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07:12 < kanzure> 038r8iavd0[hf08
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07:41 < kanzure> "The team also calculated the planet's equivalent of computing power: the speed of DNA transcription. Given the average rate of genetic transcription for different organismal groups, they found that the biosphere processes more than 10^24 subunits of DNA per second."
07:42 < kanzure> "...Where do you see the future of the company in 5 and 10 years?" "In the next 5 years we want to be the largest manufacturer of DNA in the world. In 10 years we hope to be closer to our longterm mission of replacing all natural organisms on the planet with better synthetic ones. For instance having made the DNA for say 10% of all plant on the planet surface sounds like a reasonable goal."
07:46 < ebowden_> ...what company is this?
07:51 < kanzure> NERV
07:52 < Regex_> ebowden_: Cambrian Genomics https://www.reddit.com/r/Futurology/comments/2lhvkl/interview_with_cambrian_genomics_a_singularity/
07:56 < ebowden_> I'm going to need a lot of evidence to conclude that replacing all the earth's organisms with "better" synthetic ones is a good idea.
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07:57 < ebowden_> This is "nanobots repair all da cells lysed by ice crystals!" levels of woo.
07:59 < andytoshi> http://www.scottaaronson.com/blog/?p=2862 landed in my inbox a couple days ago
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08:32 < kanzure> also page 43 http://w3.ualg.pt/~hgalvao/MPOB/BacAbundBiomGrowthActivity.pdf
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08:33 < kanzure> "Bacterial growth rates range 0.1 to 1.0 d-1 (equivalent to doubling times of ~0.7 to 7 days)."
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08:42 < kanzure> more people complaining about tdcs https://news.ycombinator.com/item?id=12151337
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09:11 < JayDugger> NERV, heh.
09:11 < JayDugger> And from the nytimes. Pfui.
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09:51 < maaku> NERV, lol
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10:00 < Reventlov> https://web.archive.org/web/20160402030146/http://www.nature.com/news/chinese-project-probes-the-genetics-of-genius-1.12985 TIL
10:03 < Reventlov> >Studies in twins indicate that genetic factors should explain significantly more than half of the variation in adult general intelligence — the abstract quantity measured in IQ tests.
10:06 < Reventlov> https://en.wikipedia.org/wiki/Heritability_of_IQ interesting read
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10:24 < CaptHindsight> how small can one currently make a stand alone micropore sequencer?
10:26 < CaptHindsight> an 8bit microntroller die at 14nm might be <3um square
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10:50 < CaptHindsight> looks like I'll have to shrink organic semiconductor lithography down to <100nm
10:53 < CaptHindsight> for a brute force attempt at making a nanoscale synthetic ligation device
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11:20 < FourFire> Hello all
11:22 < FourFire> Has adeno-tetra-phosphate or adeno-pnta-phosphate synthesis been proposed to improve metabolic energy density?
11:23 < FourFire> (assuming such molecules are stable at 37⁰
11:23 < FourFire> )
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12:15 < CaptHindsight> "porous silicon was not only biocompatible, but could even provide a health benefit because when they dissolve they become silicic acid, which is vital substance for strong bones and healthy connective tissues."
12:40 < nmz787> SiO2 is etched by neurons
12:41 < kanzure> what ligation reaction would you be doing in a "micropore" precisely?
12:42 < nmz787> I was just thinking gibson-reagents for ligating and assembling oligos post-synthesis
12:43 < nmz787> but I was recommended a few days ago to reconsider synthetic chemistry as the efficiency was said to be higher (I am skeptical, but also that diybio person was mentioning this too... but I haven't really processed what this means and if there is a simple way around it)
12:44 < kanzure> there are probably some modern chemistry approaches that could be used, i don't think chemists have been looking to update oligonucleotide synthesis
12:44 < nmz787> something about synthetic chemistry assuring you that deletions prevent further polymerization
12:44 < kanzure> but it would require someone who knows about actual chemistry
12:44 < nmz787> but I seem to remember that being not true
12:44 < nmz787> they were recommending old-style phosphoramidite
12:45 < kanzure> "you do it"
12:45 < kanzure> no really, if they want to do phosphoramidite chemistry debugging, let's just pay them to do it
12:46 < nmz787> they also said the fluorescent terminator's that i.e. helicos or another company sells should last a LONG time if you're doing micro/nano fluidics
12:46 < nmz787> and also use PCR rather than e.coli
12:47 < nmz787> I think he was more recommending baby-steps rather than thinking through the whole next-gen mega-super-integrated-system
12:47 < nmz787> which yes makes engineering sense, but is also slightly harder to convince myself to do
12:47 < nmz787> or rather be excited about
12:48 < nmz787> I also could tell this person was much more informed about sequencing than synthesis
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12:48 < nmz787> but that they also knew much about close-to-single-molecule sensing and handling schemes
12:48 < nmz787> (because of trying to do sequencing a bunch)
12:50 < nmz787> I still think my idea is possible if you scale up the reaction molecules to the limit of detection... and there could be some other electrical techniques for increasing signal to noise... maybe a lock-in amplifier
12:55 < CaptHindsight> kanzure: "what ligation reaction would you be doing in a "micropore" precisely?"
12:56 < CaptHindsight> any or all required
12:56 < CaptHindsight> brute force build a ligator vs some hybrid is the question
12:58 < CaptHindsight> anything that works at this point is a plus
12:59 < CaptHindsight> if the POSaM had been in more hands the last 10 years things would be farther along
12:59 < CaptHindsight> but hardly anyone is actually building anything, they just yap about it
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13:15 < ybit_> http://www.lix.polytechnique.fr/~fvalenci/papers/cham.pdf
13:15 < ybit_> "The Chemical Abstract Machine"
13:16 < ybit_> "We introduce a new kind of abstract machine based on the chemical metaphor used in the l? language of Ban%tre & al. States of a machine are chemical solutions where floating molecules can interact according to reaction rules. Solutions can be stratified by encapsulating subsolutions within membranes that force reactions to occur locally. We illustrate the use of this model by describing the operational semantics of the TCCS and CCS process calculi. W
13:16 < ybit_> linked from https://cstheory.stackexchange.com/questions/70/what-are-the-historical-roots-of-milners-bigraphs
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17:29 < CaptHindsight> the ligatron 1000
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20:09 < kanzure> this "compartmentalized self-replication" paper has some details i wasn't expecting, http://diyhpl.us/~bryan/papers2/polymerase/Directed%20evolution%20of%20polymerase%20function%20by%20compartmentalized%20self-replication%20-%20Ghadessy.pdf
20:10 < kanzure> in particular they were putting ecoli into each water-in-oil bubble compartment
20:10 < kanzure> and they are not explicitly mentioning a protein expression system
20:10 < kanzure> but i'm pretty sure they have to be using protein expression from the leftover ecoli components. how else are they getting new polymerase enzymes to be created?
20:17 < yashgaroth> no protein expression, just dna replication, then they transform cells with the pcr products; they're heat-lysing the cells, so the ribosomes won't survive
20:17 < yashgaroth> "better" polymerases just copy their own DNA more so they're selected for in the next round of transformations, repeat
20:21 < yashgaroth> protein expression happens in those transformed host cells, which are assumed to only take up one copy of the gene
20:32 < kanzure> huh? what next round of transformations?
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20:32 < kanzure> what? they are breaking the emulsions?
20:33 < kanzure> oh they are re-creating the emulsions after each round of transformation?
20:33 < yashgaroth> ya
20:34 < kanzure> where is that mentioned >:(
20:34 < yashgaroth> figure 1
20:34 < kanzure> fuck everyone
20:34 < kanzure> btw i really think keeping it all in emulsion would be better. why not use protein expression system in each droplet?
20:35 < yashgaroth> well they picked the easiest enzyme to improve with this method
20:36 < yashgaroth> as long as there's positive selection of information you're okay, and that's easy with a polymerase since it copies its own gene
20:36 < kanzure> right, yes. but it seems like a ot of work to break down everything and make new cultures.
20:36 < kanzure> *lot
20:37 < yashgaroth> you can miniaturize and automate a lot of it, and even one mL of e.coli has a billion cells
20:38 < kanzure> yeah i'm just disappointed.    maybe the microfluidic paper has a better system.
20:40 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/A%20general%20strategy%20for%20expanding%20polymerase%20function%20by%20droplet%20microfluidics%20-%202016.pdf
20:40 < kanzure> nope looks like same thing. what..
20:40 < yashgaroth> "but with microfluidics"
20:45 < kanzure> wat.
20:46 < kanzure> there was a version of this where things would be attached to the ribosome instead of fully detaching
20:46 < kanzure> or the gene would be physically attached to the polymerase
20:46 < kanzure> as a tag
20:46 < yashgaroth> * display, eg ribosome display, dna display
20:46 < kanzure> maybe that's just my imagination, and i need to tell other people about that method?
20:46 < kanzure> yes but it was a compartmentalized self-replication method
20:47 < yashgaroth> do cells count as compartments
20:47 < kanzure> sure
20:47 < yashgaroth> then cell display counts I guess
20:50 < kanzure> huh..
20:52 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/Ultrahigh-throughput%20screening%20in%20drop-based%20microfluidics%20for%20directed%20evolution%20-%202010.pdf
20:52 < kanzure> yeast surface display stuff
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21:05 < kanzure> huh, nope. same technique.
21:06 < kanzure> "We break the emulsion to release the cells from the drops, allow the cells to replicate and then repeat the growth, induction, and sorting process."
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21:19 < kanzure> yashgaroth: found it, i was thinking of "in vitro compartmentalization" not "compartmentalized self-replication" http://diyhpl.us/~bryan/papers2/polymerase/Directed%20evolution%20by%20in%20vitro%20compartmentalization%20-%202006.pdf
21:21 < yashgaroth> is this for doing the actual synthesis reaction, or directed evolution of the enzymes, or both?
21:21 < kanzure> page 3 box 1
21:21 < kanzure> it's for directed evolution things
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21:23 < kanzure> "IVC has several advantages over other in vitro selection techniques such as phage-display, ribosome display, mRNA-peptide fusion, and SELEX[16]: firstly, it is possible to efficiently select for properties other than binding, such as catalytic or regulatory activities; and, secondly, it is possible to select for true intermolecular catalysis in trans (where the substrate is not linked to the catalyst), thus enabling the selection of ...
21:23 < kanzure> ... enzymes for multiple-turnover. Enzymes that have been selected for catalysis through the use of IVC include DNA methyltransferases[1,5,21], DNA polymerases[10,22], phosphotriesterases[4], restriction endonucleases[11], β-galactosidases[2], and thiolactonases[6]. IVC has also been used to select peptides and proteins for ligand binding[12–14,23,24] and regulatory activity[3]. Additionally, by replacing the in vitro ...
21:23 < kanzure> ... transcription-translation system with a transcription-only system it has been possible to select for ribozymes (catalytic RNAs) that catalyze Diels-Alder cycloaddition[8] and RNA ligation[25] in trans and with multiple turnovers."
21:23 < yashgaroth> yeah could be useful, selecting for stuff like independence from template length limits, stuff like that
21:25 < yashgaroth> for TdT that is, but yeah it's a good technique
21:27 < kanzure> i was v. confused seeing all that "put a cell in an emulsion droplet" stuff. it was not this "IVC" technique at all.
21:31 < kanzure> "A variety of strategies can be used to select for catalytic, binding or regulatory activities. To select for catalysis, the substrate, and subsequently the product, of the selected enzymatic activity can be physically linked to the gene, either directly[1,5,11,21] or via a microbead[4,25]. Genes encoding active enzymes will be associated with the product and, after breaking the emulsion (Steps 14–17), can be separated from genes ...
21:31 < kanzure> ... encoding inactive proteins attached to unmodified substrate by, for example, affinity purification[1,5,11,21] or fluorescence-activated ‘cell’-sorting of microbeads[4,25]. If the conditions for performing a selection are incompatible with the transcription-translation system then a useful strategy is to attach single genes to microbeads, express the genes in emulsion droplets and use a ligand or antibody on the microbeads to ...
21:31 < kanzure> ... capture the translated proteins. These microbeads can then be selected for catalysis by breaking the emulsion (Steps 14–17), washing and resuspending the microbeads in the desired buffer and re-emulsifying the microbeads by homogenization (refer to Step 11) to create a more monodisperse emulsion[4]. Alternatively, the microbeads can be selected for ligand binding[12]. After completing the selection, execute Steps 18–24 to recover ...
21:31 < kanzure> ... the selected genes."
21:52 < kanzure> CaptHindsight: you might be interested in this one,
21:52 < kanzure> "A bulk sub-femtoliter in vitro compartmentalization system using super-fine electrosprays" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873800/
21:53 < kanzure> "The extreme miniaturization of biological and chemical assays in aqueous-droplet compartments enables spatiotemporal control for large-scale parallel experimentation and can thus permit new capabilities for “digitizing” directed molecular evolution methodologies. We report a remarkably facile bulk method to generate mega-scale monodisperse sub-femtoliter aqueous droplets by electrospray, using a prototype head with super-fine inkjet ...
21:53 < kanzure> ... technology. Moreover, the electrostatic inkjet nozzle that injects the aqueous phase when immersed within an immiscible phase (an optimized oil/surfactant mixture) has the advantage of generating cell-like sub-femtoliter compartments for biomolecule encapsulation and successive biological and chemical reactions. Sub-femtoliter droplets of both liquid (water-in-oil, volumes ranging from 0.2 to 6.4 fL) and gel bead (agarose-in-oil, ...
21:53 < kanzure> ... volume ranging from 0.3 to 15.6 fL) compartments with average sizes of 1.3 μm and 1.5 μm, respectively, were successfully generated using an inkjet nozzle at a speed of more than 105 droplets per second. We demonstrated the applicability of this system by synthesizing fluorescent proteins using a cell-free expression system inside electrosprayed sub-femtoliter droplets at an accelerated rate, thereby extending the utility of ...
21:53 < kanzure> ... in vitro compartmentalization with improved analytical performance for a top-down artificial cellular system."
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22:00 < CaptHindsight> electrostatic needle
22:01 < CaptHindsight> red blood cell volumes
22:01 < CaptHindsight> print the insides and quickly wrap with/form a membrane
22:05 < CaptHindsight> I mentioned a few weeks ago that you could print enough wells on a single slide for an entire genome
22:07 < ebowden_> What kind of additive manufacturing stuff is done at your factory?
22:08 < CaptHindsight> R&D and materials development
22:08 < CaptHindsight> nano-yodas
22:08 < ebowden_> That makes it sound like more of a laboratory.
22:09 < CaptHindsight> it's more one/few of a kind type stuff
22:09 < ebowden_> So, nanoscale printing?
22:10 < CaptHindsight> some of that
22:10 < CaptHindsight> materials get formulated and manufactured
22:11 < ebowden_> Have you invented anything amazing?
22:11 < CaptHindsight> silent corduroy for the military
22:12 < CaptHindsight> no zip zip not matter how hard you try
22:12 < ebowden_> Oh cool.
22:12 < ebowden_> Chinese military?
22:12 < CaptHindsight> swiss army
22:12 < ebowden_> Huh.
22:13 < ebowden_> How much of the stuff do you make?
22:13 < CaptHindsight> oh the factory in China, just SLA/DLP/LCD type printers
22:13 < CaptHindsight> nothing exciting
22:14 < ebowden_> Ok. How much of the silent corduroy do you make?
22:14 < CaptHindsight> it's a secret
22:14 < ebowden_> Ahh. But high enough volumes to be decent money?
22:15 < CaptHindsight> once the Chinese find out they would flood the market with cheap imitations
22:15 < ebowden_> Find out that you are selling it, or how to make it?
22:16 < kanzure> yashgaroth: nmz787: okay made various updates to the draft, have written out some sections (although i'm sure the text needs to be edited a bunch to look sane)
22:16 < CaptHindsight> http://imgur.com/a/eGlOs  any Russian translators in here?
22:47 < kanzure> maaku: nintendo stock went down anyway
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