--- Log opened Wed Feb 12 00:00:37 2020
00:32 < nmz787> vacuum leaks suck
01:57 < juri_> yep!
01:57 < juri_> how bad?
02:17 < nmz787> I'm at 8.3 torr in this PVC chamber I've been building
02:17 < nmz787> pump gets down to 1*10^-2 torr with gauge directly connected
02:19 < juri_> Ugg.
02:19 < juri_> have you hit your seals with alcohol?
02:20 < nmz787> yeah
02:20 < nmz787> well, all but some brass tee fittings that were underneath the chamber
02:21 < nmz787> they're my biggest suspect at this point, I think
02:21 < juri_> no pressure bounce?
02:21  * juri_ nods.
02:21 < nmz787> nah
02:21 < nmz787> there was, but I solved that one
02:21  * juri_ sighs, really wishes she had her old SEM. :~(
02:21 < nmz787> but my vacuum didn't significantly improve
02:21 < nmz787> :(
02:22 < nmz787> gotta find a new old SEM
02:22 < nmz787> or a new less-old SEM
02:22 < juri_> yeah. been trolling ebay, but i don't have 5K to blow. :)
02:22  * nmz787 wishes my SEM was paid more attention to re: repairs
02:22 < nmz787> I have all the parts to get the column back together
02:22 < nmz787> and attempt a pumpdown with new oil
02:22 < nmz787> but... time
02:23 < nmz787> on that note, gotta go sleep
02:23 < nmz787> I'm already late for bed
02:23 < juri_> rest well.
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06:00 < lsneff> Does anyone have a copy of self-replicating kinematic machines? It appears to be out of print and my university library doesn't have it.
06:14 < lsneff> Ah nvm, I found the ebook
06:14 < lsneff> Too bad the format isn't ideal
07:27 < nsh> http://93.174.95.29/main/62000/5689cfd150f0a8c30e95bc8c33e1ec9c/Robert%20A.%20Freitas%20Jr.%2C%20Ralph%20C.%20Merkle%20-%20Kinematic%20Self-Replicating%20Machines-Landes%20Bioscience_Eurekah.com%20%282004%29.pdf
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07:35 < kanzure> lsneff: i have a pdf somewhere.
07:35 < kanzure> hrm maybe not.
07:36 < kanzure> i recall intentionally making a pdf from the website because i speculated that freitas is the type of person to continuously update his material, and it's less likely that some ebook will have the updates
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07:45 < lsneff> Thanks nsh
07:45 < lsneff> And yeah, I'd guess the same of freitas
07:45 < lsneff> I wonder what he's doing these days
07:47 < nsh> np
07:47 < kanzure> send him fan mail, i think we're his only fan club
07:47 < kanzure> rfreitas@rfreitas.com
07:51 < lsneff> I feel bad for him and merkle
07:51 < lsneff> Drexler too
07:51 < lsneff> They tried to push people to make this incredible technology and no one did it
07:52 < kanzure> because you have to build things yourself instead of asking people to do it
07:52 < kanzure> things don't get built by making passionate arguments about why they are interesting
07:52 < kanzure> things get built by doing hard work
07:52 < kanzure> and, arguably, convincing people to do your bidding for you can be significantly harder
07:53 < kanzure> like you're merkle, do you really want to gamble that your skills of persuasion are superior to your technical skills? is that really a gamble that you're going to make...?
07:56 < kanzure> on another note: given an arbitrary three-dimensional shape is it possible to show that the shape can be constructed by amino acid strings, amino-amino contact interactions, peptides, and proteins?
07:56 < kanzure> specifically i'm excluding the question of protein folding, and i'm willing to have a much more limited environment of folds and peptide-peptide or protein-protein glue
07:57 < kanzure> i think the DNA origami people came up with something for tessellating a three-dimensional object into a collection of DNA strings
07:58 < lsneff> What have they even been doing for the past 10 years?
07:58 < kanzure> what was the name.... it was the thing that the DNA origami people migrated to after nanoengineer died. it was like cadnanononono or something.
07:59 < lsneff> Cadnano
08:00 < kanzure> yeah so why don't we have this for protein-protein structures?
08:00 < kanzure> molecular nanotechnology doesn't necessarily need to solve protein folding, just building stuff out of protein and amino acids (e.g. the engineering thing where the underlying science doesn't matter as long as you have predictable effects)
08:02 < lsneff> There's a presentation that Drexler did a few years back where he talked about that
08:02 < lsneff> Positional assembly of protein structures
08:09 < lsneff> The idea was you'd fold dna into a 3d printer-like structure and it'd use a tooltip to activate bonding sites on proteins
08:10 < kanzure> no
08:11 < kanzure> i think the only tooltip you should rely on is a ribosome spitting out amino acid strings
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08:12 < lsneff> Ah, so they'd self assemble?
08:25 < lsneff> That seems more complicated to me than position assembly.
08:29 < kanzure> if position assembly was so simple then we'd already have it.
08:29 < kanzure> people have been investigating it for a while. freitas, merkle and drexler have been thinking about it for decades.
08:33 < kanzure> "Hierarchical assembly of DNA-protein nanostructures" https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=922060
08:36 < kanzure> here they use RecA protein filaments to strengthen the DNA origami nanostructure (RecA is a DNA binding protein)
08:38 < kanzure> RecA only binds 3 bp at a time? what. might as well go with dCas9 surely...
08:49 < kanzure> here is one that increases DNA filament rigidity using a "virus-inspired protein" https://pubs.rsc.org/en/content/articlelanding/2019/nr/c9nr05225a/unauth#!divAbstract
08:53 < kanzure> and here they use bovine serum albumin and "class II hydrophobin" https://onlinelibrary.wiley.com/doi/pdf/10.1002/adhm.201700692
08:56 < kanzure> they should probably use glutaraldehyde to stabilize the protein-encapsulated DNA filaments...
08:58 < kanzure> apparently they do use glutaraldehyde as a crosslinking agent in a step to convert a DNA string into a metallized conductive instrument https://www.nature.com/articles/ncomms2690.pdf?origin=ppub
08:58 < kanzure> for lithography purposes.
09:01 < kanzure> thinking some more about the problem, i think it would probably be ideal to assume the work surface is flat and that the nanofactory is mostly a "two-dimensional" structure, consisting of surface-bound components that pass materials around to different areas that are linker-functionalized to perform certain reactions.
09:01 < kanzure> instead of using encapsulation to keep reactant factors close together, i would propose using DNA-cobinding with the intermediate manufactured materials.
09:02 < kanzure> and then pass along that DNA molecule from component to component (the materials would be attached to the DNA molecule as they are moved to each step)
09:13 < kanzure> this is in comparison to the conventional three-dimensional conglomerate nanofactory idea (where the nanofactory is either a giant protein with a bunch of interior pockets, or some well-ordered positionally-assembled masterpiece)
09:13 < kanzure> masterpiece nano-cube of sorts.
09:17 < lsneff> Is a positionally-assembled masterpiece not still the end goal?
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09:20 < lsneff> I assumed you meant this nanofactory as a bootstrapping step, but perhaps I'm wrong
09:25 < kanzure> it sort of doesn't matter, as long as you have some sense of programmability and reliability
09:26 < kanzure> and being able to reliably construct designed things
09:26 < lsneff> These would be programmable in mass, right?
09:26 < lsneff> You'd have a beaker full of them that all make the same thing
09:27 < kanzure> shrug, dunno
09:28 < kanzure> metallized and graphene-linked DNA filaments seems useful for nanolithography and then it's just a few more short hops to get to nanoMEMS mechanical motion stuff https://www.nature.com/articles/ncomms2690.pdf?origin=ppub (or use DNA motors and protein motors...)
09:33 < kanzure> i think the thing to do would be something like dCas9 fusion proteins (fused to proteins or amino acid residues that perform a specific catalytic reaction step in the manufacturing process) that attach to the matched DNA segment, then they bind there forever.
09:35 < kanzure> goal is molecular assembly blocks like lego, then lego stuff together to bootstrap more nano-precision capabilities
09:37 < kanzure> but a strong argument could be made that AFM tip manipulation of DNA origami structures can't be used to make lego bricks, and that the only way to build this stuff up is with programmable DNA-protein origami nanostructures and AFM doesn't help...
09:38 < kanzure> maybe you can drag around a nanostrucure with an AFM tip (just mechanical force) until it bumps into another nanostructure that is pre-functionalized with a binding catalyst thing.
09:47 < kanzure> figure 1? https://sci-hub.tw/https://ieeexplore.ieee.org/abstract/document/8346490
09:48 < kanzure> excuse me, figure 3. this is a spider silk + FIB variation.
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09:52 < kanzure> not sure how they are inducing crosslinking by their FIB though...
09:57 < abetusk> nmz787, I forgot where I heard it, either from Ben Krasnow or the Though Emporium, but they were trying to draw a vacuum and mentioned that PVC is porous and they had to go with a different material
10:01 < kanzure> here is one for "polyphenols" for molecular lego crosslinking https://minerva-access.unimelb.edu.au/bitstream/handle/11343/120178/Caruso_NNANO-16040759A_ms_rev_acc.pdf?sequence=1&isAllowed=y
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17:22 < kanzure> https://rivalvoices.substack.com/p/fuck-it-we-ball-on-rats-postrats
17:22 < maaku> lsneff: Drexler works on AI-risk stuff for Nick Bostrom
17:22 < maaku> Merkle has some sort of startup, presumably related to his recent patents regarding mechanical computation
17:23 < maaku> Freitas, I don't know
17:24 < kanzure> merkle sold out to ethereum crowd
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17:53 < lsneff> That's what I heard about merkle yeah
17:54 < lsneff> He's being shown off because he's well-known
18:10 < lsneff> Look: https://patents.google.com/patent/US20190250187A1/en?inventor=Ralph+C.+Merkle&sort=new
18:11 < lsneff> It's assigned to cbn nano technologies, inc
18:11 < lsneff> They recently got a $40 million investment from the canadian government: https://www.canada.ca/en/innovation-science-economic-development/news/2019/07/minister-bains-announces-investment-that-will-position-canada-as-global-leader-in-nanomanufacturing.html
18:12 < lsneff> to work on mechanosynthesis
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18:18 < fenn> huh. rub shoulders with bankers because of crypto-shenanigans and they end up funding actual research
18:19 < lsneff> It could be fruitful to become more familiar with some of the people involved.
18:20 < lsneff> maaku: ^
18:20 < lsneff> and freitas is involved too.
18:20 < lsneff> I guess they all came out of retirement
18:21 < fenn> inventors Damian G. Allis, Jeremy Barton, Michael Drew, Robert A. Freitas, Aru Hill, Matthew Robert Kennedy, Ralph C. Merkle, Tait Takatani, Michael Shawn Marshall
18:21 < fenn> i don't think there's anything new in this patent
18:21 < fenn> just glancing at the figures
18:22 < fenn> but good for them, getting some real money
18:22 < lsneff> Yeah, looks like old mechanosynthesis stuff
18:22 < lsneff> This must have been the stealth startup that merkle has mentioned in the past
18:22 < fenn> "nanofactory corporation" doesn't sound particularly stealthy
18:23 < lsneff> Yes, but they have no online presence basically, I'd still call it stealth
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18:31 < lsneff> Has merkle ever found this group? He appears to be connected to a few other h+ groups
18:34 < kanzure> no he hasn't been here
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19:45 < lsneff> .yt https://www.youtube.com/watch?v=cdKyf8fsH6w
19:46 < lsneff> "An Introduction to Molecular Nanotechnology with Ralph Merkle | Singularity University"
20:05 < lsneff> I dug a little deeper into the cbn nano technologies inc stuff
20:05 < lsneff> It looks like most of the employees are from a california company that got acquired in 2018
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22:51 < nmz787> kanzure: there are only 4 DNA bases... but "Despite the use of only 22 amino acids (21 in eukaryotes[note 1]) by the translational machinery to assemble proteins (the proteinogenic amino acids), over 140 amino acids are known to occur naturally in proteins"
22:52 < nmz787> kanzure: so the complexity of doing protein origami is wayyyy higher
22:55 < nmz787> and the tessellated DNA origami is called DNA tiles and bricks
23:03 < nmz787> that DNA metallization looks really similar to silver plating via the Brashear process (http://www.ilpi.com/glassblowing/tutorial_silvering.html) except that the reaction is less reactive and the DNA is somehow activating/nucleating the deposition
23:07 < nmz787> kanzure: it says low dosage of ions from the FIB cause the crosslinking... I've also seen crosslinking as a potential outcome with things like PMMA during FIB patterning
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23:21 < nmz787> abetusk: hmm, I thought it was only "gas permeable" on a relatively low level... thanks for the tip, searching on it now. I've got quite a bit of surface area (10" diameter, about 3 ft tall)
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--- Log closed Thu Feb 13 00:00:39 2020