--- Day changed Mon Jun 02 2008
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07:04 -!- 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]
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07:04 [ fenn     ] [ nsh ] [ Phreedom] [ Vedestin] 
07:04 [ joshcryer] [ nsh-] [ Splicer ] [ ybit    ] 
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07:04 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
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10:20 < fenn> re: distributed bug tracker.. could stick it in a wiki layer, like /talk/
10:25 < fenn> and then have some rss jiggeryboo to notify mailing lists and watch for responses/integrate them into the wiki
10:26 < fenn> (not that i know anything about rss at all)
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10:47 < kanzure> http://8bitpeoples.com/
10:51 < fenn> OMG music theft! waaaaaaaa
11:00 < kanzure> http://8bitcollective.com/
11:01 < kanzure> so, fenn, where've you been up to?
11:01 < fenn> time phased
11:01 < kanzure> sleep?
11:02 < 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
11:03 < 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
11:04 < 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
11:06 < 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
11:07 < 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!"
11:08 < 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
11:09 < Vedestin> the longer a title is, the less important that position is
11:10 < fenn> so, "janitor" must be pretty high up eh
11:11 < fenn> i've got all the keyssss
11:13 < 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
11:14 < 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?
11:15 < kanzure> fenn, do you happen to remember the technical terminology behind 'cloning' (not actual cloning, but in mol-bio labs), subcloning, PCR, etc.?
11:16 < 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?
11:17 < 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.' 
11:18 < 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. 
11:19 < fenn> its more like, you have this flounder and want to extract its antifreeze gene
11:20 < 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?
11:21 < 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
11:22 < 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
11:23 < 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
11:24 < 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
11:25 < 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)
11:26 < fenn> ok, so good so far
11:27 < 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
11:28 < 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
11:29 < 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
11:30 < 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
11:31 < 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"
11:32 < 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
11:33 < fenn> um.. an enzyme to bind to a specific dna sequence? i guess some transcription promoters could qualify..
11:34 < 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
11:35 < 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?
11:36 < fenn> http://faculty.uca.edu/~johnc/thymine%20dimer%20photolyase.jpg  
11:38 < fenn> the pol-I enzyme (taq pol) is supposed to fill in the gaps after some other repair enzyme cuts out the damaged DNA
11:39 < 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
11:41 < fenn> here's a typical animation of the process: http://youtube.com/watch?v=_YgXcJ4n-kQ
11:44 < 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*
11:45 < fenn> ybit: what about it?
11:45 < fenn> seen SWORDS robots? coming to a neighborhood near you
11:46 < 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'
11:47 < fenn> if you arent meeting the quarterly profit expectations, you get removed from the mutual fund
11:47 < ybit> i hadn't seen it
11:48 < 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
11:49 < fenn> would be much smaller, better overall
11:49 < fenn> this "u-check-out" stuff is just lame
11:50 < fenn> anyway, marshall's point is that capitalism is fucked, which everyone already knew
11:51 < 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...
11:52 < 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
11:53 < fenn> ybit: yeah i just read that entire site last week
11:53 < fenn> his writing needs some work, the ideas are good though
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11:53 < kanzure> fenn: I still haven't read anything on marshallbrain.com
11:58 < fenn> a spectrophotometer seems like such an easy thing to make
11:59 < fenn> its just a prism, a white light source, and a detector
12:00 < 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
12:02 < 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
12:03 < 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
12:04 < fenn> i think they just wrote some copy that sounded good
12:05 < fenn> 'ethically acceptable' means, nobody picketing on your lawn or throwing bricks through the window?
12:07 < fenn> wow that cd spectroscope is pretty good
12:09 < 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
12:10 < 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
12:11 < kanzure> and it's solid state :) hurray
12:11 < kanzure> yep
12:11 < fenn> what's an artificial immune system made from?
12:14 < Vedestin> nanobots!
12:14 < Vedestin> with lasers!
12:14 < Vedestin> zap! zap! take that cancer!
12:16 < 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
12:17 < kanzure> so this might consist of antibodies, or possibly of microbes etc.
12:19 < fenn> actually antibody serum has been in use for about a hundred years
12:20 < fenn> typically used for snake bites
12:21 < 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?
12:22 < Vedestin> shave couldnt hurt
12:37 < 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 ...
12:38 < kanzure> IEEE Spectrum issue on the Singularity? why the hell wasn't I invited?
12:39 < 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 :)
12:40 < kanzure> who, I might remind others, showed up in here a few months ago
13:15 < kanzure> hahah
13:15 < kanzure> David didn't know he actually got in
13:15 < kanzure> they didn't tell him
13:20 < fenn> in what, the article?
13:21 < 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"
13:22 < fenn> spectrum is a big deal i guess
13:24 < 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
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13:25 < fenn> not VR that "compete with and ultimately replace real reality"
13:25 < fenn> g'dammit
13:39 [Users #hplusroadmap]
13:39 [ fenn] [ nsh] [ Phreedom] [ Vedestin] [ ybit] 
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13:40 < fenn> blech. the spectrum writers just like to take a big shit on anything that doesn't fit their hegemony
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17:36 < kanzure> fenn: you around?
17:36 < kanzure> we're making the Elowitz multi-protein/DNA/RNA oscillator but as one dsDNA molecule
17:37 < kanzure> it's just a different backbone for the repressilator model
18:01 < nsh> repressilator?
18:05 < kanzure> nsh: it goes up, down, and up again
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