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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 | 07:04 | |
| -!- Topic set by kanzure [] [Tue Apr 29 18:54:31 2008] | 07:04 | |
| [Users #hplusroadmap] | 07:04 | |
| [ fenn ] [ nsh ] [ Phreedom] [ Vedestin] | 07:04 | |
| [ joshcryer] [ nsh-] [ Splicer ] [ ybit ] | 07:04 | |
| -!- Irssi: #hplusroadmap: Total of 8 nicks [0 ops, 0 halfops, 0 voices, 8 normal] | 07:04 | |
| -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008 | 07:04 | |
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| fenn | re: distributed bug tracker.. could stick it in a wiki layer, like /talk/ | 10:20 |
|---|---|---|
| fenn | and then have some rss jiggeryboo to notify mailing lists and watch for responses/integrate them into the wiki | 10:25 |
| fenn | (not that i know anything about rss at all) | 10:26 |
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| kanzure | http://8bitpeoples.com/ | 10:47 |
| fenn | OMG music theft! waaaaaaaa | 10:51 |
| kanzure | http://8bitcollective.com/ | 11:00 |
| kanzure | so, fenn, where've you been up to? | 11:01 |
| fenn | time phased | 11:01 |
| kanzure | sleep? | 11:01 |
| fenn | yea | 11:02 |
| kanzure | I have this nasty Best Buy gift card, somebody suggested I get an Asus EEEPC 9000. | 11:02 |
| kanzure | erm, 900. | 11:02 |
| Vedestin | do it | 11:02 |
| kanzure | do it? :) | 11:02 |
| kanzure | my hand is larger than the screen | 11:02 |
| kanzure | http://images.google.com/images?client=opera&rls=en&q=EEEPC%20900&sourceid=opera&ie=UTF-8&oe=utf-8&um=1&sa=N&tab=wi | 11:03 |
| Vedestin | yeah, they're so portable | 11:03 |
| kanzure | right, but you can't type :) | 11:04 |
| Vedestin | i'm good with my hans | 11:04 |
| Vedestin | *hands.... | 11:04 |
| Vedestin | hmmm...maybe im not | 11:04 |
| kanzure | here we go - http://jimmyauw.com/wp-datajim/personal/156_eeepc.jpg | 11:04 |
| kanzure | fenn, so I went to the maker faire volunteer meetup, and apparently you exited as I was telling everyone how it went | 11:06 |
| kanzure | somehow I ended up being appointed the one to do community collaboration and so on | 11:06 |
| kanzure | jackpot? | 11:07 |
| fenn | ah, my router has been crashing a lot for some reason | 11:07 |
| fenn | obligation? | 11:07 |
| fenn | um.. clout source? | 11:07 |
| kanzure | clout? | 11:07 |
| fenn | "listen to me, mister, i'm the maker faire community collaboration executive!" | 11:07 |
| kanzure | hehe | 11:08 |
| kanzure | don't know | 11:08 |
| kanzure | but it sounds important, right? | 11:08 |
| kanzure | I've been talking with the Austin electric vehicle group, we're thinking of a badass electric vehicle carpooling stampede to show up | 11:08 |
| Vedestin | the longer a title is, the less important that position is | 11:09 |
| fenn | so, "janitor" must be pretty high up eh | 11:10 |
| fenn | i've got all the keyssss | 11:11 |
| kanzure | some people do in fact consider the janitor to be pretty high up there | 11:13 |
| kanzure | they are allowed to roam and clean up all of the messes, get to meet with everyone who doesn't avoid them right off | 11:13 |
| kanzure | and frankly, I've never seen anybody actively *avoid* talking with a janitor that says hello | 11:13 |
| kanzure | hahah, on an off-topic note - http://www.8bitporno.com/ - which I guess was bound to show up in the search results ... 8bitmusic -> 8bitporno, right? | 11:14 |
| kanzure | fenn, do you happen to remember the technical terminology behind 'cloning' (not actual cloning, but in mol-bio labs), subcloning, PCR, etc.? | 11:15 |
| kanzure | I've apparently had this sort of a, gap, and even though it's a simple matching problem I suck | 11:16 |
| kanzure | http://heybryan.org/mediawiki/index.php/Bioreactors | 11:16 |
| kanzure | the todo section; I lack the right terminology | 11:16 |
| kanzure | can you help? | 11:16 |
| fenn | er, explain more verbosely what you want to know? | 11:16 |
| kanzure | well, where would 'subcloning' be on that outline that I have on the wiki page? | 11:17 |
| kanzure | hm, Wikipedia is helpful actually - 'The simple transfer of of a cloned fragment of DNA from one vector to another.' | 11:17 |
| kanzure | why not just replicate the vectors though | 11:18 |
| kanzure | why transfer from parent plasmid to destination plasmid? | 11:18 |
| fenn | The terms "recombinant DNA technology," "DNA cloning," "molecular cloning,"or "gene cloning" all refer to the same process: the transfer of a DNA fragment of interest from one organism to a self-replicating genetic element such as a bacterial plasmid. | 11:18 |
| fenn | its more like, you have this flounder and want to extract its antifreeze gene | 11:19 |
| fenn | so you chop up its genome and insert pieces into plasmids until you get a recombinant bacterial colony that has the gene | 11:20 |
| kanzure | oh, so they're doing it all at once | 11:20 |
| kanzure | i.e., they don't know which plasmids in advance are working? | 11:20 |
| kanzure | entailing lots of selection experiments? | 11:21 |
| fenn | right | 11:21 |
| kanzure | chop up genome -> insert pieces (you don't know which) into new plasmids -> good luck figuring out which cells were competent, which cells actually took up the plasmids, and then which ones are actually expressing what you care about | 11:21 |
| kanzure | fun times | 11:21 |
| kanzure | of course, 'chop up genome' can be replaced with 'dump your oligos' | 11:22 |
| fenn | you can sequence the plasmid and study it, then insert/remove functions like antibiotic resistance or expression factors | 11:22 |
| kanzure | which plasmid? | 11:22 |
| kanzure | how would you select a single plasmid? | 11:22 |
| fenn | the one that you selected for | 11:22 |
| kanzure | okay | 11:22 |
| kanzure | heh | 11:22 |
| fenn | um.. well, you can find the colony expressing a particular protein with monoclonal antibodies (fluorescence tagged) | 11:22 |
| fenn | so then it'll glow | 11:22 |
| kanzure | why would it glow when the antibody attaches? | 11:23 |
| fenn | because it's the only place where there's antibodies | 11:23 |
| kanzure | oh, concentration? | 11:23 |
| fenn | signal to noise ratio stuff | 11:23 |
| kanzure | ok | 11:23 |
| kanzure | hrm | 11:23 |
| fenn | i'm sure there's other ways to do it | 11:23 |
| kanzure | now I just need some googleable terms that I can wrok off of | 11:23 |
| kanzure | the diybio.org guys didn't like my idea of using aptamers to do protein purification, they like affinity chromatography (phase change chromatography) | 11:24 |
| fenn | recombinant protocol | 11:24 |
| kanzure | but I'm still iffy on the hardware setup to do it | 11:24 |
| kanzure | (to do affinity chromatography) | 11:24 |
| fenn | what's wrong with aptamers? | 11:24 |
| kanzure | hold on | 11:24 |
| kanzure | http://groups.google.com/group/diybio/tree/browse_frm/thread/b5adcd35fd1072c/f05cfbf25e0b1125?rnum=1&_done=%2Fgroup%2Fdiybio%2Fbrowse_frm%2Fthread%2Fb5adcd35fd1072c%3F#doc_635acdeff7be33a7 | 11:25 |
| fenn | depends how much you're purifying i guess | 11:25 |
| kanzure | the idea was to use a bioreactor/tank-thing where you have the cells produce the proteins and metabolites and chemicals that you need to do the recombinant protocols over again | 11:25 |
| kanzure | i.e. to make the tank somewhat self-replicating (except for the scrap metal you'd need) | 11:25 |
| fenn | ok, so good so far | 11:26 |
| fenn | is taq polymerase patent expired yet? | 11:27 |
| kanzure | wtf?? | 11:27 |
| kanzure | srsly? | 11:27 |
| fenn | eh? | 11:27 |
| fenn | everything's patented, even genomes | 11:27 |
| kanzure | in the link the guy mentions that aptamers are challenging due to the specificity requirements of the backbone, but I think this could be solved with computational models, right? and then building the molecule with an oligo/DNA/RNA synthesizer | 11:27 |
| kanzure | fenn: I don't think we care if it's patented, in the end | 11:28 |
| kanzure | who gives them a monopoly on life? | 11:28 |
| fenn | well, it affects what sort of organization you're able to make | 11:28 |
| kanzure | I suppose. | 11:28 |
| fenn | i.e. hard to get grants from "respected" organizations if you're flagrantly violating patents | 11:28 |
| kanzure | we'll solve that later | 11:29 |
| kanzure | I always thought that PCR was to amplify the number of DNA molecules | 11:29 |
| kanzure | however, #biology scoffed at me when I mentioned that | 11:29 |
| fenn | why did they scoff? | 11:29 |
| kanzure | because I was wrong | 11:29 |
| kanzure | let me remember | 11:30 |
| fenn | PCR is to amplify a sequence of DNA | 11:30 |
| fenn | you have to know the sequence (~10-20bp) at both ends of the sequence | 11:30 |
| fenn | and its only good for like 2kbp | 11:30 |
| kanzure | why do you need to know the ends of the seq? | 11:31 |
| fenn | otherwise the enzyme won't stick | 11:31 |
| kanzure | what enzyme? | 11:31 |
| fenn | also it allows you to specify which sequence to amplify, which is more important | 11:31 |
| fenn | pol-III i think? its "taq polymerase" | 11:31 |
| kanzure | but do you have an enzyme to bind with any 20 bp seq? | 11:32 |
| kanzure | that caps the strand you want to amplify? | 11:32 |
| fenn | pol-I | 11:32 |
| fenn | um.. an enzyme to bind to a specific dna sequence? i guess some transcription promoters could qualify.. | 11:33 |
| fenn | but in general, DNA repair enzymes recognize specific features of dna, based on how the covalent bonds or the lack of them alters the structure | 11:34 |
| kanzure | I Mean, why do you need to know the seq at both ends of your main sequence in your pool of DNA that you want to amplify ?? I mean, what difference does it make if you know bp #5 versus not knowing bp #8 ? does this influence which enzyme you choose in your experiment? | 11:35 |
| fenn | http://faculty.uca.edu/~johnc/thymine%20dimer%20photolyase.jpg | 11:36 |
| fenn | the pol-I enzyme (taq pol) is supposed to fill in the gaps after some other repair enzyme cuts out the damaged DNA | 11:38 |
| fenn | so, it can't start writing a new strand, it can only add on to an existing strand | 11:39 |
| fenn | the sequences at the ends, "primers" allow it to begin writing the new strand | 11:39 |
| fenn | here's a typical animation of the process: http://youtube.com/watch?v=_YgXcJ4n-kQ | 11:41 |
| ybit | http://www.marshallbrain.com/manna1.htm thoughts on the Manna system and potential robot wars would be nice to hear | 11:44 |
| fenn | they never showed us any animations when i was in college, can you believe that? | 11:44 |
| ybit | thoughts/feedback* | 11:44 |
| fenn | ybit: what about it? | 11:45 |
| fenn | seen SWORDS robots? coming to a neighborhood near you | 11:45 |
| ybit | i wonder how the manna system might evolve and how that may be prevented | 11:46 |
| fenn | i think the manna system already exists, its called 'business metrics' | 11:46 |
| fenn | if you arent meeting the quarterly profit expectations, you get removed from the mutual fund | 11:47 |
| ybit | i hadn't seen it | 11:47 |
| fenn | i'd actually prefer a robot store with just one demo model of each item.. then you add it to your 'virtual shopping cart' and the conveyor belt spits out a box with all the stuff as you exit the store | 11:48 |
| fenn | would be much smaller, better overall | 11:49 |
| fenn | this "u-check-out" stuff is just lame | 11:49 |
| fenn | anyway, marshall's point is that capitalism is fucked, which everyone already knew | 11:50 |
| kanzure | fenn: I still don't know why it matters whether or not the cap string of bp is AAAAAAAAA versus AAAAAATAAAAAA and what that would mean for my enzyme selection when trying to do PCR... | 11:51 |
| fenn | oh.. the primer sequence can be off somewhat and still work | 11:52 |
| fenn | there's rules/equations for determining how well a given primer and template will work together | 11:52 |
| ybit | i found it fascinating... well, i'm off to work | 11:52 |
| fenn | ybit: yeah i just read that entire site last week | 11:53 |
| fenn | his writing needs some work, the ideas are good though | 11:53 |
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| kanzure | fenn: I still haven't read anything on marshallbrain.com | 11:53 |
| fenn | a spectrophotometer seems like such an easy thing to make | 11:58 |
| fenn | its just a prism, a white light source, and a detector | 11:59 |
| fenn | i guess most scientific gear is like that, real simple once you understand how it works | 12:00 |
| fenn | like the RT pcr thermocycler - a lightbulb and a fan | 12:00 |
| kanzure | http://synbiosafe.eu/forum/viewtopic.php?f=18&t=47 "Based on the current state-of-the-art, please let us know what kind of recommendations you would like to give in order to ensure a safe, secure and ethically acceptable development in synthetic biology." ugh | 12:02 |
| fenn | what's "development" mean in this context? | 12:02 |
| kanzure | fenn, there are some spectroscopes on the net that are just cereal boxes + sticks + a CD + flashlight | 12:02 |
| kanzure | I don't know what they mean by "acceptable". Do I have to approve 'synthetic biology' in order to let it occur? | 12:03 |
| fenn | i dont think a flashlight would be a good light source, since most of the wavelengths you're interested in are UV | 12:03 |
| kanzure | http://ioannis.virtualcomposer2000.com/spectroscope/toyspectroscope.html | 12:03 |
| kanzure | ah, he uses many different light sources for testing | 12:03 |
| fenn | i think they just wrote some copy that sounded good | 12:04 |
| fenn | 'ethically acceptable' means, nobody picketing on your lawn or throwing bricks through the window? | 12:05 |
| fenn | wow that cd spectroscope is pretty good | 12:07 |
| kanzure | I don't even know how to fix it, but I would desperately like the EU or somebody like that to focus on developing distributed tech for the enhancement of personal immune systems and so on | 12:09 |
| kanzure | not to march around saying "This is wrong, blah blah blah" ;-) but to actually focus on testing face masks, hvac filtration tech, water purification, desalinization, artificial immune systems (made up of microbes, no less), and deploying tools to keep people armed to the teeth with knowledge | 12:10 |
| fenn | the LED spectrums are very broad, looks like they would be a good light source | 12:10 |
| kanzure | and it's solid state :) hurray | 12:11 |
| kanzure | yep | 12:11 |
| fenn | what's an artificial immune system made from? | 12:11 |
| Vedestin | nanobots! | 12:14 |
| Vedestin | with lasers! | 12:14 |
| Vedestin | zap! zap! take that cancer! | 12:14 |
| kanzure | "Now, the basic problem is this: the problem of being finite is an infinitely frustrating one; how can this be?" | 12:16 |
| kanzure | hahah indeed! on guard! | 12:16 |
| kanzure | nah, I mean to import from other experimental immune systems in the lab | 12:16 |
| kanzure | so this might consist of antibodies, or possibly of microbes etc. | 12:17 |
| fenn | actually antibody serum has been in use for about a hundred years | 12:19 |
| fenn | typically used for snake bites | 12:20 |
| kanzure | so, I'm heading out to the lab soon | 12:21 |
| kanzure | need to prepare or make myself decent | 12:21 |
| kanzure | a shave? | 12:21 |
| Vedestin | shave couldnt hurt | 12:22 |
| kanzure | hm | 12:37 |
| kanzure | http://heybryan.org/~bbishop/cgi-bin/blosxom.cgi | 12:37 |
| kanzure | "Two paths to the singularity" | 12:37 |
| kanzure | Gershenfeld v. Kuzweil | 12:37 |
| kanzure | An interesting development ... | 12:37 |
| kanzure | IEEE Spectrum issue on the Singularity? why the hell wasn't I invited? | 12:38 |
| kanzure | http://www.spectrum.ieee.org/jun08/6313 | 12:39 |
| kanzure | Well before Gershenfeld and Kurzweil's different visions of the future merged, their thoughts came together to influence the mind of David Dalrymple, now age 16 and an MIT graduate student. Dalrymple began corresponding with Gershenf | 12:39 |
| kanzure | jld;sj;klasdf;jafjkl;asd | 12:39 |
| kanzure | Dalrymple :) | 12:39 |
| kanzure | who, I might remind others, showed up in here a few months ago | 12:40 |
| kanzure | hahah | 13:15 |
| kanzure | David didn't know he actually got in | 13:15 |
| kanzure | they didn't tell him | 13:15 |
| fenn | in what, the article? | 13:20 |
| kanzure | (2008-06-02 12:25:40) David Dalrymple: fabuntu is Ed Baafi's pet project, isn't it? | 13:21 |
| kanzure | yeah | 13:21 |
| fenn | i'm sure he shows up in lots of magazine articles, for "freak show value" | 13:21 |
| fenn | spectrum is a big deal i guess | 13:22 |
| fenn | they dont say anything about distributed sensor networks :( | 13:24 |
| fenn | you can use "gershenfeld reality" style fungible computing to build up a highly detailed realtime model of reality, and then explore that with augmented reality interfaces | 13:24 |
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| fenn | not VR that "compete with and ultimately replace real reality" | 13:25 |
| fenn | g'dammit | 13:25 |
| [Users #hplusroadmap] | 13:39 | |
| [ fenn] [ nsh] [ Phreedom] [ Vedestin] [ ybit] | 13:39 | |
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| fenn | blech. the spectrum writers just like to take a big shit on anything that doesn't fit their hegemony | 13:40 |
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| kanzure | fenn: you around? | 17:36 |
| kanzure | we're making the Elowitz multi-protein/DNA/RNA oscillator but as one dsDNA molecule | 17:36 |
| kanzure | it's just a different backbone for the repressilator model | 17:37 |
| nsh | repressilator? | 18:01 |
| kanzure | nsh: it goes up, down, and up again | 18:05 |
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