--- Log opened Thu Jul 14 00:00:41 2011
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13:15 < kanzure> back
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14:43 < kanzure> genspace was ok. typical molecular biology lab.
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14:59 < kanzure> they had three or four inconspicuous copies of "THE SINGULARITY IS NEAR" on their shelves but play dumb about transhumanist topics
14:59 < QuantumG> of that transhumanist topics are dumb
15:00 < kanzure> like gene therapy?
15:00 < kanzure> c'mon, viral infection of plasmids is just like gene therapy
15:00 < kanzure> with lots of other constraints
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18:20 < fenn> hm, if outer_space comes back tell him to call steve langford from ideas signs in san antonio... i helped build his CNC router for cutting out acrylic letters and i'm sure he gets a lot of down time
18:21 < fenn> nevermind i'll just email him
18:30 < fenn> hm. "agrocircle" neat idea
18:30 < fenn> i guess it's a robot arm mounted on a track on one of those rotating water pipes
18:44 < fenn> woah. http://twentytwowords.com/2011/06/16/what-childrens-skulls-look-like-as-they-prepare-to-lose-their-baby-teeth/
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20:26 < fenn> i really like how the "3d view" mode works in 3d warehouse http://sketchup.google.com/3dwarehouse/details?mid=670d50f5e360dd034201e75d2c2bc4bd&prevstart=0
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21:10 < kanzure> fenn: did you read the backlog and/or notes
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21:40 < fenn> backlog yes notes no
21:40 < fenn> should i read the notes?
21:40 < fenn> anselm rants about the gene synthesis costs thing all the time
21:41 < fenn> who in particular is doing bio at noisebridge? and when i looked in the box marked "bio stuff" it was full of makerbot pieces
21:44 < kanzure> rikke and rolf
21:44 < kanzure> rolf is ex-SGI/SIGGRAPH
21:44 < kanzure> rikke is ex-germany? or something
21:44 < kanzure> they are also probably the same folks taking over the mycelium cultures..
21:46 < kanzure> the notes have some details that haven't been talked about before, so i'd say read them
21:49 < fenn> oh. i know rikke, not rolf
21:49 < kanzure> is ex-germany the right way to describe her :p
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21:54 < fenn> SCIENCE http://www.flickr.com/photos/laen/5745373098/in/photostream
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22:00 < kanzure> "distilling water from orange dyed water" SCIENCE
22:00 < fenn> sorry add some snark marks ~~~~ ~~~~
22:03 < fenn> rikke rasmussen and rolf van widenfelt, if namespace conflicts
22:03 < kanzure> sounds right
22:03 < kanzure> i'm still trying to defend an attack of Culture after a visit to times square for a meal
22:03 < fenn> Culture?
22:03 < kanzure> you know.. that thing
22:03 < fenn> NYC is not Culture
22:04 < kanzure> well all the ads
22:04 < kanzure> and lights
22:04 < fenn> they're money grubbers, don't kid yourself
22:04 < fenn> gah, have you even read Iain Banks?
22:04 < kanzure> i think that's one that i lie about and say i have
22:04 < fenn> well, read some fo re4lz
22:05 < fenn> they're all pretty good, i started with "consider phlebas"
22:06 < fenn> you might enjoy "excession"
22:06 < kanzure> i am not near my hard copies of banks at the moment
22:06 < fenn> "Banks has noted that he spent much time playing the Civilization computer game (appearing to refer to the first version of the game series) before writing the book and that it was one of the inspirations for the concept of the 'Outside Context Problem' central to the novel."
22:07 < fenn> want a soft copy?
22:07 < kanzure> no i'd rather just get the torrent thingy and be done with it
22:07 < fenn> uh. what?
22:07 < kanzure> you know.. the full collection torrent thing
22:07 < kanzure> am i making this up
22:09 < fenn> bring a TB drive to cali
22:09 < kanzure> okie dokie
22:09  * fenn mutters something about music server not mounting external drive properly
22:10 < kanzure> i like that anselm is complaining about dna synthesis too
22:10 < fenn> mostly the cost and how it inhibits research
22:10 < kanzure> yeah how else are you going to have relevant large permutation libraries
22:10 < fenn> you only need a few nanomoles but you get like millimoles of dna (and most of the cost is reagents, but nobody is doing small scale synthesis for cheap for some odd reason)
22:11 < fenn> you dont need to do gene synthesis just for permutation
22:11 < kanzure> well this researcher at duke seems to be doing subnanomolar oligonucleotide synthesis
22:11 < fenn> mostly it's for convenience.. simpler to synthesize from scratch and ligate with gibson reaction than to do some complicated restriction enzyme from existing dna
22:12 < fenn> yeah it's definitely possible, it's just not a commercial reality
22:13 < kanzure> oh here we go
22:13 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Parallel%20on-chip%20gene%20synthesis%20and%20application%20to%20optimization%20of%20protein%20expression.pdf
22:13 < kanzure> $0.001/bp for 30kb sequence
22:13 < kanzure> so $1/kbp
22:13 < kanzure> so $10k for a handful of megabases :/
22:14 < kanzure> er wait why am i doing bad math
22:14 < fenn> because you don't use 'units'
22:15 < kanzure> "handful" is probably where i screwed up.. a handful=1
22:15 < kanzure> handful=10
22:15 < fenn> $1k/MB using your numbers
22:15 < fenn> you end up using about 2x the number of synthesized bases per base of gene product though, so more like $2k
22:15 < fenn> there's lots of single strand overlap, that's how the assembly process works
22:15 < kanzure> because of errors?
22:16 < kanzure> no i don't like assembly
22:16 < fenn> btw yeast do some really cool recombination stuff
22:16 < kanzure> i have an irrational distaste for multiplexed gene synthesis
22:16 < fenn> "i dont like assembly" meaning what exactly, you are going to run a chemical reaction a million times?
22:16 < kanzure> well polymerase seems to be doing an ok job at a reaction spanning many hundreds of megabases
22:16 < fenn> you're a fool then
22:16 < fenn> it's a trivially parallelizable problem, no reason at all not to
22:17 < kanzure> cost increase
22:17 < kanzure> 2x cost
22:17 < fenn> 2x cost for 1000x speedup
22:17 < fenn> not to mention it actually works, whereas your 1MB "oligo" would be plagued with errors
22:17 < kanzure> you might as well be arguing that nobody should bother to improve dna synthesis
22:17 < kanzure> since it's all parallelizable as it is now
22:17 < fenn> no i'm just saying parallelization is a good thing
22:18 < kanzure> besides, you should assume i would reduce the error rate
22:18 < fenn> how?
22:18 < kanzure> there are very common flaws that have uncommon solutions
22:18 < fenn> specifics please
22:18 < kanzure> i put a  lot of time into looking up the typical and abnormal failure modes
22:18 < kanzure> well
22:18 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Error%20analysis%20of%20chemically%20synthesized%20polynucleotides.pdf
22:19 < kanzure> oh geeze where did the other papers & notes go
22:19 < fenn> i'd like to point out there's a few orders of magnitude difference between 100 bases and 1000000 bases
22:19 < kanzure> that's not the paper i was thinking of anyway, it's way less detailed
22:20 < kanzure> i figure it would be nice to aim for 1/2000 error rates
22:20 < fenn> so basically they use a three step reaction to reduce error rate
22:20 < kanzure> well modern parallel oligo synthesizers just do dna sequencing on each reaction as well
22:20 < fenn> the assembly process lets you sequence intermediate (say 1kb) products
22:21 < kanzure> yep
22:21 < fenn> so if it's wrong, you can just re-do the assembly process, run pcr again, get a single sequence
22:21 < fenn> sequence, lather rinse repeat
22:21 < fenn> (hint: it's wrong, a lot)
22:22 < fenn> once you get over ~5kb PCR becomes a pain
22:23 < fenn> there are newer enzymes which don't fall off as easily, but i don't really know how well they work on extra long sequences
22:23 < kanzure> you could attempt to optimize polymerases for being able to hold on
22:23 < fenn> yes that's been done
22:23 < kanzure> like very long sequences that don't end before the stop codonz
22:24 < fenn> i think you should go to bed.
22:24 < kanzure> how bad is it
22:24 < fenn> bbl, i'm going to nb to build some toys
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22:58 < ybit> The Quest for Consciousness by Christof Koch
22:58 < ybit> That's a book I can't find online :\
23:05 < kanzure> consciousness is a  scam
23:06 < kanzure> http://en.wikipedia.org/wiki/Sense_of_agency
23:06 < kanzure> i am reading that at the moment
23:06 < kanzure> i find it suspect
23:06 < kanzure> like i can't figure out how they figured out "sense of agency" is a real thing other than asking themselves if they thought it was real
23:06 < kanzure> i'd rather see "sense of agency" studies on dissociative mice or something
23:17 < ybit> kanzure: care to expand on why you think conciousness is a scam?
--- Log closed Fri Jul 15 00:00:42 2011