--- Log opened Thu May 18 00:00:57 2017
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06:17 < kanzure> huh, there's actually a bunch of private islands in the world, like >100k
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11:22 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=3e2b98e7 Bryan Bishop: include reference for a confusing statement >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-bitcoin-selection-cryptography/
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13:19 < kanzure> for "iterative in vitro enzyme decoding of an encoded DNA molecule" it could work like this: exclusively use alternative unnatural nucleotides. maybe 16. one of them needs to be a "NOP". then we engineer a bunch of enzymes that fuzzymatch long stretches of a certain unnatural nucleotide and replace it with a single normal nucleotide (ATGC). in between these stretches, have lots of NOPs, and th...
13:19 < kanzure> ...e enzymes should fall off as soon as they hit a NOP sequence. later, use an enzyme that exclusively removes NOPs from a dna molecule.
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13:20 < kanzure> the most magic component there would be the enzyme doing the fuzzymatch of long stretches of a certain unatural nucleotide, and replacing that segment with a single nucleotide.  that's not something that resembles any existing enzymatic activity. and for especially long stretches like >20 bp you basically need the ezyme to "grab" the begining of the segment ad hold on to it for a while. which ...
13:20 < kanzure> ...is not a behavior we see.
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13:33 < kanzure> https://en.wikipedia.org/wiki/Repetition_code
13:33 < kanzure> "The chief attraction of the repetition code is the ease of implementation."
13:34 < kanzure> .wik repeat-accumulate code
13:34 < yoleaux> "In computer science, repeat-accumulate codes (RA codes) are a low complexity class of error-correcting codes. They were devised so that their ensemble weight distributions are easy to derive. RA codes were introduced by Divsalar et al." -- https://en.wikipedia.org/wiki/Repeat-accumulate_code
13:58 < kanzure> nmz787_: what is the actual cost of DNA synthesis in an inkjetting scenario, if there's no sequencing and no size limit to the molecules in each spot?
13:58 < kanzure> nmz787_: like the $0.03/bp prices are usually because of sequencing, right
13:58 < kanzure> ?
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18:00 < nmz787_> kanzure: I don't actually know, I tried asking yashgaroth about the prices of the gene arrays, since I think those are pretty much what you're asking for... but he didn't know when I asked
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18:06 < kanzure> the cost that twist quotes is probably including sequencing and stuff..
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18:24 < nmz787_> well, they were also requiring 100s of megabases to be purchase
18:25 < nmz787_> and as yash said "I'll believe it when I see it"
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19:02 < nmz787_> we gotta get "I'll believe it when I see it" t-shirt logo designs
19:03 < yashgaroth> the vast majority of gene synthesis cost at 3c/bp is sequencing and assembly, mostly sequencing
19:06 < yashgaroth> plus paying off all their fancy machines; I'd say profit too but I doubt twist is profitable
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19:08 < nmz787_> testing the permutations of swapping at mis-alignment sites would be something like MAGE?
19:12 < nmz787_> tracking combinations could be tricky
19:14 < yashgaroth> similar
19:33 < nmz787_> so this whole FIB transport thing and requirement of forklift rentals, has me really interested in mech suits
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--- Log closed Fri May 19 00:00:58 2017