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| kanzure | david pearce is still doing his one-file-per-domain-name thing http://www.biointelligence-explosion.com/biointelligence-explosion.pdf | 07:29 |
|---|---|---|
| kanzure | owait freeman dyson is still alive? | 07:29 |
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| kanzure | "the world becomes so weird that money no longer has value; e.g. we all become inert mathematical abstractions." eh there are worse fates i guess. | 07:49 |
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| justanotheruser | not hip enough. Should be biointelligence-explosion.io | 09:03 |
| justanotheruser | or biointelligence-explodr.io | 09:03 |
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| kanzure | justanotheruser: the context here is that david pearce is well known for having purchased 10,000 domain names and keeping only a single page of content on each one | 10:09 |
| kanzure | http://diyhpl.us/~bryan/irc/david-pearce-domains.url.txt | 10:09 |
| kanzure | of course this is only 3700 of his domains | 10:09 |
| chris_99 | that's insane | 10:11 |
| chris_99 | that must cost a fortune too | 10:11 |
| archels | Pearce owns jetpress.org? I didn't know that | 10:12 |
| archels | nah, whois says James Hughes | 10:13 |
| kanzure | james hughes and david pearce are friends and colleagues so it's not surprising | 10:13 |
| kanzure | at minimum, david pearce *hosts* jetpress.org | 10:13 |
| kanzure | "that's insane" correct | 10:14 |
| archels | cool | 10:14 |
| kanzure | what's really funny is that faceface/dbolser once introduced me into the korean equivalent of david pearce, a dude named jong bhak who owns the 10,000 domains starting with bio- | 10:15 |
| justanotheruser | oh wow, you're actually serious about thousands of domains | 10:16 |
| kanzure | http://jongbhak.com/index.php/Latest_CV_of_Jong_Bhak | 10:16 |
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| justanotheruser | what, cocaine.org | 10:16 |
| archels | isn't this all pretty meaningless? domain squatting is so 1990s | 10:17 |
| justanotheruser | is he just a squatter hoping some of them become valuable? | 10:17 |
| kanzure | yes i think he's sold some of the domains or let them expire | 10:17 |
| archels | if you actually do something and link them up like Pearce did with (I guess a subset of) them, that's cool | 10:17 |
| kanzure | well when you're fucking loaded with money, playing games like this is totally trivial | 10:17 |
| archels | heh | 10:17 |
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| kanzure | other than that, i have no explanation | 10:21 |
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| kanzure | ]/win 5 | 10:30 |
| kanzure | frlkjasdf | 10:30 |
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| kanzure | "Trapping a transition state in a computationally designed protein bottle" http://www.bakerlab.org/system/files/Mills_Science_2015A.pdf | 12:14 |
| kanzure | "Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score" http://nar.oxfordjournals.org/content/43/11/5340 | 12:15 |
| kanzure | instead of trying to use a limited subset of amino acids to get easier-to-predict protein structures, you could have protein subunits with simple linkers that you could enable/disable. the minimum size of your nanostructures would be much larger, and you'd essentially only have a cube to work with, and you would probably need a laborious chemical procedure to assemble your final structure, but you'd essentially have structural protein legos. | 12:38 |
| kanzure | you would need to find some protein-protein subunit linking method that would ideally be more than a single bond, plus the linker method would have to be easily disabled by misprinting the sequence for one of the residues (so that you can disable different linkers on a single cube) | 12:39 |
| kanzure | i suspect this would not work for large nanostructures because of yield problems... if it takes you 800 reactions to assemble your protein structure monstrosity, yield problems will cause a lot of trouble for you trying to reach the final state. | 12:41 |
| drethelin | what is the goal here anyway | 12:41 |
| drethelin | like what are we trying to build | 12:41 |
| kanzure | well, having a general library of structural nanosystems would be useful for doing nanothings | 12:41 |
| kanzure | at the moment our ability to make nanoscale structures is rather limited | 12:43 |
| kanzure | whoops i mean nanoscale nanostructure nanothings. everything in nanoworld is more nanoified... | 12:44 |
| kanzure | .wik molecular machine | 12:46 |
| yoleaux | "A molecular machine, or nanomachine, is any discrete number of molecular components that produce quasi-mechanical movements (output) in response to specific stimuli (input). The expression is often more generally applied to molecules that simply mimic functions that occur at the macroscopic level." — https://en.wikipedia.org/wiki/Molecular_machine | 12:46 |
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| kanzure | wow these examples all suck | 12:49 |
| kanzure | you could have very large molecular differential gears https://camo.githubusercontent.com/c17786e5d6d83085c219198bc3cf8a83347f7e0b/687474703a2f2f64697968706c2e75732f7e627279616e2f6972632f6e616e6f656e67696e6565722f696d616765732f647265786c65722d6d65726b6c652d646966666572656e7469616c2d676561722e676966 | 12:50 |
| kanzure | drethelin: more broadly, see http://www.youtube.com/watch?v=vEYN18d7gHg | 12:50 |
| kanzure | eudoxia: you should make a list of useful molecular machines in the 100k-10M atoms range. | 12:57 |
| CaptHindsight | funny how the mechanisms in the first stage all have subatomic resolution | 13:27 |
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| kish | so what's tis about | 14:21 |
| kish | what gives | 14:21 |
| kanzure | we're just plotting to blow up a few dozen galaxies within the next 2 or 3 million years, nothing much | 14:24 |
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| CaptHindsight | I think that QC needs to be built into the synthesizer | 15:02 |
| CaptHindsight | nano synthesizer with something like a nanopore that does QC as it builds | 15:05 |
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| CaptHindsight | how well is DNA ligase understood? | 15:55 |
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| ParahSailin_ | there are some thermostable ligases that will tolerate a G-T wobble hybridization | 15:59 |
| ParahSailin_ | to my knowledge there isnt even a publication mentioning this | 15:59 |
| ParahSailin_ | its more of lab lore | 15:59 |
| CaptHindsight | heh | 15:59 |
| CaptHindsight | how to build in base excision repair, nucleotide excision repair and mismatch repair | 16:05 |
| CaptHindsight | start building nano machines that contain repair proteins | 16:07 |
| FourFire | CaptHindsight, how is that easier/superior to inserting the genes into the genome? | 16:09 |
| FourFire | (with crispir/next gen of that tech) | 16:10 |
| CaptHindsight | FourFire: I'm just looking at ways to build QC into a synthesizer | 16:11 |
| CaptHindsight | so what you insert is what you wanted, now whats to stop mechanisms from correcting or removing what you want to insert is another story | 16:12 |
| FourFire | CaptHindsight, yeah, I need to study more | 16:13 |
| CaptHindsight | me too | 16:13 |
| FourFire | CaptHindsight, even if one method is actually superior to another, i consider it worthwhile for all the obvious routes to be developed in parallel incase one is 10 yrs easier to implement | 16:16 |
| CaptHindsight | have to start somewhere | 16:17 |
| CaptHindsight | I still wonder how much of this is known but kept private | 16:18 |
| FourFire | what I'm saying is if you've got an idea, go for it, don't be discouraged by me questioning it's effacy | 16:18 |
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| kanzure | traditionally the quality control is just a matter of dna sequencing, mass spec, etc. | 16:55 |
| kanzure | "deep space network now" http://eyes.nasa.gov/dsn/dsn.html | 16:57 |
| kanzure | this is a sort of dumb page... | 16:58 |
| kanzure | .wik midazolam | 17:02 |
| yoleaux | "Midazolam (/mɪˈdæzəlæm/, marketed in English-speaking countries and Mexico under the trade names Dormicum, Hypnovel, and Versed,) is a short-acting central nervous system (CNS) depressant of the benzodiazepine class developed by Hoffmann-La Roche in the 1970s." — https://en.wikipedia.org/wiki/Midazolam | 17:02 |
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| CaptHindsight | if you have built in error correction to synthesis that is very error prone and the error correction step takes as long as each step in the synthesis what do you gain? | 17:16 |
| CaptHindsight | if you perform synthesis in massive parallel operations what do you lose by doing QC only at the end of synthesis? | 17:18 |
| CaptHindsight | just the cost of operation and the chemicals | 17:19 |
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| kanzure | well you have to spend more of your parallelism on doing the same thing, basically | 17:41 |
| kanzure | (if you do quality control only at the end) | 17:42 |
| fenn | this seems amenable to mathematical analysis | 17:55 |
| fenn | is there a mathematician in the house! | 17:56 |
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| CaptHindsight | you can also do synthesis in massive parallel operation and error correct on the way | 18:01 |
| CaptHindsight | how efficient do you want/need to be? | 18:01 |
| CaptHindsight | How much does it cost either way? | 18:01 |
| CaptHindsight | how long does each step take? | 18:02 |
| CaptHindsight | with and without error correction | 18:02 |
| CaptHindsight | with inkjet, it's what ~96 samples per tray? | 18:03 |
| CaptHindsight | with DLP it's 2.3 million per tray | 18:04 |
| CaptHindsight | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741231/ | 18:12 |
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| CaptHindsight | no far fewer " The actual device contained 128 × 31 (total 3698) individual pico-reaction chambers" | 18:14 |
| CaptHindsight | but if you can get a 1:1 mirror to reaction chamber ratio then you're back to 2.3 million | 18:20 |
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| CaptHindsight | hmm, Roche NimbleGen used DLP to make maskless | 19:09 |
| CaptHindsight | microarrays | 19:09 |
| CaptHindsight | but got out of the business 3 years ago | 19:09 |
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| CaptHindsight | https://www.youtube.com/watch?v=eSr5CxAdiww Agilent uses inkjet and gets >99% efficiency | 19:21 |
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| nmz787_i | papermonkey: 10.1002/adma.201502092 | 19:51 |
| nmz787_i | .title http://onlinelibrary.wiley.com/doi/10.1002/adma.201502092/abstract | 19:51 |
| yoleaux | nmz787_i: Sorry, that doesn't appear to be an HTML page. | 19:52 |
| nmz787_i | High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks | 19:58 |
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| nmz787_i | http://onlinelibrary.wiley.com/store/10.1002/adma.201502092/asset/supinfo/adma201502092-sup-0001-S1.pdf?v=1&s=607028810176411d8bde875bf2214e98a04cde21 | 20:00 |
| kanzure | so this is just printing over the same location multiple times? | 20:05 |
| CaptHindsight | yes, with multiple inkjet fluids | 20:10 |
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| kanzure | how is there no splash? | 20:11 |
| kanzure | .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741231/ | 20:12 |
| yoleaux | Photoelectrochemical synthesis of DNA microarrays | 20:12 |
| kanzure | yeah it's a little strange that there were only 3698 reaction chambers in that example | 20:13 |
| kanzure | 1024x1024 micromirror array even when suboptimally used should still get you more than 10k reactions in parallel... not just 3700.... | 20:13 |
| CaptHindsight | who knows, maybe they were running DOS | 20:15 |
| kanzure | what does ">99% efficiency" actually man | 20:15 |
| kanzure | *actually mean | 20:15 |
| kanzure | also this is for oligo probe hybridization stuff (not the end of the world, of course) | 20:16 |
| kanzure | (i mean, the difference is that oligo probe hybridization stuff is not designed to be combined into larger sequences (since you just insert your molecular junk and then look at the hybridization results visually)) | 20:16 |
| kanzure | (((the agilent video))) | 20:17 |
| kanzure | fenn: there is a lack of good documents on the interwebs about useful molecular machines to do with basic nanotechnology, perhaps you have a few in mind that could be added to the wiki? | 20:20 |
| kanzure | useful and er simple molecular machines. not the do-everything molecular mechanisms. | 20:21 |
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| --- Log closed Mon Jul 06 00:00:02 2015 | ||
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