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| kanzure | bloop. | 06:30 |
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| kanzure | "Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity" http://science.sciencemag.org/content/early/2016/09/22/science.aag1465 | 07:08 |
| kanzure | "Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically-plausible (including unnatural but functionally relevant) side-chains is not readily accessible. We describe C (sp3)–C (sp3) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free radical chemistry, ... | 07:08 |
| kanzure | ... and use them to form Cβ–Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide-diversity of natural, unnatural, posttranslationally-modified (methylated, glycosylated, phosphorylated, hydroxylated) and labeled (fluorinated, isotopically-labeled) side-chains to be added to a common, readily-accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This ... | 07:09 |
| kanzure | ... approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for accessing diverse proteins." | 07:09 |
| kanzure | "Towards deep symbolic reinforcement learning" https://arxiv.org/abs/1609.05518 | 07:10 |
| kanzure | .tw https://twitter.com/fchollet/status/775388595871809536 | 07:11 |
| yoleaux | A reasonable candidate for replacing backprop in deep learning: ADMM (alternating direction method of multipliers). (@fchollet) | 07:11 |
| kanzure | "Capacity-approaching DNA storage" http://dnafountain.teamerlich.org/ http://biorxiv.org/content/early/2016/09/09/074237.1 | 07:12 |
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| kanzure | "The multilayer connectome of Caenorhabditis elegans" https://arxiv.org/abs/1608.08793 | 07:14 |
| kanzure | "Accurate de novo prediction of protein contact map by ultra-deep learning model" http://biorxiv.org/content/early/2016/09/03/073239 | 07:15 |
| kanzure | paperfuge (yes already mentioned but whatever..) http://biorxiv.org/content/early/2016/08/30/072207 i guess i mentioned the foldscope not the paperfuge. | 07:17 |
| kanzure | "small tool for searching small guide DNA for CRISPR-Cas9 target sequence" https://github.com/hanyue36/sgs | 07:18 |
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| juul | ybit: oh great! i've been traveling but will put up the individual talks soon | 09:04 |
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| kanzure | http://www.cs.virginia.edu/~robins/YouAndYourResearch.html | 10:26 |
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| poppingtonic | http://www.openphilanthropy.org/dr-adam-marblestone-mit-synthetic-neurobiology-group-and-mit-media-lab-and-dr-eric-drexler-future | 11:54 |
| yoleaux | 19 Sep 2016 15:22Z <kanzure> poppingtonic: see http://gnusha.org/logs/html/2016-09-19.log.html#t08:19-93 | 11:54 |
| poppingtonic | kanzure: good! it's been a while since I was here. | 11:56 |
| poppingtonic | The OpenPhil link is a page linking to a pdf. Some good stuff about a recent workshop with US DOE people about atomically precise manufacturing and an exploratory project to build a 1st generation molecular 3D printer. | 11:59 |
| fenn | is that what they're calling it these days? | 12:01 |
| poppingtonic | what, atomically precise manufacturing? Drexler has been calling it that for years now, I think...and the interview is with him and Adam Marblestone.. | 12:03 |
| fenn | "molecular 3D printer" is a phrase i hadn't heard yet | 12:04 |
| poppingtonic | matter compiler? | 12:05 |
| kanzure | what was wrong with atomically precise manufacturing | 12:07 |
| poppingtonic | the name, or the entire idea? | 12:08 |
| kanzure | the name! | 12:08 |
| poppingtonic | I don't see anything wrong with it, it's more precise. Heh. | 12:08 |
| kanzure | i should probably go ask adam to pitch dna synthesis for molecular manufacturing reasons. not sure if he is doing that already. | 12:09 |
| kanzure | http://www.openphilanthropy.org/sites/default/files/Eric_Drexler_Adam_Marblestone_09-01-16_%28public%29.pdf | 12:09 |
| poppingtonic | kanzure: I remember reading about that somewhere, not sure whether it was Marblestone or Church who wrote it. I'll look in Regenesis again and see.. | 12:11 |
| kanzure | " spiroligomer bricks" | 12:11 |
| poppingtonic | "A molecular 3D printer made entirely out of self-asssembled nanoscale components would be massively parallel by design. [...] If such printers could work with blocks on a 1nm scale, they would compete with the best self-assembly methods." | 12:14 |
| poppingtonic | "despite advances in DNA origami and other areas, there is a considerable probability of failure in the approach pursued by each lab, due to the inherent difficulty of biomolecular research" | 12:17 |
| poppingtonic | kanzure: re DNA synthesis, I think they both are. See the estimates on funding costs spread over 3-6 large, successful labs. | 12:18 |
| kanzure | ok emailed adam 588df395c9a74880b6e7433d8d31ca030392b9d90ab5445293462f4e871b1387 | 12:21 |
| poppingtonic | kanzure: from Regenesis pp115: "The synthetic minimal cell would enable the production of materials too large or otherwise incompatible with the more elaborate functioning systems of a complex cell. It also represents our best shot at a general nanotech assembler, the dream of Eric Drexler and many nanotechnology enthusiasts since he first described it in his 1986 book Engines of Creation." | 12:28 |
| kanzure | weird that they want an entire cell for that. | 12:29 |
| kanzure | in vitro protein synthesis already works yo | 12:29 |
| poppingtonic | I think the goal with the cell is to figure out (really "grok") the minimal set of proteins that make a cell "alive", for some sufficient definition of the term given in the book. | 12:30 |
| kanzure | for molecular manufacturing, we can do many tihngs without an entire cell--- for example, there was a paper from a few years ago that showed how to make arbitrary 3d polyhedral objects using dna origami. | 12:30 |
| kanzure | well, not completely arbitrary, there is a size constraint on the low end i think, and probably an upper size constraint on the high end. and also not all possible shapes can be made by polyhedrons. | 12:31 |
| kanzure | poppingtonic: about making biology more like programming http://gnusha.org/logs/html/2016-09-08.log.html#t19:11-111 | 12:33 |
| poppingtonic | I see. Not end-user modifiable. DRM'd up the wazoo. | 12:36 |
| poppingtonic | That's a good thread, kanzure. Thanks. | 12:42 |
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| kanzure | poppingtonic: yep sure. | 12:48 |
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| kanzure | schedule is up https://scalingbitcoin.org/event/milan2016#schedule | 14:36 |
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| kanzure | "Friday is the last day for registration for the Igem Giant Jamboree" | 15:19 |
| kanzure | synbiobeta conference is tomorrow http://synbiobeta.com/conferences/synbiobeta-sf-2016/ | 15:20 |
| kanzure | "on Saturday Seattle carries out a sheep brain dissection for beginning neuro-biologists" | 15:23 |
| kanzure | ( https://www.meetup.com/HiveBio-diyBio-Seattle-Science-Meetup/events/233371985/ ) | 15:23 |
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| kanzure | "The future of whole-cell modeling" https://covert.stanford.edu/publicationpdfs/DMacklin2014.pdf | 18:58 |
| kanzure | "A whole-cell computational model predicts phenotype from genotype" http://www.cell.com/cell/fulltext/S0092-8674(12)00776-3 | 18:58 |
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| kanzure | hmph | 21:13 |
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| --- Log closed Tue Oct 04 00:00:12 2016 | ||
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