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06:30 < kanzure> bloop.
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07:08 < 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, ...
07:09 < 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."
07:10 < kanzure> "Towards deep symbolic reinforcement learning" https://arxiv.org/abs/1609.05518
07:11 < 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)
07:12 < kanzure> "Capacity-approaching DNA storage" http://dnafountain.teamerlich.org/ http://biorxiv.org/content/early/2016/09/09/074237.1
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07:14 < kanzure> "The multilayer connectome of Caenorhabditis elegans" https://arxiv.org/abs/1608.08793
07:15 < kanzure> "Accurate de novo prediction of protein contact map by ultra-deep learning model" http://biorxiv.org/content/early/2016/09/03/073239
07:17 < 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.
07:18 < kanzure> "small tool for searching small guide DNA for CRISPR-Cas9 target sequence" https://github.com/hanyue36/sgs
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09:04 < juul> ybit: oh great! i've been traveling but will put up the individual talks soon
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10:26 < kanzure> http://www.cs.virginia.edu/~robins/YouAndYourResearch.html
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11:54 < 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
11:56 < poppingtonic> kanzure: good! it's been a while since I was here.
11:59 < 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.
12:01 < fenn> is that what they're calling it these days?
12:03 < 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..
12:04 < fenn> "molecular 3D printer" is a phrase i hadn't heard yet
12:05 < poppingtonic> matter compiler?
12:07 < kanzure> what was wrong with atomically precise manufacturing
12:08 < 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.
12:09 < 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
12:11 < 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"
12:14 < 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."
12:17 < 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"
12:18 < poppingtonic> kanzure: re DNA synthesis, I think they both are. See the estimates on funding costs spread over 3-6 large, successful labs.
12:21 < kanzure> ok emailed adam 588df395c9a74880b6e7433d8d31ca030392b9d90ab5445293462f4e871b1387
12:28 < 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."
12:29 < kanzure> weird that they want an entire cell for that.
12:29 < kanzure> in vitro protein synthesis already works yo
12:30 < 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.
12:31 < 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.
12:33 < kanzure> poppingtonic: about making biology more like programming http://gnusha.org/logs/html/2016-09-08.log.html#t19:11-111
12:36 < poppingtonic> I see. Not end-user modifiable. DRM'd up the wazoo.
12:42 < poppingtonic> That's a good thread, kanzure. Thanks.
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12:48 < kanzure> poppingtonic: yep sure.
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14:36 < kanzure> schedule is up https://scalingbitcoin.org/event/milan2016#schedule
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15:19 < kanzure> "Friday is the last day for registration for the Igem Giant Jamboree"
15:20 < kanzure> synbiobeta conference is tomorrow http://synbiobeta.com/conferences/synbiobeta-sf-2016/
15:23 < 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/ )
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18:58 < 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
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21:13 < kanzure> hmph
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--- Log closed Tue Oct 04 00:00:12 2016