--- Log opened Mon Jun 18 00:00:49 2018
--- Day changed Mon Jun 18 2018
00:00 < archels> fenn: extracting the pins from a DIL socket went remarkably well
00:01 < archels> I used a heat gun, and slowly increased the temperature until the plastic starts getting soft, then I just use a pair of needle-nose pliers to wiggle the pins out one by one
00:05 < fenn> nice
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05:45 < kanzure> .title
05:45 < yoleaux> From Bacteria to Buildings: Additive Manufacturing Outside of the Box - S. Keating - MIT PhD Defense - YouTube
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06:47 < kanzure> linear molecular nanotechnology (programmable linear polymers) should be sufficiently interesting for starters. capping/decapping already works there.
06:48 < kanzure> why don't we have a protein fusion protein design person? where are they?
06:50 < kanzure> .to yashgaroth do you have any recommendations for a protein capping/decapping/additive protein fusion protocol? capping should be bulk liquid chemical, decapping should be local electron transfer or some other procedure with AFM tip or other physical switch.
06:50 < yoleaux> kanzure: I'll pass your message to yashgaroth.
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07:12 < kanzure> .wik protein tag
07:12 < yoleaux> "Protein tags are peptide sequences genetically grafted onto a recombinant protein. Often these tags are removable by chemical agents or by enzymatic means, such as proteolysis or intein splicing. Tags are attached to proteins for various purposes." — https://en.wikipedia.org/wiki/Protein_tag
07:13 < kanzure> streptavidin-biotin protein tagging would be promising...
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07:17 < kanzure> .wik biotinylation
07:17 < yoleaux> "In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb the natural function of the molecule due to the small size of biotin (MW = 244.31 g/mol)." — https://en.wikipedia.org/wiki/Biotinylation
07:18 < kanzure> biotinylation of AFM probe tips is already very common; maybe the linker is not the right structure for maaku's purposes tho.
07:19 < kanzure> .wik biotin acceptor peptide
07:19 < yoleaux> kanzure: Sorry, that command (.wik) crashed.
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07:24 < kanzure> why not just use biotinylated gold nanoparticles
07:25 < kanzure> "Submicron streptavidin patterns for protein assembly" https://pdfs.semanticscholar.org/270c/f84a760c590403ee327892907bc37492b29b.pdf
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07:28 < kanzure> maaku: what was the problem, again?
07:28 < kanzure> particularly why does maaku need tooltips if we already have many binding chemistries
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07:58 < kanzure> 1a6ce44a9ae994cf6ea49442b4c64fc35003e56a43dc80ee729f9f87b05d8461  bitcoin-papers.2018-06-18.zip
07:58 < kanzure> http://diyhpl.us/~bryan/papers2/bitcoin-papers.2018-06-18.zip
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08:08 < kanzure> 330663ef6b0e88148d27c2743fd224765a82370cd43da7954d047a696ac3c26e http://diyhpl.us/~bryan/papers2/bitcoin/filehashes.txt
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08:17 < kanzure> .tw https://twitter.com/kanzure/status/1008730113830203395
08:17 < yoleaux> sha256 hashes of various bitcoin papers http://diyhpl.us/~bryan/papers2/bitcoin/filehashes.2018-06-18.txt H(file) == 330663ef6b0e88148d27c2743fd224765a82370cd43da7954d047a696ac3c26e @otsproofbot2 (@kanzure)
08:28 < kanzure> 08:27 <+kanzure> alife simulation is good simulator but it too suffers from perma-stuck of non-evolution after like 100,000 years of simulation time
08:28 < kanzure> 08:28 <+kanzure> i was talking with the developer (some professor?) of alife and he mentioned that their simulations never spontaneously develop sexual reproduction
08:28 < kanzure> 08:28 <+kanzure> incentives for development of sexual reproduction seem to be unknown or underspecified
08:29 < kanzure> s/alife/avida
08:29 < kanzure> .wik avida
08:29 < yoleaux> "Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer programs (digital organisms). Avida is under active development by Charles Ofria's Digital Evolution Lab at Michigan State University; the first version of Avida was designed in 1993 by Ofria, Chris Adami and C." — https://en.wikipedia.org/wiki/Avida
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08:32 < kanzure> "The surprising creativity of digital evolution: A collection of anecdotes from the evolutionary computation and artificial life research communities" https://arxiv.org/pdf/1803.03453.pdf
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09:55 < kanzure> https://phys.org/news/2018-06-faster-cheaper-dna.html
09:55 < kanzure> "Arlow's idea was to securely tether an unblocked nucleotide to TdT, so that after the nucleotide is added to a growing DNA molecule, the enzyme remains attached and itself protects the end of the chain from further additions. After the DNA molecule has been extended, they cut the linking tether to release the enzyme and re-expose the end for the next addition."
09:55 < kanzure> "De novo DNA synthesis using polymerase-nucleotide conjugates" https://www.nature.com/articles/Nbt.4173
09:56 < kanzure> .tw https://twitter.com/Keasling_Lab/status/1008746730278383617
09:56 < yoleaux> New paper out from our lab in @NatureBiotech! De novo DNA synthesis using polymerase-nucleotide conjugates. Congratulations Dan and Sebastian! https://www.nature.com/articles/nbt.4173 (@Keasling_Lab)
09:58 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/De%20novo%20DNA%20synthesis%20using%20polymerase-nucleotide%20conjugates%20-%202018.pdf
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10:17 < kanzure> music https://www.youtube.com/watch?v=yFpWMspbhBU
10:24 < yashgaroth> fuck knows how you'd activate/decap proteins with an AFM tip, I could see subtractive printing if you're just ablating monomers off of a crystal/aggregate
10:24 < yashgaroth> I/we spoke to Arlow at the first gp-write, he's good
10:25 < kanzure> protein co-protein uh.. i think proteins attach to each other and unbind all the time. these mechanisms surely exist.
10:25 < kanzure> yeah it's interesting to see how long it has taken us talking about "hey someone should do TdT things" to people actively publishing on it
10:25 < kanzure> two publications in a week is pretty high for TdT-based dna synthesis techniques (the data storage one and now this)
10:29 < yashgaroth> they'll bind, but doing it site-specifically at that resolution is rough, though maybe there's some electrochemistry bonds that'll break far before the AFM tip fucks up the rest of the protein
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10:37 < yashgaroth> or some catalyst protein stuck on the tip that triggers a conformational change in free-floating bricks that makes them bind to the surface, that's probably your best bet if you can find a good candidate
10:37 < kanzure> well, maaku was okay with a two-step thing where you cap/decap and then float in your bricks so that you don't need to attach your bricks to the AFM probe tip
10:38 < yashgaroth> oh not the bricks themselves on the tip, some other protein that bends the bricks in solution so they're able to bind to surface proteins for a short timeframe before reverting back to normal
10:39 < yashgaroth> making it not cause massive chains of free-floating aggregates wherever the tip goes, well that's a different issue
10:42 < kanzure> bend -> bind?
10:42 < yashgaroth> would need to reversibly bind in order to bend
10:43 < yashgaroth> imagine uhh...one of those rubber cup things where you push it inside-out and it stays like that for a while but eventually pops back into a cup shape
10:43 < yashgaroth> and you build with stacks of inside-out cups that stick together when they're in that shape
10:44 < yashgaroth> there might be some way to cause covalent bonds betwixt proteins under an electrical field, I'll see if I can find anything
10:45 < kanzure> i was thinking something about streptavidin might have already been done.. since literally everything in biology uses streptavidin/biotinylation..
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10:48 < yashgaroth> well, biotech, yes...if you can make a channel open on the floating streptavidin in an electric field, then sure
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10:50 < kanzure> isn't this just cross-linking or something
10:51 < yashgaroth> which part? biotin/sav bond isn't crosslinking since it's not covalent
10:52 < kanzure> i mean his goal could be satisfied by cross-linking
10:52 < kanzure> there's a looot of papers about functionalizing protein nanopatterns to surfaces https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050812/   but he wants protein-protein guided by AFM.
10:57 < yashgaroth> yeah but 3d structures instead of patterns...there's gotta be some way to induce a covalent bond between two proteins that're stuck to each other if you electrocute them (and the atoms to be stuck together are lined up), but what search terms to use
10:59 < yashgaroth> with unnatural amino acids I imagine it'd be much easier to get a reliable bond
11:00 < kanzure> "Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition" http://www.pnas.org/content/100/8/4527.short
11:00 < kanzure> "Here we describe the use of self-assembling amyloid protein fibers to construct nanowire elements. Self-assembly of a prion determinant from Saccharomyces cerevisiae, the N-terminal and middle region (NM) of Sup35p, produced 10-nm-wide protein fibers that were stable under a wide variety of harsh physical conditions. Their lengths could be roughly controlled by assembly conditions in the ...
11:00 < kanzure> ...range of 60 nm to several hundred micrometers. A genetically modified NM variant that presents reactive, surface-accessible cysteine residues was used to covalently link NM fibers to colloidal gold particles. These fibers were placed across gold electrodes, and additional metal was deposited by highly specific chemical enhancement of the colloidal gold by reductive deposition of metallic ...
11:00 < kanzure> ...silver and gold from salts. The resulting silver and gold wires were ≈100 nm wide. These biotemplated metal wires demonstrated the conductive properties of a solid metal wire, such as low resistance and ohmic behavior. With such materials it should be possible to harness the extraordinary diversity and specificity of protein functions to nanoscale electrical circuitry."
11:00 < kanzure> well that's cool... bit of a more specific setup for linking proteins to electrodes.
11:00 < kanzure> even tho there's other techniques i guess.
11:01 < yashgaroth> yeah most of the papers seem to be about activating electrodes with proteins
11:02 < kanzure> "Zinc-finger proteins for site-specific protein positioning on DNA origami structures" cool but not what i wanted..
11:03 < kanzure> this one suggests using spytag/spycatcher/spyligase for adhesion https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281928/
11:06 < yashgaroth> yeah the spy tags are interesting, though as with biotin/sav you need a way of controlling the polymerization
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11:07 < kanzure> nanografting with a metalloprotein https://pubs.acs.org/doi/abs/10.1021/nl025795h
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11:08 < yashgaroth> ooo
11:12 < yashgaroth> oh they're just scraping off some of the SAM layer so that the protein can bind
11:13 < kanzure> this one does protein nanostructures using protein G/rabbit IgG/anti-IgG https://pubs.acs.org/doi/abs/10.1021/la035491q
11:18 < kanzure> "Metallic nanostructures via static plowing lithography" http://persweb.wabash.edu/facstaff/porterl/PorterGroup/Publications/Reprints/LAP_NanoLett_2003.pdf
11:19 < kanzure> this one carves out shapes in a gold monolayer https://www.temple.edu/borguet/Publication/Documents/pdf_files/2006-1.pdf
11:20 < yashgaroth> that first one wins the prize for world's tiniest ELISA but that's about it
11:21 < yashgaroth> seems to be a lot of "plowing lithography" aka just carving stuff onto a surface with an AFM tip
11:24 < yashgaroth> surely someone's trying for an ignobel prize by nano-scraping a graffito onto something
11:29 < kanzure> solution might use something like glutaraldehyde for crosslinking
11:31 < yashgaroth> yeah that'd be a good choice, but delivering it or ablating it with nanometer precision...
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11:37 < kanzure> MultiColoredHat: be greeted
11:38 < MultiColoredHat> aloha:)
11:38 < MultiColoredHat> whats gucci
11:39 < MultiColoredHat> @kanzure, whats this channel about?
11:39 < kanzure> MultiColoredHat: http://diyhpl.us/wiki/hplusroadmap
11:48 < MultiColoredHat> got it
11:49 < MultiColoredHat> i am really into cures for everything
11:49 < MultiColoredHat> @kanzure, you guys heard of sodium chlorite?
11:49 < kanzure> .wik sodium chlorite
11:49 < yoleaux> "Sodium Chlorite (NaClO2) is a chemical compound used in the manufacturing of paper and as a disinfectant." — https://en.wikipedia.org/wiki/Sodium_chlorite
12:00 < kanzure> yeah it needs to be an AFM probe tip catalyzed reaction on the protein aggregate's surface...
12:00 < kanzure> and it can be positive or negative resist, i don't really care
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16:33 < kanzure> bulk nanotechnology approach:   bunch of nanoparticles or small proteins with weird shapes + glutaraldehyde + agarose gel ->  sift through the data set and find the nanostructures you wanted
16:34 < kanzure> random cross-linking should eventually create most small structures, or structures that you could experimentally use for various purposes
16:34 < kanzure> hence i have turned molecular nanotechnology into the kind of search problems that venture capitalists wake up in the middle of the night about missing out on
16:43 < kanzure> you only need to bootstrap a few dozen basic nanostructures, from which you can then make more tools
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18:49 < fenn> and it will only take 6 billion years
19:08 < kanzure> that's not clear to me, what are the actual bootstrapping parts that you really need?
19:09 < kanzure> also, what if most dust and sandstorms on earth were mostly molecular nanotech and nobody has ever really checked to see if this planet is already infested with old discarded nanotech? we have barely categorized a handful of viruses for pete's sake.
19:10 < kanzure> i think with AFM shotgun nanotech screening, the problem is what do you do when you find something- and how do you make it into something functionally useful for bootstrapping a thing
19:12 < kanzure> and most nanotech parts are going to be smaller than virus capsids
19:13 < kanzure> $500 whole genome sequencing https://us.dantelabs.com/collections/best-seller/products/whole-genome-sequencing-wgs-full-dna-analysis
19:17 < kanzure> .tw https://twitter.com/gwern/status/1004135264984489984
19:17 < yoleaux> Why I say we need to breed cats for domestication: apparently, it's perfectly normal to have a quarter (!) of your entire pet cat sample in an experiment not be examinable by a vet because they are so upset by travel/vet (& 1 couldn't even after drugged). https://www.dropbox.com/s/70h01puu1efbl7q/2017-vanhaaften.pdf?dl=0 https://pbs.twimg.com/media/De9ngY3XUAAVdzZ.jpg (@gwern)
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19:49 < kanzure> "Generation of surface amino groups on aromatic self-assembled monolayers by low energy electron beams- A first step towards chemical lithography" https://onlinelibrary.wiley.com/doi/abs/10.1002/(SICI)1521-4095(200006)12:11%3C805::AID-ADMA805%3E3.0.CO;2-0
19:49 < kanzure> (more -thiol stuff)
19:55 < kanzure> "Nanoscale site-selective catalysis of surface assemblies by palladium-coated atomic force microscopy tips: chemical lithography without electrical current" https://pubs.acs.org/doi/abs/10.1021/la000674n
19:56 < kanzure> hm that one was cited by freitas
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19:56 < kanzure> "Direct writing of electronic devices on graphene oxide by catalytic scanning probe lithography" etc..
20:02 < kanzure> "Current-less photoreactivity catalyzed by functionalized AFM tips" ok..
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20:13 < kanzure> wait... what?
20:13 < kanzure> http://cyber.sci-hub.tw/MTAuMTAzOC9ubWV0aC4yOTE4/church2014.pdf
20:15 < kanzure> http://cyber.sci-hub.tw/MTAuMTAzOC9ubWF0NDU5NA==/hughes2016.pdf
20:16 < kanzure> http://cyber.sci-hub.tw/MTAuMTAyMS9hY3NuYW5vLjViMDU3ODI=/aguilar2015.pdf
20:16 < kanzure> why was i having so much difficulty with guessing urls before?
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20:47 < kanzure> http://libgen.io/dbdumps/scimag/libgen_scimag_dbbackup-2018-06-15.rar
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20:59 < kanzure> http://moscow.sci-hub.tw/9f9b89f3c323b028e38fdf429c329789/church2014.pdf
20:59 < kanzure> http://moscow.sci-hub.tw/9f9b89f3c323b028e38fdf429c329789/xyz.pdf
21:05 < kanzure> forgot about the captchas -_-
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--- Log closed Tue Jun 19 00:00:50 2018