| --- Log opened Thu Jul 14 00:00:41 2011 | ||
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| kanzure | back | 13:15 |
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| kanzure | genspace was ok. typical molecular biology lab. | 14:43 |
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| 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 | 14:59 |
| 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 | 15:00 |
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| 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 | 18:20 |
| fenn | nevermind i'll just email him | 18:21 |
| 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 | 18:30 |
| fenn | woah. http://twentytwowords.com/2011/06/16/what-childrens-skulls-look-like-as-they-prepare-to-lose-their-baby-teeth/ | 18:44 |
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| fenn | i really like how the "3d view" mode works in 3d warehouse http://sketchup.google.com/3dwarehouse/details?mid=670d50f5e360dd034201e75d2c2bc4bd&prevstart=0 | 20:26 |
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| kanzure | fenn: did you read the backlog and/or notes | 21:10 |
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| 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 | 21:40 |
| 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 | 21:41 |
| 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.. | 21:44 |
| kanzure | the notes have some details that haven't been talked about before, so i'd say read them | 21:46 |
| fenn | oh. i know rikke, not rolf | 21:49 |
| kanzure | is ex-germany the right way to describe her :p | 21:49 |
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| fenn | SCIENCE http://www.flickr.com/photos/laen/5745373098/in/photostream | 21:54 |
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| kanzure | "distilling water from orange dyed water" SCIENCE | 22:00 |
| fenn | sorry add some snark marks ~~~~ ~~~~ | 22:00 |
| 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 | 22:03 |
| 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 | 22:04 |
| fenn | they're all pretty good, i started with "consider phlebas" | 22:05 |
| 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." | 22:06 |
| 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 | 22:07 |
| 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 | 22:09 | |
| 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) | 22:10 |
| 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 | 22:11 |
| fenn | yeah it's definitely possible, it's just not a commercial reality | 22:12 |
| 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 :/ | 22:13 |
| kanzure | er wait why am i doing bad math | 22:14 |
| fenn | because you don't use 'units' | 22:14 |
| 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? | 22:15 |
| 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 | 22:16 |
| 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 | 22:17 |
| 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 | 22:18 |
| 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 | 22:19 |
| 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 | 22:20 |
| 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) | 22:21 |
| fenn | once you get over ~5kb PCR becomes a pain | 22:22 |
| 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 | 22:23 |
| 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 | 22:24 |
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| ybit | The Quest for Consciousness by Christof Koch | 22:58 |
| ybit | That's a book I can't find online :\ | 22:58 |
| kanzure | consciousness is a scam | 23:05 |
| 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 | 23:06 |
| ybit | kanzure: care to expand on why you think conciousness is a scam? | 23:17 |
| --- Log closed Fri Jul 15 00:00:42 2011 | ||
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