--- Log opened Fri Mar 02 00:00:07 2018 00:04 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 00:04 -!- TC is now known as Guest23439 00:08 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 268 seconds] 00:33 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 240 seconds] 00:59 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 01:01 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-thpebaigdtqmhcie] has joined ##hplusroadmap 01:01 < archels> Please provide us with the web link to your Google Scholar account. This is MANDATORY! We will not consider your application without an up-to-date Google Scholar account. 01:01 < archels> summer school registration form 01:38 < nmz787> https://www.youtube.com/watch?v=SAUEUwiZXxI 01:38 < nmz787> .title 01:38 < yoleaux> Fat Abbot South Park Clip 2 School In Sumertime - YouTube 03:33 -!- ebowden [~ebowden@128.250.0.208] has quit [Remote host closed the connection] 03:38 -!- ebowden [~ebowden@1.136.110.252] has joined ##hplusroadmap 03:39 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-thpebaigdtqmhcie] has quit [Quit: Connection closed for inactivity] 03:42 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 03:45 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has joined ##hplusroadmap 03:46 -!- emeraldgreen [~user@70.ip-145-239-90.eu] has quit [Client Quit] 04:05 -!- ebowden_ [~ebowden@128.250.0.208] has joined ##hplusroadmap 04:09 -!- ebowden [~ebowden@1.136.110.252] has quit [Ping timeout: 245 seconds] 04:11 < adlai> fenn: arguably, "bitcoin mining" will require much R&D towards continuous fabrication of new hardware... especially considering the whole PoW change issue (not that i'm backing one horse or the other, but, it's an issue) 04:54 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 265 seconds] 05:24 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 265 seconds] 05:25 -!- DataPacRat [~dan@vdsl-74.itcanada.com] has joined ##hplusroadmap 05:29 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 06:12 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 06:16 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Client Quit] 06:17 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 06:28 < kanzure> gp-write now wants "dream technology suggestions" for dna delivery 06:29 < kanzure> so i guess the most obvious one is "complete transfection of every cell in a mammal" 06:29 < kanzure> i also wrote down "optically-gated natural competence pores" 06:29 < kanzure> and those bacterial nanoneedles for dna transfer would be nice 06:29 -!- pasky [~pasky@nikam.ms.mff.cuni.cz] has quit [Ping timeout: 265 seconds] 06:29 < kanzure> and "transfection helper genes"- increase efficiency of electroporation, sonoporation, chemical transfection, lipofection, etc., by fiddling with upfront genetic contributions to the efficiency of those techniques 06:30 < kanzure> and more insane-level things like "make chromosomes non-essential to mammalian cell lifecycle" (and then you don't have to deliver big DNA fragments, just a bunch of small stuff) 06:30 < kanzure> "Better debugging and molecular reporters of delivery and integration efficiency (perhaps a DNA molecule reporter that can be sequenced from the bloodstream)" 06:31 -!- pasky [~pasky@nikam.ms.mff.cuni.cz] has joined ##hplusroadmap 06:36 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 06:57 -!- drewbot [~cinch@54.234.48.173] has joined ##hplusroadmap 07:09 < kanzure> "Interstellar communication message decontamination is impossible" https://arxiv.org/pdf/1802.02180.pdf 07:10 < kanzure> hmm typos "participate in a conversion with the ai" 07:18 -!- WeirdTolkienishF [~Weird@unaffiliated/weirdtolkienishf] has joined ##hplusroadmap 07:26 < kanzure> alright that was a waste of time 07:33 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 265 seconds] 08:21 -!- ebowden_ [~ebowden@128.250.0.208] has quit [Read error: Connection reset by peer] 08:21 -!- ebowden [~ebowden@128.250.0.208] has joined ##hplusroadmap 08:30 < maaku> .wik Micro black hole 08:30 < yoleaux> "Micro black holes, also called quantum mechanical black holes or mini black holes, are hypothetical tiny black holes, for which quantum mechanical effects play an important role. The concept that black holes may exist that are smaller than stellar mass was introduced in 1971 by Stephen Hawking." — https://en.wikipedia.org/wiki/Micro_black_hole 08:31 < maaku> hrm, that's not hte interesting bit 08:32 < JayDugger> Good morning. 08:34 -!- juri_ [~juri@205.166.94.162] has quit [Ping timeout: 256 seconds] 08:43 -!- augur [~augur@2600:380:8668:2097:1db7:cbb5:bad5:5b07] has joined ##hplusroadmap 08:46 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-kqcamarofdqsoatq] has joined ##hplusroadmap 09:01 -!- juri_ [~juri@205.166.94.162] has joined ##hplusroadmap 09:04 -!- DataPacRat [~dan@vdsl-74.itcanada.com] has quit [Ping timeout: 248 seconds] 10:15 -!- razzy` [~user@2001:718:2601:38f::21] has joined ##hplusroadmap 10:16 -!- razzy` [~user@2001:718:2601:38f::21] has quit [Remote host closed the connection] 10:24 < kanzure> .tw https://twitter.com/peterktodd/status/969504515215917056 10:24 < yoleaux> Interesting legal analysis of the new Blockchain Defensive Patent License that ASICBOOST will be licensed as (patent not yet granted). https://www.emergingtechlaw.org/analysis/creating-the-blockchain-defensive-patent-license420182 (@peterktodd) 10:30 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 256 seconds] 10:46 -!- augur [~augur@2600:380:8668:2097:1db7:cbb5:bad5:5b07] has quit [Remote host closed the connection] 11:24 < kanzure> http://growyourink.lapaillasse.org/ 11:29 < kanzure> .title https://www.reddit.com/r/Bitcoin/comments/813n2i/opening_asicboost_for_defensive_use_asicboost/ 11:29 < yoleaux> Too Many Requests 11:29 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 11:40 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 248 seconds] 11:41 < maaku> .title https://www.nytimes.com/2018/02/05/science/mutant-crayfish-clones-europe.html 11:41 < yoleaux> This Mutant Crayfish Clones Itself, and It’s Taking Over Europe - The New York Times 11:41 < maaku> self-replicating crayfish via a rather unique form of asexual replication 11:53 -!- drewbot [~cinch@54.234.48.173] has quit [Remote host closed the connection] 11:55 -!- augur [~augur@104-244-24-85.PUBLIC.monkeybrains.net] has joined ##hplusroadmap 12:11 -!- MrHindsight [~2020@unaffiliated/capthindsight] has quit [Read error: error:1408F10B:SSL routines:SSL3_GET_RECORD:wrong version number] 12:11 -!- MrHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 12:13 < TMA> I wonder if it is edible/tasty as several other crustaceans are 13:05 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 13:12 < maaku> well they probably all taste the same... 13:30 < kanzure> hmm we need enzymes to help prevent long DNA from breaking in vitro. 13:33 -!- Hooloovo0 [Hooloovoo@hooloovoo.blue] has quit [Ping timeout: 256 seconds] 13:34 -!- Hoolootwo [Hooloovoo@hooloovoo.blue] has joined ##hplusroadmap 13:44 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 13:50 -!- HEx1 [~HEx@hexwab.plus.com] has quit [Remote host closed the connection] 13:51 -!- HEx [~HEx@hexwab.plus.com] has joined ##hplusroadmap 13:51 -!- HEx is now known as Guest73008 13:52 -!- Guest73008 is now known as HEx1 13:53 -!- augur [~augur@104-244-24-85.PUBLIC.monkeybrains.net] has quit [Remote host closed the connection] 14:01 < kanzure> "Resetting the yeast epigenome with human nucleosomes" https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(17)31269-2 14:02 < kanzure> very cool paper. 14:22 < kanzure> "Humans and yeast are separated by a billion years of evolution, yet their conserved histones retain central roles in gene regulation. Here, we "reset" yeast to use core human nucleosomes in lieu of their own (a rare event taking 20 days), which initially only worked with variant H3.1. The cells adapt by acquiring suppressor mutations in cell-division genes or by acquiring certain aneuploid ... 14:22 < kanzure> ...states. Converting five histone residues to their yeast counterparts restored robust growth. We reveal that humanized nucleosomes are positioned according to endogenous yeast DNA sequence and chromatin-remodeling network, as judged by a yeast-like nucleosome repeat length. However, human nucleosomes have higher DNA occupancy, globally reduce RNA content, and slow adaptation to new conditions ... 14:22 < kanzure> ...by delaying chromatin remodeling. These humanized yeasts (including H3.3) pose fundamental new questions about how chromatin is linked to many cell processes and provide a platform to study histone variants via yeast epigenome reprogramming." 14:22 -!- DataPacRat [~dan@vdsl-74.itcanada.com] has joined ##hplusroadmap 15:00 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 15:55 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 15:57 -!- CandleGlow [~CandleGlo@unaffiliated/candleglow] has joined ##hplusroadmap 16:17 < fenn> re "dream technology" for DNA delivery, my idea is an intracellular protein based CPU that participates in the internet via DNA, RNA, and optical data packets. obviously it can also synthesize DNA and RNA for use in the cell by directing an engineered polymerase to do so 16:30 -!- red-001 is now known as red-3-2-2019 16:37 < nmz787> yes, remote-control (and data exfiltration) via RF is a definite 'want' 16:38 < nmz787> fenn: do you trust protein more than d/rna? stronger bonds? 16:38 < kanzure> ok added 16:38 < kanzure> dna delivery conversation was today 16:39 < kanzure> sending link by pm 16:39 < MrHindsight> nanodrones that look like tiny Dominos trucks? 16:40 < kanzure> there were a lot of complaints from bench biologists about the difficulties and time cost of doing microinjection straight into a cell's nucleus 16:40 < kanzure> seemed really manual for some reason 16:40 < kanzure> my recommendation was to automate it with some computer vision stuff 16:41 < nmz787> I can get some microinjectors for nothing if needed, the machine is programmable that makes them, so we can adjust params for final diameter and length and such 16:41 < nmz787> I guess throwing that on a piezo speaker buzzer thing would get some movement 16:41 < kanzure> also, microinjection into nucleus can only tolerate about 500 kb at the high end. i asked why that might be the case and the only answer was shear force. i'm not completely convinced (why not just inject more slowly, over multiple hours? if people are doing this manually then they probably don't want to be sitting there pipetting for 5 hours.) 16:42 < nmz787> hmm, maybe the injection volume and DNA concentration? 16:42 < nmz787> i.e. their needle is too long or something 16:42 < nmz787> too much dead volume 16:42 < MrHindsight> yeah, they use nanopositioners on a microscope stage with tiny needles 16:42 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-kqcamarofdqsoatq] has quit [Quit: Connection closed for inactivity] 16:43 < nmz787> I wonder if they push the DNA fluid with solvent or gas 16:43 < kanzure> the problem, they claim, is that the dna breaks apart. but i'm not convinced that this has been thoroughly experimentalized... 16:43 < fenn> nmz787: yes, protein is faster and more reliable because it uses covalent bonds rather than squishy thermodynamics concepts that are hard to see directly 16:43 < nmz787> fenn: ribozymes are also covalent though, right? 16:43 < fenn> compared to strand displacement reactions or whatever 16:44 < fenn> sure ribozymes are similar to what i'm thinking. it doesn't need to be protein specifically, but it is a mechanical object 16:44 < kanzure> one idea that was brought up was that you could use intracellular parasites to maybe deliver dna to the nucleus 16:44 < kanzure> parasites are good hosts for this because they have already co-evolved to be similar to the hyperhost machinery 16:45 < nmz787> kanzure: we should definitely ask how they eject the DNA solution into the nucleus, if by liquid or gas... I highly doubt they have a physical plunger, based on knowing how most microinjectors are pulled from glass capillaries 16:45 < nmz787> kanzure: liquid would mean diffusion, and thus limit their working time 16:45 < nmz787> so they'd have to work fast 16:45 < nmz787> and thus break shit 16:45 < kanzure> the reference i linked earlier regarding humanized chromatin in yeast was mentioned on the call. pretty neat concept. the concern is that dna donated from yeast conjugated to a mammalian cell wont be usable by the mammalian cell due to packaging and other stuff. so you could just force the yeast to do more mammalian-similar things. 16:46 < kanzure> likewise, one of the recommendations was to search for protozoa or eukyarotic algae that can do homologous recombination with similar efficiency as yeast, since eukaryotic algae is going to be much more similar to mammalian chromosome compatibility system things 16:46 < nmz787> mmm, that sounds like a good idea 16:47 < nmz787> euk algae are close than euk yeast? 16:47 < kanzure> cell fusion and conjugation are a good idea but i'm not convinced that it will cause dna to get into the nucleus in multi-cellular eukaryotic organisms 16:47 < kanzure> one possible way to overcome this is to disable the dna digestion enzymes that get expressed in the cytoplasm before the nucleus 16:47 < kanzure> nobody mentioned eukaryotic yeasts 16:47 < fenn> yeast is eukaryotic 16:48 < kanzure> welp. 16:48 < kanzure> anyway yes algae is closer 16:48 < kanzure> unfortunately nobody has really exhaustively searched for protozoa or algae that are really good at homologous recombination 16:50 < kanzure> "If you think about what delivers mammalian bp DNA through the cytoplasm into the nucleus, the only thing I can think of is sperm, some sort of synthetic delivery inspired yb that, some sort of organelle type thing with propulsion and protection for the DNA. That's where I would take inspiration from, in nature, otherwise I would be looking at mechanical engineered based mehtod to inject into ... 16:50 < kanzure> ...the nucleus directly." 16:50 -!- Gurkenglas [~Gurkengla@dslb-178-005-162-043.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 260 seconds] 16:51 < nmz787> hmm, that sounds very strange that algae would be closer... I mean, algae have photosynthesis, yeast don't, we don't... maybe I am misinterpreting how big photosynthesis seems to be of a difference 16:52 < nmz787> I guess it could have nothing to do with DNA packaging stuffs 16:53 < nmz787> kanzure: maybe there's a way to enable sperm to transcribe and translate DNA->protein, so they can self-select when you add DNA to the sperm (SMGT) 16:54 < nmz787> inject DNA+cell-free-expression-kit during SMGT 16:54 < nmz787> ? 17:05 < kanzure> you mean antibiotic selection thing? 17:08 < nmz787> something like that, but even fluorescent for a FACS machine to sort out, etc 17:08 < kanzure> ya that's the current proposal from yashgaroth (FACS things) 17:09 < nmz787> FACS!=facsimile 17:09 < nmz787> (yes I know you know) 17:15 < nmz787> note to self, just megadosed on 100kU of vitamin D 17:16 < fenn> you might want to keep a log book for that sort of thing 17:17 < nmz787> yeah, I actually was grepping these logs a few days ago looking for the link to the OK-safety paper on it, and saw I first did it last April 17:17 < nmz787> and had some other chat logs in gmail from December, which I guess was the last time 17:19 < fenn> sure looks like yeast is closer http://tolweb.org/Eukaryotes/ 17:19 < kanzure> there's a lot of different algae tho 17:19 < kanzure> and some complex algaes 17:20 < kanzure> hrm. i guess that's not a good argument. 17:22 -!- DataPacRat [~dan@vdsl-74.itcanada.com] has quit [Ping timeout: 245 seconds] 18:02 < fenn> https://www.roswellbiotech.com/ developing a semiconductor chip-based single-molecule sequencing technology that relies on molecular electronics. Roswell Biotechnologies Harnesses Molecular Electronics for Chip-Based DNA Sequencing 18:03 < fenn> Jan 10, 2018 | Julia Karow 18:03 < fenn> Premium 18:03 < fenn> NEW YORK (GenomeWeb) – Roswell Biotechnologies of San Diego is developing a semiconductor chip-based single-molecule sequencing technology that relies on molecular electronics. 18:03 < fenn> The technology, dubbed Electronic Nano-Device Sequencing (ENDSeq), measures changes in current that occur when a polymerase that is part of an integrated circuit incorporates nucleotides into a growing DNA strand. 18:03 < fenn> derp 18:06 < fenn> apparently they are measuring the resistance across a polymerase, and the shape of the resistance spike is related to the type of base incorporated 18:06 < fenn> each sensor is 10nm across 18:13 < fenn> oh 10nm is roughly the diameter of a polymerase molecule 18:39 < fenn> neat stuff: https://en.wikipedia.org/wiki/Dip-pen_nanolithography 18:41 < fenn> it should mention beam pen lithography, where transparent pens are coated in a metal, then the tip is cut off to make an aperture smaller than the wavelength of light to do nanoscale photolithography 18:42 < fenn> the pen acts as a waveguide 18:51 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 245 seconds] 18:51 -!- aeiousomething [~aeiousome@124.123.12.253] has joined ##hplusroadmap 19:36 -!- aeiousomething [~aeiousome@124.123.12.253] has quit [Ping timeout: 256 seconds] 19:41 -!- aeiousomething [aeiousomet@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 19:51 < fenn> "the centromeres in yeast are very different from the rest of the eukaryote kingdom" 19:52 < fenn> i think the GP-write guy just happened to be working with eukaryotic algae 19:52 -!- Hoolootwo is now known as Hooloovo0 19:56 -!- drewbot [~cinch@54.159.162.39] has joined ##hplusroadmap 19:59 < fenn> .wik magnetofection 19:59 < yoleaux> "Magnetofection is a simple and highly efficient transfection method that uses magnetic fields to concentrate particles containing nucleic acid into the target cells." — https://en.wikipedia.org/wiki/Magnetofection 20:00 < fenn> why the hell does this work? 20:01 < fenn> i guess it just shoves the particles into the cells 20:05 < fenn> omg it's literally just a permanent magnet 20:14 < fenn> you could encapsulate a chromosome in a magnetic nanoparticle and hope it gets into the nucleus by chance. it's not bad odds since the nucleus takes up a fairly large cross sectional area 20:15 < fenn> well i guess it's more like a microparticle than a nanoparticle 20:15 < fenn> anyway you could make a thing big enough to hold your dna and add magnetic stuff to the material you make it with 20:15 < fenn> it would slowly dissolve and then release the dna 20:18 < fenn> microfluidics is great at doing this sort of encapsulation of liquids with polymers 20:18 < fenn> the trick would be getting one chunk of DNA in one capsule 20:19 < fenn> maybe viral packaging machinery could help out here, but i don't know anything about that 20:23 < fenn> there's also cambrian's method of shooting micro beads off a slide with a laser 20:23 < fenn> shoot the beads into a cell nucleus directly 20:25 < kanzure> AAV can't package too many bp, that's the primary bottleneck in virus stuff; everyone is familiar with AAV and not as much interest in branching out to the bigger viruses. probably HSV-1 will be used more in the future tho, which can deliver significantly more bp like 100 kbp i think? 20:28 < fenn> human chromosomes are ~250Mbase 20:28 < kanzure> i think a chromosome is going to be much larger than a magnetic nanoparticle 20:28 < fenn> 10 micron 20:29 < fenn> width 1.4micron 20:29 < kanzure> thank you, dr. dimensional analysis. 20:31 < kanzure> roswell is a really cool name. i talked with them for a bit and i don't think they really understand what their tech can do. they either played dumb or they lack imagination. 20:31 < kanzure> their focus on sequencing is really weird. sure it can be used for sequencing. if you are a mortal. 20:31 < fenn> it makes me think of 1950s UFO aliens or the intel Haswell chips 20:32 < fenn> what would you do besides sequencing? 20:32 < kanzure> pm 20:32 < fenn> right 20:33 < kanzure> done 20:39 -!- adlai [~adlai@unaffiliated/adlai] has quit [K-Lined] 20:39 -!- streety [~streety@li761-24.members.linode.com] has quit [Ping timeout: 248 seconds] 20:40 * fenn waves to the spooks 20:41 -!- streety [~streety@li761-24.members.linode.com] has joined ##hplusroadmap 20:51 < kanzure> music! https://www.youtube.com/watch?v=_uGPS40cUAU&t=8m 21:08 < kanzure> .title https://www.fbo.gov/index?s=opportunity&mode=form&tab=core&id=27bb04c4f4027dd010792d7dd7dc19be 21:08 < yoleaux> kanzure: Sorry, that command (.title) took too long to process. 21:17 < kanzure> .wik crud coupled device 21:17 < yoleaux> "A distributed database is a database in which storage devices are not all attached to a common processor. It may be stored in multiple computers, located in the same physical location; or may be dispersed over a network of interconnected computers." — https://en.wikipedia.org/wiki/Distributed_database 21:17 < kanzure> uhrm... 21:20 < kanzure> ah, charge coupled devices 21:43 -!- DataPacRat [~dan@adsl-195.itcanada.com] has joined ##hplusroadmap 22:23 -!- jtimon [~quassel@41.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 240 seconds] 22:26 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: ORGANS IN MAINS] 23:16 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 23:17 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 240 seconds] 23:24 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] --- Log closed Sat Mar 03 00:00:08 2018