--- Log opened Fri Jun 15 00:00:46 2018
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08:37 < kanzure> ugh
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10:17 < archels> https://www.nexans.co.uk/eservice/UK-en_GB/fileLibrary/Download_540329718/UK/files/High%20Power%20PoE_2017_v4_1.pdf
10:17 < archels> so PoE can push about 100 W now? not bad
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12:49 < jrayhawk> https://www.youtube.com/watch?v=G61Q0AIuP3o general overview of PacBio sequencing workflows
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15:56 < maaku> kanzure: would you sign alert-retirement messages for altcoins that ask?
15:57 < maaku> .title https://www.youtube.com/watch?v=1bw6Zi17DBI
15:57 < yoleaux> Radical abundance: how a revolution in nanotechnology will change civilization - YouTube
15:57 < maaku> .title https://www.youtube.com/watch?v=dAA-HWMaF9o
15:57 < yoleaux> Dr. Eric Drexler - The Path to Atomically Precise Manufacturing - YouTube
15:58 < maaku> This is the first time I've seen Drexler's 3d-printing-with-protein pathway to nanomachines, and it seems eminently doable
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16:46 < heath> .tw https://twitter.com/DanHooperAstro/status/1007618336329551873
16:46 < yoleaux> (1/6) I just put out a new paper, in which I indulge in some wide-eyed futurism. Let me walk you though the idea. http://arxiv.org/pdf/1806.05203.pdf https://pbs.twimg.com/media/DfvEbTuVAAED0CJ.jpg (@DanHooperAstro)
16:47 < heath> maaku: thanks for that link
16:51 < maaku> The piece I was missing was that Drexler is proposing making lego-like tileable protein blocks, but with some sort of capped surface
16:52 < maaku> So they will only bind if the surface is activated
16:54 < maaku> Start with an array of these on the surface. Use an STM/AFM tip to decap/activate some. Bathe the surface in protein lego blocks for sufficient time to get each activated site bound to a block.
16:55 < maaku> Then rinse and repeat. In this way you get 3d printing of structures composed of small protein blocks, using off-the-shelf STM/AFM and synthetic biology.
16:57 < maaku> And although the design for the blocks is TDB, examples of protein engineering done so far demonstrate structural regdity and mechanical capabilities necessary to do Merkle-Freitas atom-by-atom diamondoid assembly
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16:59 < maaku> He even points to a cool set of proteins I didn't know about which have highly reliable light-activated transformations that would be used to provide programmable X-Y-Z motion for protein arm assemblages with sub-nanometer precision, using laser light sources of different colors
17:01 < maaku> heath: likewise thanks for your link, that's interesting reading
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17:12 < kanzure> maaku: okay sure
17:12 < kanzure> maaku: yes i'll sign a thing
17:13 < kanzure> maaku: i've bee nfailing to communicate with you if opsins are new to you
17:14 < kanzure> and azobenzenes were in the drafts of that polymerase engineering doc i shared with you :-)
17:14 < kanzure> from 17min 30sec
17:16 < maaku> kanzure: I didn't realize 1. how precise or 2. how reliable these were
17:17 < kanzure> and fast
17:17 < maaku> yeah
17:17 < kanzure> maaku: one of the tricks that a lab did was to put an azobenzene into an amino acid alternative, which got encoded into a protein
17:18 < maaku> basically before I thought any of these things were still boxing gloves compared to the Merkle-Freitas tooltips, and therefore only marginally useful as a stepping stone but not solving the problem
17:18 < kanzure> azobenzenes can also be added into nucleotides if you want to do dna-level switching... but i think protein/amino-acid switching is more interesting.
17:18 < maaku> but that assumption I had seems to be incorrect
17:18 < kanzure> we're really close to being able to do cool things with proteins, the trouble is making lots of novel proteins (custom/synthetic dna costs too much)
17:19 < kanzure> and you still sort of don't know what to build- have to experiment by building
17:19 < kanzure> hence the reason for new custom dna each experiment
17:19 < maaku> yeah but money can by synthetic dna, and money is a solveable problem.
17:20 < kanzure> well it becomes into a "burn money on a large search space" sorta problem, which investors consider to be blue sky
17:20 < maaku> vs. the straight-to-diamandoid APM path which requires uncertain technical advances
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17:21 < maaku> I imagine that finding an ideal set of protein building blocks is a literal genetic search problem
17:21 < maaku> This can be solved relatively cheaply, IF you had a specification for what you wanted and a metric for evaluating it.. I wonder what that would look like
17:22 < kanzure> goal for me is build thing to make lots of dna cheaply; if you want to jump past that, then you probably want stuff like protein-based nanofactory-whatever..
17:24 < maaku> I doin't think you'd need to make a whole lot of DNA. Use a synthetic bioreactor to output the lego blocks, microfluidics to transfer them from storage to worksite, and off-the-shelf tungston AFM probe for worksite activation
17:25 < maaku> you need some expensive DNA to start the bioreactors, but then it's self-replicating
17:25 < kanzure> ok you want protein lego delivery by AFM?
17:25 < kanzure> there are some non-AFM methods where you use protein-protein targeting based on dna, recognition motifs, or other methods
17:25 < maaku> no, this design is delivery by liquid bath of the worksite
17:26 < maaku> but the lego bricks will only bind to surfaces that have been selectively activated by the AFM tip
17:26 < kanzure> i see what you mean. so not entirely self-assembly. AFM-assisted self-assembly.
17:27 < kanzure> AFM-assisted selective self-assembly
17:27 < maaku> correct
17:27 < kanzure> what does that get you?
17:27 < maaku> let's say the bricks have open A binding sites and closed B binding sites. A binds to B. the tooltip is used to activate/open a B
17:28 < kanzure> i mean how far does that get you
17:28 < maaku> if drexler's claims about engineered protein rigidity are correct (no reason to think otherwise), then this really is all you need for most things
17:29 < maaku> but if you want carbon nanotube and diamond structures for the full vision or electronics, then it appears protein bricks with azobenzenes can be used to make arms that are precise enough to precision the Merkle-Freitas "minimal toolset" tips
17:30 < maaku> which you can then use to do any kind of diamandoid construction, via a set of laser sending positional commands to a azobenzine-protein robotic assembly arm
17:31 < kanzure> world-to-nano interfaces can be things like giant scissors or giant gears (downstepping your kinetic input into smaller motions at a work site), doesn't necessarily need to be laser/optical, but yes.
17:32 < maaku> The AFM tooltip is just a scaffolding crutch to build those robotic arms
17:34 < kanzure> ok well anyway, for the AFM chemistry that you want, you'd probably look into click chemistry + capping/decapping
17:35 < kanzure> and "protecting groups"
17:35 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Enzymatic%20protecting%20group%20techniques.pdf
17:50 < kanzure> maaku: agree?
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18:02 < maaku> was afk, but yes that looks right. thanks for the search terms and link
18:04 < kanzure> i think the actual selective chemistry for reversible capping/protection will be the difficult part there
18:07 < maaku> The ideal cap would be something that "collapses" into a lower-energy state when a large mechanical force is applied, with an activation energy higher than brownian motion
18:09 < maaku> This is something easy enough to find in simulation, but I wonder what the topology of the search space would look like. If a mechanically actuaated one-time switch is fragile, it might be difficult to find
18:10 < kanzure> .wik protein acetylation
18:10 < yoleaux> "Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into a chemical compound. Deacetylation is the removal of an acetyl group." — https://en.wikipedia.org/wiki/Protein_acetylation
18:11 < kanzure> .wik post-translational modification
18:11 < yoleaux> "Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling." — https://en.wikipedia.org/wiki/Post-translational_modification
18:12 < kanzure> .wik protein phosphorylation
18:12 < yoleaux> "Protein phosphorylation is a post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or modifying its function." — https://en.wikipedia.org/wiki/Protein_phosphorylation
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19:00 < kanzure> maaku: unclear to me what the first things to build. nanomanipulators and then you get magic nanofactories after that?
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19:34 < maaku> kanzure: in what sense? the first thing to do is figure out a minimal toolbox and make a synthetic bio pipeline creating them, sorting them, storing them in high purity
19:35 < maaku> but the first thing to make once you have the 3d printer? I would say replacing the AFM/STM tool with a optically controlled nano-scale arm would be the first thing
19:35 < maaku> because AFM tips wear down fast, and are probably going to be the #1 source of errors
19:37 < kanzure> so.. an AFM replacement thing?
19:39 < maaku> that's just next on the pipeline to make the system more reliable. but are you asking what to do with this thing in general?
19:40 < maaku> well what got me excited was that the outputs should be precise enough to bootstrap diamandoid assemblers
19:41 < maaku> but drexler makes the good point that protein-based machines have a better bio-compatability story, and these lego components could be small enough to do all the nanomedicine things
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20:02 < kanzure> .wik railroad worm
20:02 < yoleaux> "A railroad worm is a larva or larviform female adult of a beetle of the genus Phrixothrix in the family Phengodidae, characterized by the possession of two different colors of bioluminescence. It has the appearance of a caterpillar." — https://en.wikipedia.org/wiki/Railroad_worm
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--- Log closed Sat Jun 16 00:00:47 2018