skdb.git/
13:39 < kanzure> the new one is apparently /var/git/biotech.git/
13:40 < fenn> that looks a lot smaller than the .zip from biohack.sf.net
13:40 < kanzure> it's five times as large
13:40 < kanzure> at least.
13:41 < kanzure> http://heybryan.org/gitweb.cgi?p=biotech.git;a=tree;f=biotech-DIY__kanzure_2008-01-27_v1;h=ac233783b97167746ca96a34f49260b71f95453c;hb=0532022269e7dce28521ca9a8ac026a6d34f9f9f
13:42 < fenn> ok i just didnt notice the subdirectories
13:42 < fenn> before it was all just a big pile
13:43 < fenn> does sf do git hosting?
13:43 < kanzure> I think it's safe to say that it still is
13:43 < kanzure> no
13:43 < kanzure> sf does everything with cvs and their own way (centralization)
13:43 < fenn> wtf :(
13:44 < kanzure> it's why I moved the wiki; their mysql db was so huge and sucky
13:44 < kanzure> they wanted me to host the wiki on *their* wikifarm
13:44 < kanzure> but it has ads and nasty templating etc.
13:44 < kanzure> with no db dump
13:44 < fenn> no db dump!!
13:45 < fenn> there should be some 'sensible wiki features' that all wikis should have in order to be socially acceptable
13:45 < kanzure> fenn: re: dumps, http://heybryan.org/gitweb.cgi?p=biotech.git;a=tree;f=biotech-DIY__kanzure_2008-01-27_v1/oww;h=bf0e70e094c26f67a6b3c2941ef81588de917ff6;hb=0532022269e7dce28521ca9a8ac026a6d34f9f9f
13:45 < kanzure> no kidding :(
13:45 < fenn> 100% organic wiki
13:46 < kanzure> the real organic wiki /should/ be ikiwiki
13:46 < fenn> ikiwiki sucks
13:46 < kanzure> fenn: so if I was to do a screencast on git usage, I'm figuring I'll show two ways
13:46 < kanzure> (1) shell (git it done in a few seconds)
13:46 < kanzure> (2) some gui or web interface or something
13:47 < kanzure> right, ikiwiki sucks is the problem
13:47 < kanzure> so if I do it via the shell, I'll just need to do "git clone http://heybryan.org/biotech.git"
13:47 < kanzure> right?
13:47 < fenn> if you want to clone th whole thing
13:48 < kanzure> and partial clones?
13:48 < fenn> might as well start out with the full clone, since its easier and makes more sense
13:48 < kanzure> right
13:48 < fenn> i dont knowh owt od o partialc loney et
13:49 < fenn> btw make sure you add gitweb to robots.txt
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13:50 < kanzure> Hey Phreedom.
13:50 < kanzure> The #git people don't know how to do partial clones. 
13:50 < fenn> so.. make sure people feel comfortable about deleting large swaths of irrelevant junk
13:50 < kanzure> right
13:50  * kanzure is playing with 'istanbul'
13:50 < Phreedom> h1
13:51 < fenn> good luck
13:51 < kanzure> btw, I'll upload the video and have one of you do a bullshit detector on it
13:51 < kanzure> shouldn't take too long
13:51 < kanzure> *detection test
13:52 < fenn> btw maybe you should show how to install git :\
13:52 < kanzure> heh, 'how to make a linux screencast' first result is a linux screencast on how to make screencasts
13:52 < kanzure> apt-get install git-core ?
13:52 < fenn> right
13:52 < fenn> 'how to open a terminal window'
13:52 < kanzure> http://www.youtube.com/watch?v=NwNZDeB1k8s
13:52 < kanzure> haha
13:52 < fenn> its not a joke :(
13:53 < fenn> i love how youtube removed the 'quality' setting so now everything plays like shit on my slow laptop
13:54 < kanzure> hm, I wonder if my screen size is going to be an issue
13:56 < fenn> what's the point of 'how to do a linux screencast' where 90% of the screencast is using windows programs?
13:57 < kanzure> that's a good question
13:57 < kanzure> I was surprised when windows was brought up
13:57 < kanzure> so I closed it
13:58 < kanzure> oh boy, 1 MB/sec
14:01 < cis-action> I recommend vimeo.com then blip.tv for the hosting, they allow much higher quality
14:01 < kanzure> I'm looking for my audio device now. I think I'm on /dev/dsp, not sure
14:02 < fenn> cis-action: i want *lower* quality though
14:02 < cis-action> it's all pretty low-quailty optimized stuff
14:03 < fenn> the proprietary flash plugin is not very efficient with cpu cycles..
14:03 < kanzure> ugh
14:03 < fenn> you used to be able to reduce the resolution to get a decent framerate
14:03 < cis-action> can you use mencoder to make h264?
14:04 < kanzure> I need something that looks like "hw:0,0"
14:04 < fenn> yes i can download the .flv with a script and play it in mplayer just fine
14:04 < fenn> but that's annoying
14:04 < fenn> kanzure: that's an alsa device address
14:04 < kanzure> fenn: yeah, I need to find the address for my soundcard
14:04 < kanzure> so that's a good start
14:29 < kanzure> well, this sound system stuff sucks :)
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14:43 < kanzure> How is it that mpg123 can play music, but then krecord says the sound card is not accessilbe?
14:43 < kanzure> Hrm. Was I offline?
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15:02 < kanzure> well, I can get audio going out the front speakers
15:02 < kanzure> from the microphone
15:02 < kanzure> does that count?
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15:32 < kanzure> fenn: you wouldn't happen to have a microphone, would you?
15:33 < fenn> as a matter of fact, i believe there is one on this computer
15:33 < kanzure> you wouln't happen to be willing to speak a few lines, eh?
15:33 < fenn> eek
15:33 < kanzure> I've been funneling text into a voice synthesizer as my alternative :-p
15:34 < fenn> in alsamixer i turned up the mic volume and then un-muted it :(
15:34 < kanzure> so your soundrecorder works after that?
15:34 < kanzure> because I am using alsa
15:34 < fenn> it plays the mic sound thru the speakers
15:34 < kanzure> and then I run stuff like krecord, gnome-sound-recorder, 
15:34 < kanzure> yeah, I can get it to play through the speakers, and the headphones, or either/or
15:34 < kanzure> but never does it seem to actually get into some user-accessible environment
15:35 < kanzure> recordmydesktop -d hw:0,0 doesn't work (the sound card is in fact index 0, so I know that's right)
15:35 < fenn> i dont have any of that stuff, so i'll try audacity
15:47 < kanzure> fenn: does it work?
15:49 < fenn> um, no
15:49 < fenn> looking at this right now: http://alsa.opensrc.org/index.php/Record_from_mic
15:50 < fenn> press tab in alsamixer to get to the capture screen
15:52 < fenn> ok it works.. somehow i was pressing the space bar wrong :\
15:56 < kanzure> press tab in alsa mixer, and then what?
15:57 < fenn> dont press tab, just arrow over to Mic and press space
15:58 < fenn> actually, press tab twice, then arrow over to Mic and press space
15:58 < fenn> you shuold see a red CAPTUR show up
15:59 < fenn> now arrow over to Capture and increase the volume
16:00 < fenn> have to press space on Capture too
16:03 < fenn> http://fennetic.net/pub/irc/alsamixer-record.png
16:04 < kanzure> looks like that for me too
16:04 < kanzure> still not getting anything on hw:0,0 or hw:1,0
16:05 < kanzure> also, Item: Mic doesn't say on nor off
16:05 < fenn> that's cause i have the mic muted so it wont cause feedback
16:06 < fenn> shouldnt matter either way
16:06 < fenn> hw:0,0 refers to the whole sound card
16:06 < kanzure> on [All], I can change the volume of the mic input going into my ear / out my speakers, but I still can't actually record
16:06 < kanzure> well, what refers to the mic jack?
16:06 < fenn> dunno. why does it want an address anyway?
16:07 < kanzure> because /dev/dsp doesn't apply for some reason?
16:07 < fenn> /dev/dsp is the synth
16:08 < fenn> oh wait, maybe i'm thinking dds
16:08 < kanzure> krecord - "cannot open soundcard: Device or resource busy"
16:08 < fenn> do you have firefox open?
16:08 < kanzure> recordmydesktop -d hw:0,0 output.ogv 
16:08 < kanzure> no
16:08 < kanzure> but I do have Opera open
16:08 < fenn> or some other music program
16:09 < kanzure> skype?
16:09 < fenn> so, this kind of problem is why alsa got invented
16:10 < kanzure> ok, krecord now works
16:10 < kanzure> now if only I can figure out what device it's on
16:10 < kanzure> ok, it works now
16:11 < kanzure> is there anyway I can demand Opera does not steal me audio?
16:13 < fenn> no, you are destined to be a slave to opera forevermore
16:13 < kanzure> :(
16:13 < kanzure> actually, I'll just record /while/ booting up Opera
16:13 < kanzure> brilliant, right?
16:13 < fenn> srsly the solution is to use alsa instead of /dev/dsp
16:13 < fenn> or that
16:13 < kanzure> but I'm not using /dev/dsp
16:14 < fenn> alsa doesnt have that 'device or resource busy' problem
16:14 < kanzure> but I *am* using alsa
16:14 < kanzure> heh'
16:17 < kanzure> okay, so it works :)
16:17 < kanzure> now I have to make sure I'm not talking out of my ass when it comes to git
16:18 < fenn> just make it short and if people need more info they can get it elsewhere
16:18 < kanzure> I wish I could pop up links in a youtube vid
16:18 < fenn> also, resizing your monitor to like 640x480 should help
16:18 < kanzure> wtf
16:18 < kanzure> stone age
16:18 < fenn> youtube is only like 300x400
16:19 < fenn> i hate screencasts where we see the person's pretty desktop background but cant read any words
16:19 < kanzure> I guess I can resize
16:19 < kanzure> grr
16:19 < cis-action> use vimeo.com
16:20 < fenn> vimeo is the same size?
16:20 < cis-action> crosspost to youtube if you are concerned about visibility
16:20 < cis-action> it will show 640x480
16:21 < cis-action> http://vimeo.com/1087631
16:21 < kanzure> yeah, okay, I resized
16:22 < fenn> heh we need a theme song.. "citizen scientist"
16:22 < kanzure> fenn: so, I just need to mention apt-get install git-core; git clone
16:22 < kanzure> citizen scientist? 
16:23 < kanzure> maybe the MacGuyver theme
16:23 < fenn> cis-action: yer video has jittery audio, do you get that?
16:23 < fenn> kanzure: like the "citizen soldier" theme for the national guard
16:24 < kanzure> hrm
16:24 < cis-action> I think the first couple of seconds (certainly the first slide) is messed up
16:24 < cis-action> but I hear all the audio fine.  maybe it's... your flash player
16:25 < fenn> woo.. go flash
16:25 < fenn> welcome to the 21st century of more bullshit
16:25 < kanzure> fenn: so, how to install git, git clone http://heybryan.org/biotech.git, and then show them the gui versions (ugh)
16:25 < kanzure> that sound good?
16:25 < cis-action> hey, so if you don't want flash, use blip.tv
16:27 < fenn> really i just think video is a poor medium for knowledge exchange
16:27 < fenn> flash just aggravates the problems with it
16:30 < ybit> wow, you guys have been at it for a long time over a screencast :P
16:31 < fenn> ybit: note my first remark, "good luck"
16:33 < cis-action> fenn: I disagree a bit
16:33 < cis-action> I think screencasts can be very high-bandwidth in some situations
16:33 < cis-action> for instance, if you could be physically present, how would you teach someone how to tie their shoelaces?
16:35 < ybit> i made a screencast with istanbul once, took less than 10mins to film it capture and upload
16:35 < ybit> it's a nice program
16:36 < ybit> Phreedom: do you know of a kde alt? (i've yet to look for one)
16:36 < kanzure> hrm, I was using istanbul, but it didn't like me
16:37 < fenn> cis-action: well.. you probably like podcasts too
16:39 < kanzure> what type of crap is this?
16:39 < kanzure> it doesn't even capture text at 640x340
16:40 < ybit> lol, this is becoming entertaining :)
16:40 < parodyoflanguage> ...
16:41 < kanzure> Hey parodyoflanguage.
16:41 < parodyoflanguage> Hello.
16:41 < kanzure> What's up?
16:41 < parodyoflanguage> Just wondering what's going on :)
16:41 < parodyoflanguage> Not a whole lot, procrastinating work.
16:41 < kanzure> I'm doing a screencast on how to download the biotech toolkit.
16:42 < parodyoflanguage> ah
16:42 < parodyoflanguage> screencast == video?
16:42 < kanzure> Yep.
16:42 < parodyoflanguage> cool
16:43 < parodyoflanguage> I don't think I'm ready for that yet :)
16:43 < kanzure> For what?
16:44 < parodyoflanguage> dyi bio
16:44 < kanzure> what about kids
16:44 < parodyoflanguage> kids?
16:44 < kanzure> Yeah, you have to do "diy bio" to get kids. :/
16:44 < kanzure> Just saying. It's an example, probably a bad one.
16:45 < parodyoflanguage> You mean this stuff is kids stuff?
16:45 < kanzure> No. I mean that many people are already doing biology in their own homes.
16:45 < kanzure> We're made up of cells and so on -- we're just largely ignorant of the biological basis of day to day stuffs.
16:45 < parodyoflanguage> Oh, you mean reproduction :)
16:46  * kanzure goes off to make the screencast.
16:48 < parodyoflanguage> A book sounds like an awesome idea.
16:53 < fenn> i have a jar of kombucha going bad on the back porch
16:53 < kanzure> linux users should be able to figure out how to install git
16:53 < cis-action> later guys
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17:04 < kanzure> crap, a 72 megabyte video?
17:10 < kanzure> bleh, I don' want to do a video :(
17:10 < kanzure> this is pretty easy stuff
17:10 < kanzure> raise your hand if you can't use git, here
17:21  * Biopunk waves
17:22 < Biopunk> what video don't you want to make?
17:36 < kanzure> A video on how to use git.
17:37 < kanzure> fenn: I got some lip from biobarcamp people about the git stuff.
17:37 < kanzure> "please don't do this, this is not the way to do it"
17:37 < kanzure> and "The BioTech Geek Book was meant to only have a small chapter on DIY stuff."
17:38 < kanzure> and other BS as if the internet only has enough space for one more book
17:40 < Biopunk> "The BioTech Geek Book" is this the pimm guy?
17:42 < kanzure> No.
17:42 < kanzure> Might be.
17:42 < kanzure> they're not playing fair
17:42 < Biopunk> i was thinking you meant this one: http://pimm.wordpress.com/2008/02/28/lets-compile-a-biotech-for-it-folks-book-and-publish-it/
17:43 < kanzure> yes
17:43 < kanzure> http://biohack.sf.net/
17:43 < kanzure> that's the kit damn it :)
17:43 < kanzure> http://heybryan.org/gitweb.cgi
17:45 < kanzure> I think Atilla is angry because she has a publishing deal
17:45 < kanzure> http://groups.google.com/biobarcamp/
17:48 < Biopunk> (http://groups.google.com/group/biobarcamp/)
17:50 < kanzure> bleah
17:50 < kanzure> yes, that
17:51 < Biopunk> yup pimm
17:52 < Biopunk> It strikes me how small this world still is
17:53 < kanzure> have you ever gone outside?
17:55 < Biopunk> The aliens took me once
17:56 < Biopunk> I'm hardly on the inside... you and Atilla are.. not sure there is a demand for my ideas of subculture yet
18:01 < kanzure> heh
18:01 < kanzure> I think they don't like me posting to their mailing list or something
18:01 < kanzure> maybe they're not used to email
18:01 < kanzure> I mean, hell, ignore the message if you want
18:05 < fenn> no, this is MY temporary autonomous zone! wah!
18:07 < kanzure> please send that message in response to her
18:07 < kanzure> that would be hillarious :)
18:08 < Biopunk> it's a guy
18:08 < fenn> yep definitely male
18:08 < kanzure> oh
18:08 < kanzure> well shit :)
18:08 < kanzure> Atilla is not a female's name?
18:09 < fenn> "Attila Csordás is a research scientist in the Gene Therapy Center at Tulane University.  He is the author of Pimm"
18:10 < kanzure> http://www.youtube.com/watch?v=joVr-5NTE28
18:10 < kanzure> aha
18:10 < fenn> were there any specific pro/con type objections?
18:11 < kanzure> No, just that HIS book is Different
18:11 < kanzure> http://groups.google.com/group/biobarcamp/
18:11 < Biopunk> maybe you talk about different books... he talks about IT for biotech people on pimm
18:12  * fenn squints
18:12 < kanzure> I don't know if I like it.
18:12 < kanzure> that was like my fifth go and it sucked worse than the other ones :)
18:12 < kanzure> too many 'um's and so on, 
18:13 < fenn> looks like it blanked out 'apt-get install git-core'
18:13 < fenn> write a script
18:13 < fenn> a teleprompt script that is
18:13 < kanzure> sure
18:13 < kanzure> but it's really retardingly simple stuff though
18:14 < kanzure> it's not even really worth talking about
18:14 < kanzure> but, if we have to, there's the video
18:15 < kanzure> technically I'm missing the step where you git add origin master
18:15 < kanzure> or something :)
18:15 < fenn> heh i love how nothing works
18:15 < Biopunk> you don't sound texan
18:16 < kanzure> fenn :)
18:16 < fenn> no, push access is dumb
18:16 < fenn> it keeps people thinking in CVS paradigm
18:16 < kanzure> hrm
18:16 < kanzure> then what do we do?
18:16 < fenn> worst case scenario they can do some kind of diff/patch
18:17 < kanzure> right?
18:17 < kanzure> but then what's best ?
18:17 < kanzure> send out an email with an attached diff?
18:17 < kanzure> crap
18:17 < kanzure> "maybe OpenWetWare will be interested in this"
18:17 < kanzure> centralization sucks :(
18:18 < kanzure> I guess I'll redo the video.
18:20 < Biopunk> kanzure... why is git better than a wiki? git it has a learningcurve
18:20 < kanzure> a wiki is git, except more sucky
18:20 < kanzure> this is better because nobody 'owns' it
18:20 < fenn> you could have an ikiwiki interface
18:20 < kanzure> well, in theory :)
18:20 < fenn> right
18:21 < Biopunk> but it's a repository?.. so someone has to hold it in anycase?
18:21 < kanzure> doesn't somebody have to have a wiki ?
18:21 < Biopunk> If it has a learning curve like that.. people just won´t use it I think
18:21 < fenn> Biopunk: for one thing, there's a lot of bad script/conversion output that made lots of little files. that's really hard to deal with from a wiki interface
18:21 < kanzure> you drag and drop files
18:22 < kanzure> how hard could this be
18:22 < Biopunk> it's not hard for me.. but i'm not sure I'd spend the time to find out
18:23 < kanzure> do you run linux?
18:23 < Biopunk> no
18:23 < kanzure> so
18:23 < kanzure> yeah.
18:23 < kanzure> http://kerneltrap.org/Linux/Git_on_Windows
18:24 < kanzure> maybe I'll just make a slideshow and talk
18:24 < Biopunk> ;)
18:25 < fenn> this whole free software rushing headlong into the singularity would be a lot more exciting if we didnt have to drag the rest of the world along with us
18:25 < fenn> kicking and screaming
18:30 < Biopunk> On the topic of the singularity: http://luci.ics.uci.edu/blog/archives/2006/09/ubicomp_2006_br_1.html
18:31 < Biopunk> It's a talk by Bruce Sterling on UbiComp 2006
18:31 < fenn> i hate that word 'spime'
18:31 < Biopunk> hehehe.. yeah
18:31 < fenn> spite/slime
18:32 < Biopunk> I liked the part where he talked about how writers talking about the singularity were in no particular hurry
18:33 < fenn> the ones predicting a rosy future maybe
18:34 < Biopunk> yeah ...they had smooth lines pointing into the future... it would happen without them doing much.. and they would be proven right and reap the benefits of being prophets
18:34 < Biopunk> The guy gives a great speech
18:34 < fenn> really? the only bruce sterling talk i saw was horrendous
18:35 < Biopunk> I thought you saw this one... he mentions splimes
18:36 < kanzure> cool, I think I did well this time
18:37  * kanzure sits around waiting for it to render
18:40 < fenn> http://savannah.gnu.org/maintenance/UsingGit pretty good summary
18:41 < fenn> you really need an alpha tester to see if its understandable though
18:41 < fenn> i.e. not me
18:41 < kanzure> meep
18:48 < kanzure> uploading (again)
18:49 < kanzure> fenn: is it worth doing more videos?
18:49 < kanzure> I mean, for other things
18:49 < kanzure> I'm not sure I like this, it doesn't encourage intellectualism
18:50 < kanzure> of course, there's nothing wrong with that
18:50 < kanzure> but.
18:50 < fenn> videos are worth negative time unless they have some editing and production put in
18:50 < kanzure> perhaps
18:51 < fenn> if its not a video you get: hyperlinks, searchability, skimmability, language translation, modifiability, etc
18:51 < fenn> pretty much automatically
18:52 < Biopunk> if a wiki would be the better option... you are putting time into making something worse... maybe you should ask people if they are prepared to use git for this
18:54 < Biopunk> you have a lot of traffic... a survey on the site might be worth while
18:54 < kanzure> what type of bullshit is that?
18:54 < kanzure> a wiki is /not/ a better option
18:54 < kanzure> and there's already a wiki
18:54 < kanzure> http://heybryan.org/mediawiki/
18:55 < fenn> settle down boy
18:55  * kanzure settles
18:55 < fenn> a wiki is a good interface for some things
18:55  * Biopunk is still sobbing a little
18:55 < fenn> and bad for some other things
18:56 < kanzure> we can do a wiki interface
18:56 < kanzure> however, if you want to rewrite the backend that'd be awesome
18:56 < fenn> now, i'm still not sure what you're trying to do
18:58 < kanzure> hm?
18:58 < kanzure> oh, the git stuff?
18:59 < fenn> what's the desired end-product of the biohack kit project supposed to look like?
18:59 < kanzure> well, it's supposed to be the bioreactor ;-)
18:59 < kanzure> but in the mean time we need to keep some people entertained, it seems
19:00 < kanzure> so, information on how to do Stuff
19:00 < kanzure> and at the moment it's not the best of information
19:00 < kanzure> I mean, it's just all thrown together
19:00 < kanzure> so there's opportunity for improvement
19:00 < fenn> yeah
19:01 < Biopunk> The quality is what would give the value
19:01 < fenn> i think it might be better if, instead of trying to sort everything in place, you sort through the pile of junk and build something structured in a separate place
19:01 < kanzure> sure
19:01 < kanzure> I hate ontologies
19:01 < kanzure> :-/
19:01 < kanzure> it pains to me save stuff in ~/cache/ellingtonia/polymerase/ (and not just because I have to keep on typing that out when saving PDFs at the end of a session)
19:02 < fenn> wikipedia doesnt really have an ontology, but it's structured, and filtered, and in a standard format
19:02 < kanzure> but rather because it's *not* Just about polymerase
19:02 < kanzure> okay, new version is live
19:02 < kanzure> http://www.youtube.com/watch?v=ZXKbzbeipmI
19:02 < fenn> and non-redundant for the most part
19:02 < fenn> a tagged filesystem perhaps?
19:03 < kanzure> where's Enk-2?
19:03 < kanzure> he's the one doing that sort of thing
19:03 < kanzure> go pester him
19:07 < fenn> last version is acceptable :)
19:07 < kanzure> hurray
19:07 < kanzure> amphetamine - it works ;-)
19:07 < fenn> heh
19:13 < Biopunk> what's supposed to be in the repository that's not in the wiki?... the wiki imposes a certain standard which is not a bad thing
19:13 < kanzure> what's in a wiki?
19:13 < kanzure> content, right?
19:13 < kanzure> words, text, stuff?
19:14 < Biopunk> yes
19:14 < kanzure> Where does this get stored?
19:14 < Biopunk> db
19:14 < kanzure> ok, why?
19:14 < Biopunk> it's manageable.. searchable
19:15 < Biopunk> is this a backend to a wiki?
19:15 < kanzure> okay, so, as opposed to that database
19:15 < kanzure> we can use git
19:15 < kanzure> the frontend is totally modularable, it could be a wiki
19:15 < kanzure> the only wiki currently anywhere near ready for a git backend is ikiwiki
19:15 < kanzure> however, ikiwiki sucks
19:16 < Biopunk> yeah.. but are you planning to have separate suff in git and ind the wiki?
19:16 < kanzure> no
19:17 < fenn> wiki is just a different view of the data
19:17 < Biopunk> i look at your clip... you say it's a wikipedia without the clicking and the need to download 6gig.. and I don't understand the point
19:17 < fenn> git is like a filesystem, wiki is like a filesystem browser
19:18 < fenn> imagine your filesystem was only accessible through google docs
19:18 < Biopunk> yes.. and if the data is the same.. what's the upside with git?
19:18 < kanzure> it's accessible to all of your file tools that you normally use
19:18 < fenn> big fucking pain in the ass, you have to load a webpage every time you do anything, no batch commands, no batch revisioning, no merging
19:18 < kanzure> loading a webpage is BAD
19:18 < kanzure> avoid at *all* costs
19:19 < Biopunk> but it's a standard.. it has a value
19:19 < Biopunk> people will use it
19:19 < kanzure> people will use whatever *works*
19:19 < fenn> if loading a webpage took less than 0.1 sec then it would be fine
19:19 < fenn> well, actually no nevermind
19:19 < kanzure> heh
19:19 < fenn> still have all the other problems (and you dont *own* the data)
19:19 < kanzure> the problems are a very long list
19:19 < kanzure> heh
19:19  * kanzure goes to watch Captain Ron
19:20 < fenn> most consumers are idiots and can't manage their own personal data, so that's why we have webmail and google docs
19:21 -!- kanzure changed the topic of #hplusroadmap to: Intro: http://www.youtube.com/watch?v=ZXKbzbeipmI http://diybio.org/ http://openwetware.org/ | diy bio toolkit: http://biohack.sf.net/ | Automated societal knowledge (put it to work): http://heybryan.org/exp.html | Channel wiki: http://heybryan.org/mediawiki/
19:21 < fenn> but if you know how to manage large numbers of files at once, then web based filesystems are just frustrating and backwards
19:22 < Biopunk> i'd say the way you are doing it is the way it used to be done all the time 20 years ago in BBS days
19:22 < kanzure> maybe back then it *worked*
19:22 < fenn> BBS didnt do content creation
19:23 < fenn> they just hosted files people had created
19:23 < Biopunk> release a dump on a torrent once a month
19:23 < kanzure> this is the dump
19:24 < Biopunk> all I'm saying is that if you wan't people to use it.. there can't be a learning curve
19:24 < kanzure> hey, would you like to package a new torrent of it?
19:24 < Biopunk> in windows format?
19:25 < fenn> windows format?
19:25 < kanzure> wtf?
19:25 < fenn> kanzure: making a tarball of the git repo actually isnt a terrible idea.. because then you dont need git to access the plain .html or whatever wiki markup
19:26 < fenn> but the repo information is still there if they ever decide to commit
19:26 < kanzure> huh?
19:26 < Biopunk> ;)
19:26 < kanzure> oh, a tarball of the first master commit?
19:26 < kanzure> or whatever
19:27 < fenn> does wikipedia have mysql fields for stuff like categories? or only last modified date, user, etc
19:27 < kanzure> I could check. but I'm going.
19:27 < kanzure> will be back
19:28 < fenn> seeya
19:28 < kanzure> uhm, also, 
19:28 < kanzure> I'm still stuck on the evolvable polymerases
19:28 < kanzure> there's technically no advantage that we can give to polymerases that copy only one nucleotide
19:28 < kanzure> :-/
19:29 < Biopunk> cu
19:58 < kanzure> fenn: researchers have found a way to do fluorotagging but for magnetism
19:59 < kanzure> so supposedly we can come up with some super-high-resolution MRI machines and get an image of cellular resolution.
20:06 < Biopunk> I want to see robots performing automatic keyhole surgery at high speed with that info
20:06 < kanzure> brain scanning
20:06 < kanzure> subcellular resolution
20:09 < Biopunk> it would be cool if we would come to understand the brain through understanding how the organism builds it... somehow the blueprint for how it works is in the DNA.. waiting to be understood.
20:10 < Biopunk> probably
20:10 < kanzure> the blueprint isn't really encoded in the DNA though
20:10 < kanzure> that's what all this 'amorphous compiler' stuff is about
20:13 < ybit> [17:10] <kanzure> http://www.youtube.com/watch?v=joVr-5NTE28 - whatever that was, it's already been removed
20:13 < fenn> kanzure: sweet, that's another fantasy of mine
20:13 < kanzure> hm?
20:13 < kanzure> oh, subcellular resolution
20:13 < ybit> ah
20:13 < kanzure> ybit: try the link in the topic
20:14 < ybit> already have, everything went well
20:14 < kanzure> I'm trying to come up with some other possible uses of it.
20:14 < ybit> and you made me laugh at the part where you stated that you already had the material, etc.
20:14 < kanzure> it's a membrane-bound integral protein.
20:14 < kanzure> ybit: material?
20:14 < ybit> one sec.. i'll get the quote..
20:14 < fenn> computer debugging
20:14 < kanzure> fenn: how so?
20:15 < kanzure> cool, 27 views on the vid
20:15 < fenn> DNA FPGA crystal growth errors
20:15 < ybit> "we can ignore that, because *I* already have it"
20:15 < ybit> heh
20:15 < kanzure> ybit: :)
20:15 < fenn> or poisoning
20:15 < kanzure> dunno if that works though
20:15 < kanzure> it's built into the membrane
20:16 < fenn> got a link?
20:17 < kanzure> "We have found a very simple way to make mammalian cells have a  
20:17 < kanzure> magnetic signature," says Hu, who is director of Emory's Biomedical  
20:17 < kanzure> Imaging Technology Center and a Georgia Research Alliance Eminent  
20:17 < kanzure> Scholar.
20:17 < kanzure> erm
20:17 < kanzure> http://www.biologynews.net/archives/2008/06/03/gene_that_magnetically_labels_cells_shows_potential_as_imaging_tool.html
20:18 < fenn> apparently birds use something like this to navigate.. it shows up in their vision (maybe its present in retinal cells?)
20:19 < Biopunk> i bet it would set of the shoplifter alarm in a supermarket
20:19 < fenn> i wouldnt mind fourier-transform-vision
20:20 < Biopunk> i saw a talk about functional body hacking... the woman talking had had a magnet in one of her fingertips for a while
20:21 < Biopunk> she could feel electromagnetic fields
20:21 < fenn> so, i dont really get the connection between matgnetite and MRI
20:21 < fenn> MRI is based on nuclear spin precession
20:22 < fenn> ferromagnetic substances have a high spin, but does that mean it will absorb radio waves better than just hydrogen?
20:23 < kanzure> hm
20:23 < kanzure> apparently it's used to "sense the earth's gravity field"
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20:24 < fenn> magnetite lines up with magnetic field lines like a compass
20:24 -!- ybit [n=h@unaffiliated/ybit] has joined #hplusroadmap
20:24 < fenn> (it IS a compass actually)
20:25 < kanzure> grr, still haven't figured out my polymerase selections
20:25 < kanzure> this is kind of annoying
20:25 < kanzure> the real sucky part is that I don't have a good way of automating it
20:25 < kanzure> it requires lots and lots of gels
20:25 < kanzure> to see if a certain batch writes a longer DNA molecule with only a specific nucleotide
20:25 < ybit> grr, that's the first crash in a long time
20:25 < kanzure> and at the same time that's not selecting for a limited nucleotide acceptance
20:26 < ybit> for the discussion earlier... git is good for the diybio devs, the updated info package on sourceforge is good for the non-technical people interested in the project 
20:26 < ybit> wiki might be good to host the information in different languages
20:26 < kanzure> I was mentioning the idea of having four different *types* of other ddNTP-like-molecules, but that just shifts the problem to DNA repair mechanisms needing to translate 'ddNTP-analog to one of the four specific ddNTPs' and again I might as well just had that "get the right ddNTP" in the first place
20:26 < kanzure> ybit: the wiki frontend is good in general for anybody, but the backend is also important
20:26 < kanzure> perhaps even more importnat.
20:26 < kanzure> *important.
20:27 < ybit> updating a wiki via git is quite interesting
20:27 < fenn> dokuwiki has a flat text structure, perhaps we could use it, along with some update hooks on both ends, to turn it into a sort of ikiwiki
20:27 < kanzure> I met somebody a few days ago who's working with Wikimedia, the Internet Archive, and the Open Library Project and is supposedly automating updated content transfers between the different organizations
20:27 < kanzure> however, the problem is that he doesn't seem to "git it"
20:28 < kanzure> aha, dokuwiki /me goes to check
20:28 < kanzure> even uses the word 'repository'
20:28 < fenn> there are other flat text wiki's (instiki for exaple) but dokuwiki has a nice interface and decent set of features
20:29 < kanzure> http://wiki.splitbrain.org/wiki:plugins?plugintag=git hrm, none?
20:29 < kanzure> oh
20:29 < kanzure> http://wiki.splitbrain.org/plugin:gitlink
20:29 < kanzure> 'Links git commit hashes and references to a gitweb application and displays information about them'
20:29 < fenn> hah look at all those tags
20:30 < kanzure> those tags are not git-specific
20:30 < fenn> oh, those are plugin names sorry
20:30 < kanzure> it seems to be a byproduct of their wiki setup 
20:30 < kanzure> i.e., the page for plugins is a template or something
20:30 < kanzure> which includes a list of all plugins on each page wtf
20:31 < fenn> i dont know what gitlink is supposed to do
20:31 < kanzure> me either
20:31 < kanzure> hrm, so the "force an ecoli to evolve a writozyme" idea sucks for a few reasons:
20:31 < kanzure> (1) it takes longer to signal a sequence to be synthesized than it takes for ecoli to divide (as you mentioned)
20:32 < kanzure> (2) transcriptional circuits are in vitro only, and I'm not too keen on quickly passing ddNTPs and other stuff as messengers through ecoli membranes quickly
20:32 < kanzure> the usual method of polymerase evolution is 'compartmentalized self-replication' where you have polymerase copy the polymerase DNA strand, and then the one that is the most efficient and the least error-prone, is the one that will win in your selections
20:33 < kanzure> however, the retarded polymerases that I want will not do that
20:33 < kanzure> you'd have to use all four of them in a system that you assume already works, to make genes that help the organism survive
20:33 < kanzure> well, not organism, but whatever
20:33 < kanzure> it needs to be an automated self-evolving system in order for the selection to actually work
20:33 < kanzure> and that's not going to happen in vitro really
20:34 < fenn> you could do in-vitro with magnetic beads attached to dNTP's? so the one that incorporates bead-ATP the fastest wins?
20:34 < kanzure> how's that?
20:34 < kanzure> magnetic beads attached to the nucleotides
20:34 < kanzure> bead-ATP ??
20:34 < fenn> then give it a scaffold strand that doesn't code for that nucleotide (so only retarded enzymes will add A to it)
20:35 < kanzure> oh, I guess we could just select for the polymerase that hangs out around the beads, making the assumption that these polymerases will be fit to use the nucleotides there?
20:35 < kanzure> I think that a surface, either a bead or a giant 2D plane, will be important here
20:35 < fenn> then you can sequence the protein.. :(
20:35 < kanzure> I was thinking that it might be useful to bind them to a surface
20:35 < kanzure> the polymerases, I mean
20:35 < kanzure> and if we can bind them and keep them in a specific spot, then we can take advantage of them in a new way
20:35 < kanzure> sequence the protein? the protein can't write itself
20:36 < kanzure> so we'd have to remember where we put each bead and what polymerases we started off in that area or something
20:36 < fenn> yeah nevermind, bad idea
20:36 < kanzure> what possible evolutionary advantage does retardation have?
20:36 < kanzure> there's a way to "flip" all of thus on its head
20:37 < Biopunk> I have a feeling too that there is some crazy simple way to do DNA synthesis... the kind that when some kid discovers it everyone goes: fuck, why didn't I think of that
20:37 < kanzure> but I'm not well versed in selection experiments, so I can't cite it
20:37 < kanzure> Biopunk: yeah, it's called oligonucleotide synthesis
20:37 < kanzure> my lab has a box in a corner that does it
20:37 < kanzure> it's roughly the size of a toaster
20:37 < fenn> really?
20:37 < kanzure> no, I think it might be the size of an icechest or something
20:37 < fenn> the polonator?
20:37 < kanzure> no
20:37 < kanzure> the polonator is George Church's lab
20:37 < kanzure> up at Harvard.
20:38 < kanzure> (Church is collaborating with this lab, though, so :-))
20:38 < kanzure> what if we make all of the nucleotides degrade except for one of the four
20:38 < kanzure> and then we select for the weight of DNA
20:39 < kanzure> whichever polymerase can make the most heavy DNA that /lasts/, wins
20:39 < Biopunk> the polonator is _not_ cheap
20:39 < kanzure> Biopunk: how so?
20:39 < kanzure> Church is planning supercheap genomics for everybody on the planet
20:39 < Biopunk> isn't it like quater of a million?
20:39 < kanzure> uh?
20:39 < Biopunk> i'll recheck
20:39 < fenn> kanzure: isnt that what i just said? (but using magnetic beads instead of degrading dna)
20:39 < kanzure> uhm
20:40 < kanzure> oh
20:40 < kanzure> so you mean to say that you have four nucleotides swimming around
20:40 < kanzure> three of those are attached to beads
20:40 < kanzure> one is free-floating
20:40 < fenn> no, only one is attached to beads
20:40 < fenn> or biotin or whatever
20:40 < kanzure> hrm
20:41 < kanzure> well, let's say only one is attached to the bead
20:41 < kanzure> what would you select? the polymerases around that bead? or everything else?
20:41 < fenn> so the idea is the retarded enzyme will incorporate that nucleotide more rapidly than aproperly functioning one
20:41 < Biopunk> "Danaher Corp., based in Washington, said it shipped its first $150,000 Polonator sequencer this week. 
20:41 < Biopunk> "
20:41 < kanzure> Biopunk: Heh. Well. There are other ways to do sequencing. http://heybryan.org/mediawiki/index.php/DNA_sequencer
20:41 < fenn> ffs $150k
20:41 < Biopunk> ..not quater of a million but still
20:42 < kanzure> no kidding
20:42 < fenn> i thought it was the "$0 genome project"
20:42 < kanzure> me too
20:42 < kanzure> I thought that's the same Polonator Project
20:42 < kanzure> otherwise I'm very very confused
20:42 < Biopunk> I never understood how many bp it could manage
20:42 < Biopunk> the software is OS
20:43 < kanzure> aha
20:43 < kanzure> so it's bullshit
20:43 < kanzure> I'll stop linking to it.
20:44 < kanzure> fenn: how would it do that?
20:44 < kanzure> how would it incorporate *that* nucleotide (attached to the bead) more quickly?
20:45 < fenn> because it's retarded, so it'll be crazily adding just that nucleotide
20:45 < fenn> like a machine gun with a sticky trigger
20:45 < kanzure> how does it happening to be in that location have anything to do with a selective pressure on forcing polymerase to *only* accept one nucleotide type ?
20:46 < kanzure> okay, so what about my radiation idea?
20:46 < kanzure> make the nucleotides degrade in an amount of time that (1) gives polymerase a time to use them but (2) by the time I run the gels or weigh the DNA, I can find the one that weighs the most (has the most nucleotides)
20:47 < kanzure> the polymerase that makes the 'most errors' will lose
20:47 < kanzure> the trick is that the polymerase might learn to discriminate between "bad A, T, C" (with the radioisotope) and "good A, T, C" (without it)
20:48 < fenn> if phosphorous decays the dna falls apart right?
20:48 < fenn> are there isotopes of P that decay fast enough?
20:48 < fenn> and then you get to worry about high levels of radiation
20:48 < kanzure> hurray for radiation
20:48 < kanzure> btw, it's a BSL2 lab, so they work with radiation daily
20:48 < fenn> i think P32 half life is like 2 years
20:48 < kanzure> crap
20:48 < fenn> oh lucky you.. 14.2 days
20:49 < kanzure> bwahah
20:49 < fenn> how the hell does that work
20:49 < Biopunk> build it in an extremophile
20:49 < kanzure> so, I'm pretty sure that I need the DNA backbone to stay in tact
20:49 < Biopunk> *grin*
20:49 < kanzure> it's just the nucleotides that I need to fall off
20:50 < kanzure> or maybe there's some selective radiation where I can blast the hell out of DNA and get rid of specific nucleotides
20:50 < kanzure> wouldn't that be nice?
20:50 < fenn> cant you just do affinity chromatography for your nucleotide?
20:50 < kanzure> hrm?
20:50 < fenn> you want the strand with the most A's right?
20:51 < kanzure> yes
20:52 < fenn> so set up a column with T's stuck to itthe substrate
20:52 < kanzure> "stuck to it <RANDOM UNICODE HERE>the substrate"
20:52 < fenn> sry my wifi is being a butt-head
20:52 < kanzure> k
20:53 < kanzure> okay, so affinity chromatography looks like DNA hybridization
20:53 < kanzure> in DNA hybridization selections, we'd have a machine that has a tip with the DNA strand that we want to match
20:53 < fenn> yes same thing
20:53 < kanzure> then, it goes to each well and if we detect a change in current pull, we know we have a matching
20:53 < kanzure> except it looks like affinity chromatography is more high throughput?
20:54 < fenn> right, i'm thinkig something like a gel that weights strands based on their bp content
20:54 < kanzure> well, one idea I had earlier was to do a gel with fluoroescently labeled nucleotides
20:54 < kanzure> and then we just look at (1) how far it travels (weight) and (2) brightness under lamp
20:54 < kanzure> we could do calculations for roughly how bright it should be methinks
20:55 < kanzure> *fluorescently
20:55 < kanzure> but that's not good
20:55 < fenn> how do you get the polymerase sequence once it makes this messed up dna?
20:55 < kanzure> you're running lains and different containers for the reactions, so you know
20:55 < kanzure> but you see, that's not selection really
20:55 < kanzure> that's human selection I guess
20:56 < kanzure> in most polymerase selections, the polymerase gets to make itself
20:56 < kanzure> but there's no vital functionality encoded by AAAAAAA that allows it to replicate itself :(
20:56 < fenn> didnt you have some paper with 'reduced substrate repertoire' polymerase? or was it increased repertoire
20:56 < kanzure> increased
20:56 < kanzure> wrong direction. 
20:57 < kanzure> the authors should had been kind enough to include some thoughts on going in the opposite direction of their work
20:57 < fenn> what if you had a plasmid with the polymerase gene, and then nicked the plasmid so the polymerase had somethig to latch onto
20:57 < fenn> then pull the plasmid out with some biotin nucleotide thing
20:58 < fenn> plasmid <ori><polymerase>AAAAA<restriction sequence>AAAAAAAAAAA
20:58 < kanzure> biotin nucleotide?
20:58 < kanzure> hm
20:58 < kanzure> and then what? 
20:58 < kanzure> so a normal polymerase would come by
20:58 < kanzure> and make the hacked polymerase
20:59 < kanzure> which could then copy AAAAA I guess
20:59 < fenn> you could inhibit the normal polymerase somehow after introducin the restriction enzyme
20:59 < kanzure> and what makes this delete the functionality for incorporating G, T, or C?
20:59 < fenn> oo here's another idea
21:00 < kanzure> we need to make G, T, C a wate of its time
21:00 < kanzure> but at the same time, we need to make AAAAAA a way for it to replicate itself (to let us see it)
21:00 < kanzure> by 'replicate' I mean 'a way to get noticed by us'
21:00 < fenn> inhibit the normal polymerase, and then promote some kind of poison gene product that kills the cell, so only a retarded polymerase will survive
21:01 < kanzure> it wouldn't survive anyway
21:01 < fenn> and use radiolabeled dNTP to measure polymerase activity
21:01 < fenn> it doesnt hve to replicate, just not explode
21:02 < kanzure> another random idea - need to make an evolutionary pressure that forces polymerase to 'compartmentalize' into four different polymerases, each specialized for a specific nucleotide
21:02 < fenn> so then, you un-do the poison and reenable the good polymerase, and the cells with messed up polymerase will then replicate
21:02 < kanzure> how long could it wait?
21:02 < fenn> long time, months at least
21:02 < fenn> unless something else eats it
21:02 < kanzure> I mean, how long could a cell go without polymerase activity
21:03 < fenn> hmm. plasmids get degraded continuously, so i dont really know
21:03 < fenn> "it depends"
21:04 < fenn> you understand the scheme though?
21:04 < fenn> two polymerases, one is sensitive to poison (the infrastructure) and the other is not (the experiment)
21:05 < kanzure> it just seems very flimsy to me
21:05 < fenn> of course its flimsy :P
21:05 < kanzure> won't they die?
21:06 < kanzure> even without the poison?
21:06 < kanzure> polymerase is pretty vital, and the polymerase I want is totally retarded
21:06 < fenn> cells not replicating are fragile but they dont just vanish into vapor like un-powered RAM
21:06 < kanzure> no, not just "not replicating", but not making any new proteins whatsoever
21:06 < fenn> you dont nee DNA polymerase to make protein
21:07 < fenn> you're confusing it with RNA polymerase
21:07 < kanzure> hm
21:07 < kanzure> oh, DNA polymerase is for replication
21:07 < kanzure> template strand synthesis
21:07 < kanzure> well, not template
21:07 < kanzure> but it uses template to synthesize the complementary strand
21:08 < kanzure> hrm, I'm wondering if anybody has starved cells of polymerase like that before
21:08 < kanzure> and observed any sort of "ability to recover"
21:09 < fenn> i'm sure they have
21:09 < fenn> otherwise how would you observe polymerase activity
21:09 < fenn> in vitro i guess
21:10 < fenn> we did some thing in school with radio labeled NTP's to monitor polymerase activity.. i dont remember the details now
21:10 < fenn> i remember spilling tritiated TTP on my pants (actually wearing those pants right now)
21:11 < Biopunk> you might be a superhero then
21:11 < fenn> maybe we were just seeing if the cells were alive
21:11 < fenn> the idea being if they didnt use the ntp's then the cells were dead
21:12 < fenn> chinese hamster kidney
21:13 < fenn> as you can see, my schooling really stuck with me
21:13 < kanzure> :)
21:15 < Biopunk> "one thing I'd like to propose to all you garage biohackers is it: As the topic title implies,a group project.
21:15 < Biopunk> Toss ideas out, what should this group try to strive for as a project? Do you even want to undertake a co-operative project?
21:15 < Biopunk> My idea would be to create a theoretical enzyme that could dissolve the tar from cigarette smoke left in the lungs.
21:15 < Biopunk> "
21:15 < kanzure> Where?
21:15 < kanzure> link?
21:15 < Biopunk> http://www.biopunk.org/group-wide-projects-t50.html
21:15 < kanzure> Biopunk: Is that you?
21:15 < kanzure> okay
21:15 < kanzure> not
21:15 < kanzure> do you allow HTML in posts?
21:16 < Biopunk> i think so.. i'll open it now
21:17 < fenn> link spammer!
21:18 < kanzure> I am a link spammer, aren't I?
21:20 < Biopunk> yeah.. I am.. I know
21:20 < Biopunk> mm... no setting for html in phpbb3
21:20 < kanzure> Biopunk: I just wanted to post the youtube video instead of the link to it
21:20 < kanzure> but I remember you doing that in another thread once
21:21 < Biopunk> ah.. that's a BB code
21:21 < Biopunk> [youtube] id [/youtube]
21:22 < Biopunk> like this: http://www.biopunk.org/how-to-use-the-board-t16.html
21:24 < Biopunk> I like it, this is good for the board... thanks kanzure
21:24 < kanzure> :)
21:24 < kanzure> it's the reason why I'm so obsessed with this stupid polymerase
21:24 < kanzure> (literally, it's supposed to be a stupid polymerase)
21:25 < Biopunk> maybe is should make 'GAAAAAAA'
21:28 < kanzure> I need a way to do a selection for death instead of a selection for living
21:28 < kanzure> except I need death to entail self-replication :-p
21:31 < fenn> inhibit good polymerase, look for polymerase activity where there should be none, clone cells with activity, un-inhibit good polymerase to replicate those cells
21:32 < fenn> do you have access to a flow cytometry machine
21:32 < kanzure> probably
21:32 < kanzure> yes
21:33 < kanzure> technically they have me and the rest of the guys in the attic
21:33 < kanzure> but the attic has more equipment and more fun stuff :)
21:33 < fenn> heh
21:33 < fenn> flow cytometry means you can pluck a glowing cell out of solution, pretty much
21:34 < kanzure> right
21:34 < kanzure> yeah, we have one, I remember asking or seeing it
21:35 < fenn> another 'basically an inkjet printer' sort of thing
21:38 < kanzure> wouldn't polymerase just evolve to get around your inhibition
21:42 < fenn> maybe
21:42 < fenn> you could do some site-directed mutagenesis on the one you're trying to mess with though
21:44 < kanzure> there's little guarantee that the mutation will be towards what I want
21:44 < kanzure> I need to select for the product of the polymerase in different situations of availability
21:44 < kanzure> (availability of nucleotides
21:44 < kanzure> )
21:45 < kanzure> if it doesn't self-replicate then it's not subject to selection experiments
21:45 < kanzure> I think that's the simple conclusion we have to make there.
21:46 < kanzure> well
21:46 < kanzure> not subject to "directed evolution" experiments
21:47 < fenn> mhmm i wonder about this http://en.wikipedia.org/wiki/Directed_mutagenesis
21:49 < kanzure> I saw that paper in my searches.
21:49 < kanzure> don't know where I put it / processed it
21:50 < Biopunk> there is always lamarcism
21:55 < fenn> Biopunk: there was some discovery recently about genes being transferred by some other mechanism than DNA
21:55 < fenn> the "kit" gene i think
21:56 < fenn> http://seedmagazine.com/news/2008/01/redefining_genes.php
21:58 < fenn> i wonder how the RNA replicates
21:58 < kanzure> oh, there was a paper that I was reading last night that unsurprisingly suggested that evidence shows that DNA-like-systems evolved at two different points in evolutionary history
21:58 < kanzure> which is kind of a "duh" thing
21:58 < kanzure> but.
21:59 < kanzure> hrm, let's turn it totally upside down
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21:59 < kanzure> we don't need polymerase to only write a certain letter
21:59 < kanzure> we can hack polymerase to use a ghost template strand
21:59 < kanzure> i.e., make the 'template strand portion' of the molecule the same as the incoming nucleotide portion
22:00 < kanzure> however, it'd be retrofitted for a different type of molecule 
22:00 < kanzure> one of the NTP-likes
22:14 < kanzure> noserub = distributed social network project
22:14 < kanzure> hrm
22:14 < kanzure> http://noserub.com/
22:17 < ybit> so.. how do you propose interfacing with the brain.. i'm not in the mood to read through my entire log atm
22:17 < ybit> or what have you fenn arrived to so far..
22:17 < kanzure> re: my polymerase woes; (2008-06-07 21:21:08) Tony: Or you do what we are doing (or trying to) with our hosting: use what we have as a spec and presume a ground up design might be several orders more efficient because what we have now is dependent on a highly contingent history.
22:17 < kanzure> ybit: okay, so brain interfacing
22:18 < kanzure> this can work a number of ways: invasive, noninvasive
22:18 < kanzure> invasive: physically touching up with the brain, neurochemicals, lesions, implants, stem cells, etc.
22:19 < kanzure> noninvasive: neurofeedback, fMRI, http://heybryan.org/mediawiki/index.php/Neuroimaging , rTMS, 
22:19 < kanzure> for physical wirings, try microelectrode arrays (electrical stimulation)
22:20 < kanzure> http://heybryan.org/docs/neuro/
22:20 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has joined #hplusroadmap
22:20 < kanzure> http://heybryan.org/recursion.html for some other approaches
22:20 < kanzure> I haven't significantly investigated biofeedback yet.
22:23  * kanzure wants some biophysical simulations of mutation
22:27 -!- xp_prg2 [n=knoppix@c-67-169-126-205.hsd1.ca.comcast.net] has joined #hplusroadmap
22:27 < xp_prg2> hi all!
22:27 < kanzure> huh
22:27 < kanzure> Hey xp_prg2 :)
22:27 < xp_prg2> ok, anyone here understand dispersion of chemical graidents for controlling gene expression?
22:28 < kanzure> fenn: Here's a new one. "An Error-Prone T7 RNA Polymerase Mutant Generated by Directed Evolution" (Brakmann, Grzeszik). I thought this sort of thing couldn't happen. According to this paper, viruses are at the maximal mutational rate.
22:28 < kanzure> xp_prg2: I understand it, but I can't cite any mathematical models or anything.
22:28 < kanzure> Basically, gene expression is controlled by activators and inhibitors, so if an inhibitor is present, guess what. :)
22:30 < xp_prg2> I heard that plastics usedthis approach
22:30 < kanzure> How so?
22:31 < xp_prg2> the guy I talked to said that plastics naturally form nano structures based on chemical gradients
22:31 < kanzure> Hrm. Viable viral offspring is only 0.5 to 1.5% of a viral population. Interesting. (exponentials)
22:31 < kanzure> Sure, you mean the polymerization process?
22:31 < xp_prg2> ya I think so, tell me more
22:33 < kanzure> I don't know much more. :) What are you doing?
22:33 < kanzure> fenn: you called it :)
22:33 < kanzure> The isolation of an error-prone RNA
22:33 < kanzure> polymerase from a plasmid library
22:33 < kanzure> containing random sequence substi-
22:33 < kanzure> tutions was enabled through a strin-
22:33 < kanzure> gent positive selection scheme, that
22:33 < kanzure> is, by rewarding inaccurate transcrip-
22:33 < kanzure> tion by a T7 RNAP mutant with the
22:33 < kanzure> survival of bacteria. Therefore, a
22:33 < kanzure> system of two compatible plasmids
22:33 < kanzure> was constructed, which couples mu-
22:33 < kanzure> tant polymerase genes in a feedback
22:33 < kanzure> loop to the essential, but inactivated
22:33 < kanzure> tetracycline resistance gene (Fig-
22:33 < kanzure> ure 1).
22:33 < xp_prg2> no that is not it then
22:33 < kanzure> What?
22:33 < xp_prg2> I need to speak to a chemical engineer
22:34 < kanzure> Ah, I see.
22:34 < kanzure> Why, though?
22:34 < xp_prg2> cuz he might know of industry practices that use chemical dispersion with gradients
22:35 < kanzure> fenn: oh, evolving with viruses is obviously better because of their high mutational rates
22:35 < kanzure> Right, but what are you getting at though?
22:35 < kanzure> Why are you interested in gradients?
22:35 < xp_prg2> that is how body forms are created in an embryo
22:35 < kanzure> to some extent
22:37 < kanzure> 'Towards this goal, Brakmann and Grzeszik used a reversion selection to evolve an error-prone T7 RNAP '
22:37 < kanzure> 'reversion selection'
22:37 < kanzure> heh, I called it inversion
22:37 < kanzure> I was so close :)
22:46 < kanzure> I guess we don't need to keep anything separated
22:46 < kanzure> just throw everything into a giant pot
22:47 < kanzure> lots of strands of DNA that encode polymerase, some that encode bad polymerase, etc., then have your nucleotide fluorescently tagged, let it sit there in the pot replicating everything. 
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23:27 < kanzure> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=306639 On the mechanism of preferential incorporation of dAMP at abasic sites in translesional DNA synthesis. Role of proof reading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site
23:27 < kanzure> mechanisms of the A-rule
23:53 < xp_prg2> kanzure what is that?
23:53 < kanzure> xp_prg2: The A-rule is where thymine is paired to adenosine in DNA.
23:54 < xp_prg2> oh ok
23:58 < kanzure> Hrm.
23:58 < kanzure> So the Russian Mafia has contacted me.
23:58 < kanzure> By this I mean, the Russian transhuman peoples.
23:59 < kanzure> They claim they have sources of funding and an interest in using me to make, propose, and implement a roadmap to suggest to the Russian government.