--- Log opened Wed Jul 27 00:00:08 2016
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00:19 < maaku> kanzure: I saw a HN post regarding NLP machine learning talking about how much relevant features are in non-audible parts of speech
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00:19 < maaku> specifically the commenter was complaining that opus can't be configured to keep this information very well in some cases
00:20 < maaku> e.g. because it forces conversion to 48kHz
00:20 < maaku> not sure actually why that would specifically be a concern, but he claimed it was and I flagged it for followup
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08:09 < kanzure> 0924ta0ijgidaf020fajd
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10:29 < kanzure> hmph
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12:38 < kanzure> ugh https://letstalkbitcoin.com/blog/post/eb141-ralph-merkle-revolutionizing-democracy-using-daos
12:39 < kanzure> ralph we need you more on tooltips than this
12:40 < eudoxia> when's the DSDM book gonna be finished Merkle
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12:44 < kanzure> sup Albatross
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13:44 < maaku> https://www.youtube.com/playlist?list=PLZlLHCryX93L40ZLylvbO8zqfbz3ZNwmm
13:44 < maaku> AGI-16 conference
13:44 < maaku> this time with lots of deep learning
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14:01 < kanzure> indiebio demo day videos https://www.youtube.com/channel/UC0FFccwm1wbmYtKfX6HDncw/videos
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15:02 < kanzure> "next twenty billion years of biology"
15:19 < kanzure> tor and load balancing http://tor.stackexchange.com/questions/13/can-a-hidden-service-be-hosted-by-multiple-instances-of-tor/24#24 versus onionbalance https://news.ycombinator.com/item?id=12171768
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18:18 < chris_99> anyone heard of the ant mirror test experiment? if the results are valid, i'm curious what that means for the mirror test
18:29 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5c695187 Bryan Bishop: some things from agi-16 >> http://diyhpl.us/diyhpluswiki/transcripts/agi-16/deep-neural-networks-cant-make-agi/
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18:51 < kanzure> "Also, I do not feel that the abstract does a great job of describing electronic polymerase, I'm still not sure whether it's computer simulated or something more like nanobots"
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20:07 < docl> The idea is to use computer controlled electronic circuitry to control literal polymerase molecules, right?
20:16 < docl> So as I'm picturing it you'd have a chip, and on that chip would be a region (or many regions) populated by our custom built polymerase molecules, likely evolved from taq or ecoli. The molecules would respond to electrical current from the chip to tell them which nucleotide to assemble next in the chain.
20:25 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=856629b3 Bryan Bishop: a lecture about directed evolution >> http://diyhpl.us/diyhpluswiki/transcripts/montclare-protein-engineering/directed-evolution/
20:26 < kanzure> docl: yep, that's right
20:27 < kanzure> docl: although personally i think the electrical interface would only be for electrical detection of sequence or nucleotides, and some other form of stimulation will be required re: actual control of the enzyme
20:28 < kanzure> with a sufficiently good directed evolution experiment setup, i think almost all of these problems just go away
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20:29 < kanzure> juul was suggesting a version where you transmit to ecoli through light some sort of signal that would tell it how to synthesize some DNA to counteract some toxin (or something)
20:29 < kanzure> unfortunately if the polymerase is not already responsive to light stimulation, then it's unlikely that any of the polymerase enzymes on your petri dish are going to respond productively
20:30 < docl> maybe you could evolve a polymerase that selects its next nucleotide based on the frequency of light shining on it?
20:30 < kanzure> however, if your entire colony was made of random mutants that had light-responsive polymerases, then perhaps some would have some response to optical stimulation -- although i still doubt that any would correctly synthesize the optically transmitted DNA data
20:30 < kanzure> in the draft polymerase paper, one of the refs we are citing is an unnatural amino acid that is photoswitchable because it incorporates azobenzene
20:31 < kanzure> so you could place this amino acid at multiple places inside a single enzyme (or you could have a second amino acid with not azobenzene but some alternative to azobenzene that would be responsive to other wavelengths)
20:32 < kanzure> the advantage of juul's approach-- if a viable selection strategy can be designed-- is that you get to skip all the difficult rational protein design steps (questions like "which amino acid should be replaced with a photoswitchable amino acid?")
20:32 < kanzure> s/wavelength/frequency
20:33 < kanzure> in selection experiments, if you are evolving for thermostability, you can introduce lots of mutations, then gradually increase the temperature and see which mutants are still active at high temperatures. the interesting question here is, what is the equivalent and feasible selection strategy for "responsive to optical stimulation" or "responsive to relevant outside stimulation of any kind"?
20:34 < docl> you could also maybe have a mechanical system that delivers the specific nucleotide you want next, and use a more general purpose polymerase that just assembles whatever's there.
20:34 < kanzure> with optical stimulation, you are at first less interested in exact sequence specifity-- the data transfer can be highly faulty but still an interesting result to start working with.  so what selection method? length of synthesized DNA?
20:35 < kanzure> yes isolation and confinement is also discussed in the draft, although i have been somewhat perplexed by the lack of literature about sub-attoliter droplets for the physical encapsulation of only one molecule
20:36 < kanzure> a thermostability example was discussed in this lecture which i just typed hehe http://diyhpl.us/diyhpluswiki/transcripts/montclare-protein-engineering/directed-evolution/
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21:03 < kanzure> instead of selecting for DNA length (corresponding to how long you predict the DNA should be if the optically-responsive polymerase was not faulty), you could maybe have fluorescent dNTPs that stop fluorescing at incorporation, then you measure fluorescence of an entire emulsion droplet, and you select for the compartments that have a fluorescence amount matching the programmed plan of stimulaton you gave to the polymerases.... but ...
21:03 < kanzure> ... distinguishing between 800 less fluorescent events in a compartment with billions is, probably not realistic.
21:24 < kanzure> it would be interesting to somehow con the optogenetics people into answering that question, you could trick them into doing that sort of project for their own optically gated protein evolution project
21:36 < kanzure> "We've known for quite a time that induction to pluripotence leads to cellular rejuvenation. The work of Laure Lapasset showed that cells derived from human centenarians could be induced to pluripotence without showing any differences with cells derived from young people. Indeed the work of JB Gurdon showed that nuclear transplantation could rejuvenate a nucleus of an aged cell and make it capable of generating an entire organism. ...
21:36 < kanzure> ... Cellular aging is a non-cell autonomous trait for the most part." "Harold, we discussed the Lapasset data, and you agreed that they do not show cellular rejuvenation. Now you are back to the old story?"
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21:42 < kanzure> "The government has a dispensation for the use of experimental drugs in the case of a mortal illness with no hope of cure by traditional means: doesn't aging fit that description?"
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22:36 < kanzure> ebowden_: your connection is broken
22:40 < ebowden_> kanzure, whenever I go AFK my laptop does that, it disconnects when it goes to sleep.
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