--- Day changed Wed May 27 2009
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01:28 < fenn> heh "DNA + 151 rum"
01:28 < fenn> inosine is already a common additive
01:34 < fenn> zoinks
01:34 < fenn> '' reader One Comment 
01:34 < fenn> 70GB PDF library workflow on OSX
01:34 < fenn>  I have a 70GB library of textbooks and technical journal articles in (mostly) PDF format.
01:34 < fenn> (mac cowell)
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01:36 < fenn> why are microsd cards all black? you cant label the damn things so they're near impossible to tell apart
01:39 < genehacker> because then you lose the card easier and have to buy more
01:39 < genehacker> otherwise they'd be fluourescent yello
01:40 < genehacker> I need to find some SD cards that have some pictures....
01:41 < genehacker> otherwise I have to take apart my old computer and figure out how to get the data off it...
01:48 < fenn> hmm those holographic data cards were fluorescent yellow
01:49 < fenn> but a micro SD card holds more
01:49 < fenn> and the reader costs 10,000 times less
01:51 < fenn> http://en.wikipedia.org/wiki/Holographic_Versatile_Card
01:56 < fenn> OLPC display looks way better than the kindlee
01:59 < fenn> hmm part of that is because it zooms properly
02:04 < fenn> for "the standard" in typesetting programs, LaTeX output sure looks like crap
02:05 < fenn> maybe it's just whatever font is installed as default on (all of) my computers (ever) but the text is all humpty dumpty looking, the tops and bottoms are not at the same height and the letters are different size
02:05 < genehacker> I think I need to read more about the connection machine
02:05 < genehacker> heck I think I saw one of them...
02:07 < fenn> i think it's "computer modern" that looks the worst
02:08 < fenn> genehacker: big black box with red led's all over the front
02:08 < fenn> "you can't miss it"
02:09 < genehacker> oh it was just the frame it seems
02:09 < fenn> quite possibly the sexiest computer case ever designed
02:09 < genehacker> http://www.computerhistory.org/collections/accession/102691297
02:09 < genehacker> no the sexiest computer case ever designed was this one supercomputer
02:09 < fenn> OH YEAH?
02:10 < genehacker> it glowed red
02:10 < genehacker> it looked like a casemod, a casemod as tall as a man
02:11 < genehacker> yikes, space could be a whole bunch of randomly connected cellular automata
02:12 < fenn> now you must do penance by bashing your forehead with "new kind of science" ten thousand times a day
02:13 < genehacker> no I don't think you get it
02:13 < fenn> why not?
02:13 < genehacker> my worst worry is that the universe is a screensaver
02:13 < fenn> i was thinking about this stuff before you were born :P
02:15 < genehacker> heck I've ran cellular automata that form random networks capable of sustaining waveforms
02:15 < fenn> about the only response i got was "well, so what if it is?" from my brother
02:15 < fenn> you have?
02:15 < genehacker> I just hope I didn't make anything sentient
02:15 < genehacker> well  this is probably just crazy talk
02:15 < fenn> i'm going to have to arrest you for violating intergalactic law
02:16 < fenn> hold still while we send a ship to your dimension
02:16 < genehacker> well then how do I know you didn't accidently create a sentient entity just by breathing?
02:17 < genehacker> I think I need to read more about cellular automata
02:18 < genehacker> damn fluid dynamics just using cubes that can move in 6 directions
02:19 < genehacker> heh I wonder If I could implement that in DNA...
02:22 < fenn> can cubes move in more than 6 directions?
02:23 < genehacker> http://www.cs.washington.edu/homes/ruzzo/
02:23 < genehacker> not here
02:25 < fenn> hmm i wonder why max used the word 'ultrahuman' instead of just 'superhuman'
02:25 < fenn> doesn't ultra mean "last"?
02:26 < genehacker> because it is ultraawesome
02:26 < fenn> it should have been "hyperhuman" following the typical progression of superlatives
02:26 < fenn> am i supposed to trademark that now?
02:28 < fenn> genehacker: how much truth behind that page?
02:30 < genehacker> none unfortunately
02:33 < fenn> no time cube for you then
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03:22 < fenn> huh. danny hillis from 1998 "Why Y2K (as we experts so fondly call it) instead of bio-terrorism, the next energy crisis, or the return of the swine flu?"
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07:31 < kanzure> "I'm Mac Cowell. I'm an amateur biologist. I'm a part of diybio.org. I'm interested in synthetic biology and refactoring and reengineering existing biological tools and techniques to be cheaper, easier, safer, and more accessible."
07:31 < kanzure> sounds untrue :/
07:32 < kanzure> oh well. /me goes off to hop a bus.
07:39 < kanzure> fenn: joseph jackson seems to think that he's on a "social mission" more than anything else.
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08:24 < splicer> fenn: sthf = Svenska TransHumanistForbundet, The swedish transhumanist association
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10:35 < kanzure> "Reminds me of those experiments that we used to to do in cub scouts - sticking a small mirror onto a thin sheet of clingfilm and watching how sound waves changed the direction of reflected light - to demonstrate how sound was just air moving rapidly."
10:40  * drazak_ never heard of that
10:41 < kanzure> isn't that a photo-microphone or something?
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11:08 < kanzure> http://openwetware.org/index.php?title=DIYbio/FAQ&action=history
11:08 < kanzure> why doesn't anybody else edit it
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11:37 < kanzure> not bad
11:37 < kanzure> http://en.wikipedia.org/wiki/Oligonucleotide_synthesis
11:37 < kanzure> I think it's time to re-read wikipedia
11:37 < kanzure> yay it has references
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11:44 < kanzure> ^ Schulhof, J. C.; Molko, D.; Teoule, R. The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups. Nucleic Acids Res. 1987, 15, 397-416.
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12:16 < kanzure> synthetic neurobiology "labcast" from ed boyden: http://labcast.media.mit.edu/?p=63
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12:50 < ultraleibniz> I like this.
12:50 < ultraleibniz> http://heybryan.org/books/papers/www/biochem118/cmgm.stanford.edu/biochem118/Papers/
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13:07 < drazak_> "Jim in four weeks created the GigAssembler by working night and day,"
13:07 < drazak_> Dr. Haussler said. "He had to ice his wrists at night because of the
13:07 < drazak_> fury with which he created this extraordinarily complex piece of
13:07 < drazak_> code."
13:11 < katsmeow-afk> the odor of overheated flesh permeated the dorm facility.....
13:11 < xp_prg> kanzure I don't understand why it is hard to assemble dna
13:11 < katsmeow-afk> the devoted gathered is quiet adoration outside in the fields.....
13:12 < katsmeow-afk> his Name was spoken in respectfully hushed tones, with bowed heads.....
13:13  * katsmeow-afk stops now
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13:26 < kanzure> xp_prg: it's more of an art of statistis
13:26 < kanzure> *statistics
13:26 < kanzure> because you need to find overlapping pieces of the genome
13:26 < kanzure> you don't sequence everything linearly, you sequence it in chunks
13:26 < kanzure> and those chunks are out of order
13:30 < drazak_> katsmeow-afk: that was muad'dib, not Jim
13:30 < drazak_> :P
13:32 < kanzure> his Name was spoken in respectfully hushed tones, with bowed heads...
13:32 < kanzure> At long last the creator spoke and he was vastened, and all was Good.
13:33 < kanzure> 'Avast, ye heathen mortals! There be code to conquer, sources to write.'
13:33 < kanzure> And the good people mumbled amongst themselves in awe, for before them stood a God--
13:33 < kanzure> vanishing, He left them all with the most beautiful program ever
13:34 < kanzure> written completely in LISP and without comments and was consequently utterly useless.
13:34 < kanzure> a big thanks goes to the big G.
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14:12 < kanzure> er, so, even in my dreams I'm promising people I'll write code for them for different things
14:12 < kanzure> the latest one was something about writing a hierarchical tournament generator thingy for a coach
14:13 < kanzure> "you're doing that by hand? gah!"
14:18 < drazak_> you, my friend, need to meet randall monroe
14:47 < kanzure> have you met him?
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15:40 < genehacker> kanzure?
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16:00 < kanzure> genehacker: yes?
16:08 < kanzure> genehacker: do you have all of the references to KSRM yet?
16:12 < kanzure> fenn: how many metalworking/machine shops would you estimate have an actual inventory list? have you seen enough to get a good bayesian clue?
16:13 < kanzure> I'm thinking of telling [AustinMetalworkingEtc] that if any of them buy me lunch, I'll type up their inventory for them :p
16:29 < kanzure> huh?
16:29 < kanzure> http://en.wikipedia.org/wiki/Single_Molecule_Real_Time_Sequencing
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16:43 < kanzure> "The ZMW holes are ~70nm in diameter and ~100nm in depth. Due to the behavior of light when it travels through a small aperture, the optical field decays exponentially inside the chamber [4]. The observation volume within an illuminated ZMW is ~20 zeptoliters (20 X 10-21 liters). Within this volume, the activity of DNA polymerase incorporating a single nucleotide can be readily detected."
16:43 < kanzure> http://heybryan.org/books/papers/craighead/ for the papers & wikipedia article
16:44 < kanzure> er, that was 1E-21 not 10-21 
16:46 < kanzure> fenn: sounds like they have to immobilize the polymerase
16:46 < genehacker> references?
16:46 < genehacker> huh?
16:46 < kanzure> genehacker: in the link
16:46 < kanzure> http://heybryan.org/books/papers/craighead/ for the papers & wikipedia article
16:46 < kanzure> "The Pacific BiosciencesTM company expects to commercialize the SMRTTM sequencing in 2010 or 2011. The prototype of the SMRTTM chip contains 1000 ZMW holes that allow the parallelized DNA sequencing. Each of the ZMW holes produces approximately 1,500 bp(base pair)in read lengths at the speed of 10 bp per second."
16:46 < kanzure> I wonder if we could make it before 2010
16:48 < genehacker> me two
16:48 < genehacker> I wonder if we could sell it in china or some place with lax copyright laws like hong kong
16:48 < kanzure> you mean patent laws
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16:51 < kanzure> what was the size of the smallest genome again? something like 600 kbp ?
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16:53 < kanzure> 580,073
16:56 < genehacker> is the size of the mycoplasma genitalium genome
16:56 < genehacker> in BP
16:58 < kanzure> http://en.wikipedia.org/wiki/Talk:Single_Molecule_Real_Time_Sequencing#Application
16:58 < kanzure> made a comment about the fishyness of it all
17:01 < genehacker> so what were you saying  before 580,073/
17:02 < kanzure> was just trying to remember the size of the genome of mycoplasma genitalium 
17:02 < kanzure> because I was pointing out that it's the only whole genome that the ZWT method or whatever could sequence with 1k holes, 10 bp/sec, and 1.5k bp max per hole.
17:10 < fenn> 1000 holes seems too few
17:10 < kanzure> "while you're down there", you might as well bother with some more
17:10 < fenn> katsmeow-afk: http://www.engadget.com/2009/04/15/solaren-corp-to-supply-california-with-space-based-solar-power/
17:11 < fenn> katsmeow-afk: note the use of concentrating mirrors on solar cells
17:11 < fenn> of course i'm highly skeptical it will actually get built
17:14 < kanzure> hm. so it turns out that time warner cable doesn't like me hosting stuff on my servers.
17:14 < kanzure> I have a 2 second lag in this channel, and I can hardly load anything over the web
17:15 < kanzure> and I think people are downloading the low-cost PCR book from the server
17:16 < fenn> yep
17:16 < fenn> it seems they just degrade your connection rather than doing something sensible like traffic shaping
17:17 < kanzure> they do that for torrenting methinks
17:17 < fenn> that = what?
17:17 < kanzure> although I'm not sure, a lot of this is me guessing and having bad experiences
17:17 < kanzure> shaping for torrenting
17:17 < fenn> yeah probably
17:17 < kanzure> although it might only be for specific ports for torrenting, I haven't tried using some other port yet
17:17 < fenn> anyway, it shouldn't ever drop 70% of packets to google.com
17:17 < fenn> try encrypted torrent packets only
17:18 < fenn> random port + encryption whee.. its like war games
17:18 < kanzure> oh, I know what I'll do 
17:18 < kanzure> I'll host it on the sata server
17:18 < fenn> no wai!
17:18 < kanzure> it's not like he's not already doing something quasi-illegal by using campus resources to host the server
17:18 < fenn> how is that illegal?
17:18 < fenn> or even quasi-illegal
17:18 < kanzure> using campus resources for a business?
17:18 < kanzure> isn't that a no-no?
17:19 < fenn> i thought that was the whole point :3
17:19 < fenn> see 'the kept university' etc etc
17:19 < kanzure> nah, uni just sells out poor souls to already established corporations
17:19 < kanzure> anyway
17:20  * kanzure goes to look at the ZWT papers
17:21 < kanzure> wonder if an immobilized polymerase can be used to electrically detect whether or not it has a certain base in its complementary hole
17:21 < kanzure> er
17:21 < kanzure> how is it that after all of this time I still do not know the precise mechanisms of DNA pol enzymes?
17:21 < fenn> it seems 'sim city' has more influence on public policy than decades of space energy research
17:22  * fenn mumbles something about arcologies
17:22 < kanzure> fenn: btw, I'm willing to make a deal with you
17:22 < fenn> let's make a deal!
17:22 < kanzure> if you stop pretending to know japanese, I'll stop pretending to know LISP
17:22 < kanzure> :p
17:22 < fenn> well at least i dont bother you with japanese on a daily basis
17:22 < kanzure> would you?
17:22 < fenn> um, no
17:23 < kanzure> what?
17:23 < fenn> huh?
17:23 < kanzure> do you or do you not bother with japanese on a daily basis?
17:23 < fenn> do not
17:23 < kanzure> fooey
17:24 < fenn> genehacker: here's your homework for today http://www.longnow.org/views/essays/articles/ArtCompSciNG.php
17:25 < genehacker> fenn I'm sewing right now
17:27 < kanzure> hm. maybe I knew how polymerase truly worked at one point?
17:27 < kanzure> http://heybryan.org/mediawiki/index.php/Polymerase
17:27 < kanzure> "A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis"
17:28 < genehacker> btw how do immune cells synthesize different antibodies?
17:29 < kanzure> I would suggest picking up a good immunology book from the server :p
17:30 < fenn> sequence shuffling
17:30 < fenn> it's really quite interesting'
17:33 < genehacker> http://www.ncbi.nlm.nih.gov/protein/193885324?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum
17:33 < genehacker> how does that immunotherapy stuff work?
17:37 < genehacker> that seems like it would be a rather handy sequence to know...
17:37 < genehacker> delightful
17:37 < genehacker> opera has flash failure too
17:37 < kanzure> what did you do?
17:38 < fenn> i love how in that story craig venter gives the professor (haussler) all the credit
17:39 < genehacker> so if we synthesize and boot up the mycoplasma laboratorium genome...
17:39 < genehacker> will he give us credit for making the first synthetic lifeform
17:39 < fenn> no
17:40 < fenn> the point was that the professor didnt do anything, it was his mysterious grad student
17:41 < genehacker> oh
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17:44 < kanzure> um, why aren't we folding proteins around nanowire support thingies
17:45 < kanzure> around scaffolds
17:45 < genehacker> ???
17:45 < kanzure> you'd be able to stuff stuff inside of the proteins and try to evolve for preserved functionality or something
17:45 < kanzure> the stuff inside could be something like a sensor for activity
17:46 < kanzure> (particularly useful for immobilization (I'm not going to consider stuffing a nanoradio into them)
17:46 < kanzure> )
17:46 < kanzure> gah! I fail at lisp
17:46 < kanzure> (immobilization useful particularly (nanoradio stuffing (nil consider))
17:50 < fenn> stuff!
17:50 < fenn> are you talking about hybrid organic/inorganic tiles?
17:50 < kanzure> tiles?
17:51 < fenn> remember the DNA FPGA thing?
17:51 < kanzure> no, I was thinking of putting wires in between the giant wrapping helices in proteins
17:51 < kanzure> no, not really
17:51 < kanzure> I mean, no, I do not mean that
17:51 < fenn> those ribbon diagrams are not entirely representative of reality
17:52 < kanzure> right, but proteins are also not wall-to-wall or the volume entirely filled with super-compressed material
17:52 < fenn> they're pretty well stuffed
17:52 < fenn> i mean, illustrations in textbooks are all way too sparse
17:53 < fenn> as far as protein concentration goes at least
17:54 < fenn> sorry i derailed your idea
17:54 < kanzure> nah, it's not a problem
17:54 < kanzure> I'm still reading up on polymerase conformational changes anyway
17:55 < fenn> i think the phrase you're looking for is "inorganic ligand"
17:55 < genehacker> nanoradios are cool
17:55 < kanzure> most ligands that I've heard about are usually external
17:56 < fenn> they're usually at the active site, because it's what makes the reaction go
17:56 < fenn> like a dill bit
17:56 < fenn> drill bit*
17:56 < kanzure> "'reveals a major conformational change wherein the C-terminal subdomain of the polymerase rotates around the axis of -helix M to produce main chain movements of up to 11 Å . This substrate-induced subdomain closure around the DNA is accompanied by numerous smaller (1−2 Å;) conformational changes "
17:56 < fenn> fantastic
17:57 < fenn> an animated 3d model would be infinitely better
17:57 < kanzure> there's a link, but it's broken
17:57 < kanzure> http://www.chem.ucsd.edu/Faculty/Kraut/bpol.html
17:58 < fenn> roadrunner hates me
17:58 < kanzure> the trick is to hate roadrunner more than it hates you
18:01 < kanzure> yay google
18:01 < kanzure> http://chem-faculty.ucsd.edu/kraut/bpol.html
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18:07 < kanzure> "If you have any comments about my movie, please click on my email Michael R. Sawaya (msawaya@ucsd.edu). A screen should pop up (its self explanatory) and there will be buttons for send and cancel. "
18:07 < kanzure> wtf
18:07 < kanzure> how ancient is this?
18:10 < kanzure> "The terminal base pair of the primer stem forms the other side of this pocket, which has a geometry that precisely accommodates a correct base pair."
18:10 < kanzure> that sounds unlikely
18:11 < kanzure> "Again, this binding pocket is defined by both nucleic acid and protein, that is, the correct 3'-terminal base pair forms one side of the pocket and specific amino acids in the O helix form the other side. The resulting slot provides a tight fit (Fig. 2) for incorporation of the correct nucleotide. "
18:17 < fenn> why does it sound unlikely?
18:17 < kanzure> because incorrect base pairs are sometimes incorporated 
18:18 < fenn> if it werent a tight fit, you'd get the wrong base 75% of the time
18:19 < fenn> you have to remember everything is constantly being battered with the equivalent of a tidal wave full of sledgehammers
18:19 < fenn> so the shape of the protein is not always exact
18:20 < fenn> i wonder why i havent heard about freedomofscience.org yet
18:21 < kanzure> really?
18:21 < kanzure> it's why joseph bothered to meet up with me
18:22 < kanzure> "One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a “short-term memory” of replication errors, responding to mismatches up to four base pairs in from the primer terminus"
18:23 < fenn> i thought you already knew him from WTA
18:23 < kanzure> no, not at all
18:23 < fenn> is he not the transhumanist bodybuilder guy?
18:23 < kanzure> it just so happens that he's well acquainted with the WTA folks
18:23 < kanzure> he is
18:23 < kanzure> but it's more of a "just so happens" rather than me meeting him through those channels
18:24 < genehacker> he might give bodybuilder a whole new meaning
18:25 < kanzure> apparently he graduated from harvard
18:25 < kanzure> he's a bit on the obsessive side :)
18:29 < fenn> "Using a Wiki format, we will create a community annotation system to review licenses and say whether they share."
18:29 < fenn> yarr
18:30 < kanzure> fenn: can you be over here by 4:30 tomorrow?
18:30 < fenn> any kind of data aggregation/standardization is better than none
18:30 < kanzure> Andrew and Linda are visiting, and she wants to meet you and such
18:30 < fenn> 4:30 i'll set my alarm
18:30 < kanzure> for 4:30 ?
18:30 < fenn> heh'
18:30 < fenn> i'm so fucked
18:31 < fenn> (just in general)
18:31 < genehacker> damn
18:31 < kanzure> good luck with that
18:31 < genehacker> I'm stuck down here
18:31 < kanzure> fenn: would pushing it out be better?
18:31 < kanzure> because she just offered to get me some food tomorrow, so if we shop first that's ideal
18:32 < fenn> hmm ok i guess
18:32 < fenn> genehacker: where are you stuck?
18:32 < genehacker> where I am right now
18:32 < genehacker> home
18:33 < genehacker> sewing up a thermal management garment
18:33 < fenn> i see. do you need someone to call emergency services to come extract you?
18:33 < genehacker> no
18:33 < fenn> ok :)
18:33 < kanzure> I want to go eat somewhere tonight
18:33 < genehacker> It's just a big hassle to get to austin from here
18:33 < kanzure> maybe freebirds. anybody want to come?
18:34 < genehacker> I could use a teleporter or at least some telepresence gear
18:34 < kanzure> er, you mean a webcam?
18:34 < genehacker> no I mean claytronic doubles
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18:35 < fenn> can you eat claytronics?
18:35 < genehacker> or a robot with stereovision, manipulators, and a low latency internet connection
18:35 < genehacker> yes, but it isn't good for you
18:37 < fenn> kanzure: i'm available tonight, as usual
18:40 < kanzure> well if you want to eat feel free to come over I guess
18:43 < xp_prg> ok kanzure thanks
18:43 < kanzure> xp_prg: ?
18:43 < xp_prg> over for dinner
18:44 < kanzure> aren't you on the wrong side of the continent?
18:44 < xp_prg> ya
18:44 < xp_prg> :)
18:44 < fenn> mail me some claytronics
18:44 < fenn> or a crossed atom beam hologram
18:45 < genehacker> or telepresence robot
18:45 < fenn> i'm telling you, you can't eat a telepresence robot
18:45 < genehacker> woo 12 feet out of 25 feet done
18:45 < genehacker> time to get moar supplies
18:46 < kanzure> fenn: sometime soon or I'll go without you :p
18:46 < fenn> oh, right
18:46 < genehacker> man one of those autonomous flying delivery vehicles would be great right about now...
18:46 < fenn> brt
18:49 < kanzure> "The polymerase, therefore, plays a significant role in defining the local and the global conformation of each mismatch structure. The type and degree of disruptions at the polymerase active site vary depending on the identity of the mismatch. We present our observations categorized by the type of base pairing."
18:51 < kanzure> nice, it has a list of different conformational changes for each type of mismatch incorporation
18:52 < kanzure> now if only it would do that for correct pairings :p
18:59 < genehacker> whoa
19:00 < genehacker> solaren says they're gonna get 4.8 gigawatts from space solar?
19:00 < genehacker> that is a lot
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23:26 < kanzure> photosensors that induce conformational changes: Vivid, White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1)
23:29 < kanzure> flavin-based photosensors,
23:29 < kanzure> comprising cryptochromes, LOV (Light, Oxygen and Voltage) and BLUF (Blue Light
23:29 < kanzure> sensing Using FAD) protein
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