| --- Day changed Sat Jun 07 2008 | ||
| kanzure | fenn_: re: getting DNA out of neurons, see DNA single-stranded binding protein (SSB) | 00:04 |
|---|---|---|
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| parodyoflanguage | !help | 01:01 |
| kanzure | Hey parodyoflanguage. | 01:03 |
| 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 ? | 01:15 |
| ybit | http://www.youtube.com/watch?v=ihVaL-FHUyk | 02:53 |
| ybit | and this one if you need something watch while chowing www.youtube.com/watch?v=V026kSw4XCs | 02:58 |
| ybit | and this is quite interesting as well: http://www.youtube.com/watch?v=sudmW97FZA0&feature=related | 03:21 |
| ybit | perhaps i should sleep :P | 04:41 |
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| -!- 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 ] | 06:33 | |
| -!- Irssi: #hplusroadmap: Total of 12 nicks [0 ops, 0 halfops, 0 voices, 12 normal] | 06:33 | |
| -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008 | 06:33 | |
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| kanzure | Hi all. | 11:56 |
| kanzure | Hrm. We actually /lost/ people. | 11:56 |
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| kanzure | Hey. | 11:56 |
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| kanzure | Fine, be that way. | 11:56 |
| -!- 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/ | 11:58 | |
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| kanzure | Hey cis-action. | 12:00 |
| cis-action | finally got my nick changed. | 12:00 |
| cis-action | hey bryan | 12:00 |
| 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. | 12:02 |
| 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 | 12:03 |
| 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 | 12:04 |
| 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 | 12:05 |
| 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 | 12:06 |
| 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. | 12:07 |
| 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 | 12:08 |
| 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/ | 12:09 |
| 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 | 12:10 |
| 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 | 12:11 |
| kanzure | it's not meant to be a bottleneck | 12:12 |
| 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! | 12:14 |
| kanzure | yep :) | 12:15 |
| 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? | 12:16 |
| 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 | 12:17 |
| kanzure | fenn: git doesn't require ssh natively, does it? | 12:18 |
| 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." | 12:19 |
| 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 | 12:20 |
| 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 | 12:21 |
| kanzure | *programmer | 12:22 |
| fenn | ugh fuck elsevier | 12:29 |
| kanzure | :) | 12:30 |
| cis-action | ha | 12:32 |
| 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 | 12:33 |
| 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 | 12:34 |
| 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 | 12:36 |
| 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 ? | 12:37 |
| fenn | oh, i forgot about the git protocol | 12:39 |
| kanzure | ? | 12:39 |
| fenn | git:// | 12:39 |
| fenn | i dont know much about it really | 12:40 |
| kanzure | so it has its own port and everything | 12:40 |
| kanzure | hrm | 12:40 |
| 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 | 12:41 |
| * 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 :) | 12:43 |
| 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. | 13:08 |
| 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? | 13:09 |
| kanzure | I don't know what youtube/dnatube/etc. wants | 13:10 |
| fenn | did you dump the diybio stuff into it? | 13:13 |
| kanzure | yep | 13:13 |
| kanzure | pushing at the moment | 13:13 |
| 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 | 13:14 |
| fenn | kanzure: do you know what a "mess" is? | 13:16 |
| 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? | 13:17 |
| kanzure | writing objects :) | 13:19 |
| fenn | ah that was pretty quick | 13:20 |
| kanzure | 2 MB/sec. Awesome. | 13:20 |
| 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 | 13:21 |
| kanzure | yep, 10 seconds ago it was 3%, it just shot up to 99%. | 13:22 |
| 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 :) | 13:23 |
| 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 | 13:24 |
| 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 | 13:25 |
| 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. | 13:26 |
| 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? | 13:27 |
| 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? | 13:28 |
| 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 | 13:29 |
| 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 | 13:30 |
| 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 | 13:32 |
| 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 | 13:33 |
| kanzure | fenn: http://heybryan.org/gitweb.cgi | 13:35 |
| kanzure | what do you think is going wrong? | 13:35 |
| kanzure | it only shows skdb | 13:35 |
| fenn | i think gitweb has to be in the same folder as biohack.git | 13:36 |
| fenn | or maybe a ln -s | 13:36 |
| 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 | 13:37 |
| 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 | 13:38 |
| 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/ | 13:39 |
| 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. | 13:40 |
| kanzure | http://heybryan.org/gitweb.cgi?p=biotech.git;a=tree;f=biotech-DIY__kanzure_2008-01-27_v1;h=ac233783b97167746ca96a34f49260b71f95453c;hb=0532022269e7dce28521ca9a8ac026a6d34f9f9f | 13:41 |
| fenn | ok i just didnt notice the subdirectories | 13:42 |
| fenn | before it was all just a big pile | 13:42 |
| 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 :( | 13:43 |
| 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!! | 13:44 |
| 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 | 13:45 |
| 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 | 13:46 |
| 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 | 13:47 |
| 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 | 13:48 |
| fenn | btw make sure you add gitweb to robots.txt | 13:49 |
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| 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 | 13:50 |
| 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 | 13:51 |
| 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 :( | 13:52 |
| fenn | i love how youtube removed the 'quality' setting so now everything plays like shit on my slow laptop | 13:53 |
| kanzure | hm, I wonder if my screen size is going to be an issue | 13:54 |
| fenn | what's the point of 'how to do a linux screencast' where 90% of the screencast is using windows programs? | 13:56 |
| kanzure | that's a good question | 13:57 |
| kanzure | I was surprised when windows was brought up | 13:57 |
| kanzure | so I closed it | 13:57 |
| kanzure | oh boy, 1 MB/sec | 13:58 |
| 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 | 14:01 |
| fenn | cis-action: i want *lower* quality though | 14:02 |
| cis-action | it's all pretty low-quailty optimized stuff | 14:02 |
| 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? | 14:03 |
| 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 | 14:04 |
| kanzure | well, this sound system stuff sucks :) | 14:29 |
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| 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? | 14:43 |
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| kanzure | well, I can get audio going out the front speakers | 15:02 |
| kanzure | from the microphone | 15:02 |
| kanzure | does that count? | 15:02 |
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| kanzure | fenn: you wouldn't happen to have a microphone, would you? | 15:32 |
| 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 | 15:33 |
| 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 | 15:34 |
| 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 | 15:35 |
| kanzure | fenn: does it work? | 15:47 |
| fenn | um, no | 15:49 |
| fenn | looking at this right now: http://alsa.opensrc.org/index.php/Record_from_mic | 15:49 |
| fenn | press tab in alsamixer to get to the capture screen | 15:50 |
| fenn | ok it works.. somehow i was pressing the space bar wrong :\ | 15:52 |
| kanzure | press tab in alsa mixer, and then what? | 15:56 |
| fenn | dont press tab, just arrow over to Mic and press space | 15:57 |
| fenn | actually, press tab twice, then arrow over to Mic and press space | 15:58 |
| fenn | you shuold see a red CAPTUR show up | 15:58 |
| fenn | now arrow over to Capture and increase the volume | 15:59 |
| fenn | have to press space on Capture too | 16:00 |
| fenn | http://fennetic.net/pub/irc/alsamixer-record.png | 16:03 |
| kanzure | looks like that for me too | 16:04 |
| kanzure | still not getting anything on hw:0,0 or hw:1,0 | 16:04 |
| 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 | 16:05 |
| 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? | 16:06 |
| kanzure | because /dev/dsp doesn't apply for some reason? | 16:07 |
| fenn | /dev/dsp is the synth | 16:07 |
| 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 | 16:08 |
| kanzure | skype? | 16:09 |
| fenn | so, this kind of problem is why alsa got invented | 16:09 |
| 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 | 16:10 |
| kanzure | is there anyway I can demand Opera does not steal me audio? | 16:11 |
| 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 | 16:13 |
| fenn | alsa doesnt have that 'device or resource busy' problem | 16:14 |
| kanzure | but I *am* using alsa | 16:14 |
| kanzure | heh' | 16:14 |
| 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 | 16:17 |
| 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 | 16:18 |
| 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 | 16:19 |
| 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 | 16:20 |
| cis-action | http://vimeo.com/1087631 | 16:21 |
| kanzure | yeah, okay, I resized | 16:21 |
| 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? | 16:22 |
| 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 | 16:23 |
| 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 | 16:24 |
| 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 | 16:25 |
| fenn | really i just think video is a poor medium for knowledge exchange | 16:27 |
| fenn | flash just aggravates the problems with it | 16:27 |
| ybit | wow, you guys have been at it for a long time over a screencast :P | 16:30 |
| fenn | ybit: note my first remark, "good luck" | 16:31 |
| 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? | 16:33 |
| 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 | 16:35 |
| 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 | 16:36 |
| fenn | cis-action: well.. you probably like podcasts too | 16:37 |
| kanzure | what type of crap is this? | 16:39 |
| kanzure | it doesn't even capture text at 640x340 | 16:39 |
| ybit | lol, this is becoming entertaining :) | 16:40 |
| parodyoflanguage | ... | 16:40 |
| 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. | 16:41 |
| parodyoflanguage | ah | 16:42 |
| parodyoflanguage | screencast == video? | 16:42 |
| kanzure | Yep. | 16:42 |
| parodyoflanguage | cool | 16:42 |
| parodyoflanguage | I don't think I'm ready for that yet :) | 16:43 |
| kanzure | For what? | 16:43 |
| 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. | 16:44 |
| 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 :) | 16:45 |
| * kanzure goes off to make the screencast. | 16:46 | |
| parodyoflanguage | A book sounds like an awesome idea. | 16:48 |
| 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 | 16:53 |
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| kanzure | crap, a 72 megabyte video? | 17:04 |
| 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 | 17:10 |
| * Biopunk waves | 17:21 | |
| Biopunk | what video don't you want to make? | 17:22 |
| kanzure | A video on how to use git. | 17:36 |
| 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." | 17:37 |
| kanzure | and other BS as if the internet only has enough space for one more book | 17:38 |
| Biopunk | "The BioTech Geek Book" is this the pimm guy? | 17:40 |
| 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/ | 17:42 |
| 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 | 17:43 |
| kanzure | I think Atilla is angry because she has a publishing deal | 17:45 |
| kanzure | http://groups.google.com/biobarcamp/ | 17:45 |
| Biopunk | (http://groups.google.com/group/biobarcamp/) | 17:48 |
| kanzure | bleah | 17:50 |
| kanzure | yes, that | 17:50 |
| Biopunk | yup pimm | 17:51 |
| Biopunk | It strikes me how small this world still is | 17:52 |
| kanzure | have you ever gone outside? | 17:53 |
| Biopunk | The aliens took me once | 17:55 |
| Biopunk | I'm hardly on the inside... you and Atilla are.. not sure there is a demand for my ideas of subculture yet | 17:56 |
| 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 | 18:01 |
| fenn | no, this is MY temporary autonomous zone! wah! | 18:05 |
| kanzure | please send that message in response to her | 18:07 |
| kanzure | that would be hillarious :) | 18:07 |
| 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? | 18:08 |
| fenn | "Attila Csordás is a research scientist in the Gene Therapy Center at Tulane University. He is the author of Pimm" | 18:09 |
| kanzure | http://www.youtube.com/watch?v=joVr-5NTE28 | 18:10 |
| kanzure | aha | 18:10 |
| fenn | were there any specific pro/con type objections? | 18:10 |
| 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 | 18:11 |
| * 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, | 18:12 |
| 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 | 18:13 |
| kanzure | it's not even really worth talking about | 18:14 |
| kanzure | but, if we have to, there's the video | 18:14 |
| 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 | 18:15 |
| 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 | 18:16 |
| 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 :( | 18:17 |
| kanzure | I guess I'll redo the video. | 18:18 |
| 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 | 18:20 |
| 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 | 18:21 |
| 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 | 18:22 |
| 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 | 18:23 |
| kanzure | maybe I'll just make a slideshow and talk | 18:24 |
| Biopunk | ;) | 18:24 |
| 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 | 18:25 |
| Biopunk | On the topic of the singularity: http://luci.ics.uci.edu/blog/archives/2006/09/ubicomp_2006_br_1.html | 18:30 |
| 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 | 18:31 |
| Biopunk | I liked the part where he talked about how writers talking about the singularity were in no particular hurry | 18:32 |
| fenn | the ones predicting a rosy future maybe | 18:33 |
| 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 | 18:34 |
| Biopunk | I thought you saw this one... he mentions splimes | 18:35 |
| kanzure | cool, I think I did well this time | 18:36 |
| * kanzure sits around waiting for it to render | 18:37 | |
| fenn | http://savannah.gnu.org/maintenance/UsingGit pretty good summary | 18:40 |
| fenn | you really need an alpha tester to see if its understandable though | 18:41 |
| fenn | i.e. not me | 18:41 |
| kanzure | meep | 18:41 |
| kanzure | uploading (again) | 18:48 |
| 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 | 18:49 |
| 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 | 18:50 |
| fenn | if its not a video you get: hyperlinks, searchability, skimmability, language translation, modifiability, etc | 18:51 |
| fenn | pretty much automatically | 18:51 |
| 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 | 18:52 |
| 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/ | 18:54 |
| 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 | 18:55 |
| 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 | 18:56 |
| kanzure | hm? | 18:58 |
| kanzure | oh, the git stuff? | 18:58 |
| 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 | 18:59 |
| 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 | 19:00 |
| 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) | 19:01 |
| 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? | 19:02 |
| kanzure | where's Enk-2? | 19:03 |
| kanzure | he's the one doing that sort of thing | 19:03 |
| kanzure | go pester him | 19:03 |
| fenn | last version is acceptable :) | 19:07 |
| kanzure | hurray | 19:07 |
| kanzure | amphetamine - it works ;-) | 19:07 |
| fenn | heh | 19:07 |
| 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? | 19:13 |
| 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 | 19:14 |
| 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 | 19:15 |
| Biopunk | yeah.. but are you planning to have separate suff in git and ind the wiki? | 19:16 |
| kanzure | no | 19:16 |
| 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 | 19:17 |
| 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 | 19:18 |
| 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 | 19:19 | |
| fenn | most consumers are idiots and can't manage their own personal data, so that's why we have webmail and google docs | 19:20 |
| -!- 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 | 19:21 |
| 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 | 19:22 |
| 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 | 19:23 |
| 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? | 19:24 |
| 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 | 19:25 |
| 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 | 19:26 |
| 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 | 19:27 |
| 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 | :-/ | 19:28 |
| Biopunk | cu | 19:29 |
| kanzure | fenn: researchers have found a way to do fluorotagging but for magnetism | 19:58 |
| kanzure | so supposedly we can come up with some super-high-resolution MRI machines and get an image of cellular resolution. | 19:59 |
| 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 | 20:06 |
| 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. | 20:09 |
| 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 | 20:10 |
| 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 | 20:13 |
| 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? | 20:14 |
| 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 | 20:15 |
| fenn | got a link? | 20:16 |
| 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 | 20:17 |
| fenn | apparently birds use something like this to navigate.. it shows up in their vision (maybe its present in retinal cells?) | 20:18 |
| Biopunk | i bet it would set of the shoplifter alarm in a supermarket | 20:19 |
| fenn | i wouldnt mind fourier-transform-vision | 20:19 |
| Biopunk | i saw a talk about functional body hacking... the woman talking had had a magnet in one of her fingertips for a while | 20:20 |
| 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 | 20:21 |
| fenn | ferromagnetic substances have a high spin, but does that mean it will absorb radio waves better than just hydrogen? | 20:22 |
| kanzure | hm | 20:23 |
| kanzure | apparently it's used to "sense the earth's gravity field" | 20:23 |
| -!- ybit [n=h@unaffiliated/ybit] has quit [Remote closed the connection] | 20:23 | |
| 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) | 20:24 |
| 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 | 20:25 |
| 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. | 20:26 |
| 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" | 20:27 |
| 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 | 20:28 |
| 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 | 20:29 |
| 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 | 20:30 |
| 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) | 20:31 |
| 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 | 20:32 |
| 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 | 20:33 |
| 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) | 20:34 |
| 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 | 20:35 |
| 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 | 20:36 |
| 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. | 20:37 |
| 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 | 20:38 |
| 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 | 20:39 |
| 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 | 20:40 |
| 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 | 20:41 |
| 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 | 20:42 |
| kanzure | aha | 20:43 |
| kanzure | so it's bullshit | 20:43 |
| kanzure | I'll stop linking to it. | 20:43 |
| kanzure | fenn: how would it do that? | 20:44 |
| kanzure | how would it incorporate *that* nucleotide (attached to the bead) more quickly? | 20:44 |
| 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 ? | 20:45 |
| 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) | 20:46 |
| 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) | 20:47 |
| 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 | 20:48 |
| 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 | 20:49 |
| 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? | 20:50 |
| kanzure | yes | 20:51 |
| 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 | 20:52 |
| 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? | 20:53 |
| 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 | 20:54 |
| 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 | 20:55 |
| 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. | 20:56 |
| 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 | 20:57 |
| 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 | 20:58 |
| 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 | 20:59 |
| 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 | 21:00 |
| 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 | 21:01 |
| 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 | 21:02 |
| fenn | hmm. plasmids get degraded continuously, so i dont really know | 21:03 |
| fenn | "it depends" | 21:03 |
| 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) | 21:04 |
| kanzure | it just seems very flimsy to me | 21:05 |
| fenn | of course its flimsy :P | 21:05 |
| kanzure | won't they die? | 21:05 |
| 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 | 21:06 |
| 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 | 21:07 |
| 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" | 21:08 |
| fenn | i'm sure they have | 21:09 |
| fenn | otherwise how would you observe polymerase activity | 21:09 |
| fenn | in vitro i guess | 21:09 |
| 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) | 21:10 |
| 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 | 21:11 |
| fenn | chinese hamster kidney | 21:12 |
| fenn | as you can see, my schooling really stuck with me | 21:13 |
| kanzure | :) | 21:13 |
| 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? | 21:15 |
| Biopunk | i think so.. i'll open it now | 21:16 |
| fenn | link spammer! | 21:17 |
| kanzure | I am a link spammer, aren't I? | 21:18 |
| 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 | 21:20 |
| Biopunk | ah.. that's a BB code | 21:21 |
| Biopunk | [youtube] id [/youtube] | 21:21 |
| Biopunk | like this: http://www.biopunk.org/how-to-use-the-board-t16.html | 21:22 |
| 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) | 21:24 |
| Biopunk | maybe is should make 'GAAAAAAA' | 21:25 |
| 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 | 21:28 |
| 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 | 21:31 |
| fenn | do you have access to a flow cytometry machine | 21:32 |
| kanzure | probably | 21:32 |
| kanzure | yes | 21:32 |
| 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 | 21:33 |
| kanzure | right | 21:34 |
| kanzure | yeah, we have one, I remember asking or seeing it | 21:34 |
| fenn | another 'basically an inkjet printer' sort of thing | 21:35 |
| kanzure | wouldn't polymerase just evolve to get around your inhibition | 21:38 |
| fenn | maybe | 21:42 |
| fenn | you could do some site-directed mutagenesis on the one you're trying to mess with though | 21:42 |
| 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 | ) | 21:44 |
| 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. | 21:45 |
| kanzure | well | 21:46 |
| kanzure | not subject to "directed evolution" experiments | 21:46 |
| fenn | mhmm i wonder about this http://en.wikipedia.org/wiki/Directed_mutagenesis | 21:47 |
| kanzure | I saw that paper in my searches. | 21:49 |
| kanzure | don't know where I put it / processed it | 21:49 |
| Biopunk | there is always lamarcism | 21:50 |
| 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 | 21:55 |
| fenn | http://seedmagazine.com/news/2008/01/redefining_genes.php | 21:56 |
| 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. | 21:58 |
| kanzure | hrm, let's turn it totally upside down | 21:59 |
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| 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 | 21:59 |
| kanzure | however, it'd be retrofitted for a different type of molecule | 22:00 |
| kanzure | one of the NTP-likes | 22:00 |
| kanzure | noserub = distributed social network project | 22:14 |
| kanzure | hrm | 22:14 |
| kanzure | http://noserub.com/ | 22:14 |
| 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 | 22:17 |
| 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. | 22:18 |
| kanzure | noninvasive: neurofeedback, fMRI, http://heybryan.org/mediawiki/index.php/Neuroimaging , rTMS, | 22:19 |
| kanzure | for physical wirings, try microelectrode arrays (electrical stimulation) | 22:19 |
| kanzure | http://heybryan.org/docs/neuro/ | 22:20 |
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| kanzure | http://heybryan.org/recursion.html for some other approaches | 22:20 |
| kanzure | I haven't significantly investigated biofeedback yet. | 22:20 |
| * kanzure wants some biophysical simulations of mutation | 22:23 | |
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| 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? | 22:27 |
| 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. :) | 22:28 |
| xp_prg2 | I heard that plastics usedthis approach | 22:30 |
| kanzure | How so? | 22:30 |
| 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 | 22:31 |
| 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 | 22:33 |
| 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 | 22:34 |
| 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 | 22:35 |
| 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 :) | 22:37 |
| kanzure | I guess we don't need to keep anything separated | 22:46 |
| kanzure | just throw everything into a giant pot | 22:46 |
| 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. | 22:47 |
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| 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 | 23:27 |
| xp_prg2 | kanzure what is that? | 23:53 |
| kanzure | xp_prg2: The A-rule is where thymine is paired to adenosine in DNA. | 23:53 |
| xp_prg2 | oh ok | 23:54 |
| kanzure | Hrm. | 23:58 |
| kanzure | So the Russian Mafia has contacted me. | 23:58 |
| kanzure | By this I mean, the Russian transhuman peoples. | 23:58 |
| 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. | 23:59 |
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