--- Log opened Sat Jul 16 00:00:58 2016 00:38 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-gxynsdtixnjcpujm] has joined ##hplusroadmap 00:51 -!- augur [~augur@2602:304:cdac:e260:4c6f:24e1:76fa:7c50] has quit [Remote host closed the connection] 00:52 -!- augur [~augur@2602:304:cdac:e260:4c6f:24e1:76fa:7c50] has joined ##hplusroadmap 00:57 -!- augur [~augur@2602:304:cdac:e260:4c6f:24e1:76fa:7c50] has quit [Ping timeout: 250 seconds] 00:58 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 01:04 -!- esmerelda [~mabel@unaffiliated/jacco] has joined ##hplusroadmap 01:13 -!- esmerelda is now known as mabel 01:18 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 01:34 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has quit [Remote host closed the connection] 01:52 -!- nmz787_i [ntmccork@nat/intel/x-dhwzyyeyiapdbzfu] has quit [Quit: Leaving.] 02:11 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 02:16 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Ping timeout: 260 seconds] 02:41 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-gxynsdtixnjcpujm] has quit [Quit: Connection closed for inactivity] 02:43 -!- nmz787_i [~ntmccork@134.134.137.71] has joined ##hplusroadmap 02:46 -!- nmz787_i [~ntmccork@134.134.137.71] has quit [Client Quit] 03:19 -!- mabel [~mabel@unaffiliated/jacco] has quit [Ping timeout: 244 seconds] 03:28 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-odyegfjenayuzmsr] has joined ##hplusroadmap 03:29 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 03:30 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 03:34 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Ping timeout: 260 seconds] 05:10 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 05:34 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 05:51 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-odyegfjenayuzmsr] has quit [Quit: Connection closed for inactivity] 06:14 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 06:17 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 06:18 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 06:19 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 06:34 -!- ebowden_ [~ebowden@1.136.97.95] has joined ##hplusroadmap 07:52 < kanzure> hmph 07:59 -!- nickjohnson [sid789@gateway/web/irccloud.com/x-dahcblljbfxjvdxt] has quit [Ping timeout: 264 seconds] 07:59 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-tclkfcxkwfetpwxu] has joined ##hplusroadmap 08:02 -!- nickjohnson [sid789@gateway/web/irccloud.com/x-cbieemzxgyjfzoku] has joined ##hplusroadmap 08:10 -!- ebowden_ [~ebowden@1.136.97.95] has quit [Remote host closed the connection] 08:27 < kanzure> fenn: why bother with sequencing with FISSEQ and proten expression labeling stuff, if you are already placing the tissue slice in front of a microscope anyway? you might as well do imaging, not sequencing. 08:27 < kanzure> for connections i think sequencing is still required. 08:29 < kanzure> https://openaps.org/ "open artificial pancreas project" 08:29 < kanzure> https://openaps.org/reference-design/ 08:29 < kanzure> https://github.com/openaps/openaps 08:30 < kanzure> https://github.com/openaps/oref0 08:53 < CaptHindsight> I'm glad they chose the pancreas, the pancreas and the spleen tend to get overshadowed by other organs in the press 08:54 < CaptHindsight> how many news articles feature the spleen? It tends to be heart, lungs and stomach 08:56 < kanzure> .wik systematic evolution of ligands by exponential enrichment 08:56 < yoleaux> "Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands." — https://en.wikipedia.org/wiki/Systematic_evolution_of_ligands_by_exponential_enrichment 08:59 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has joined ##hplusroadmap 09:09 < streety> I thought that open pancreas project was started and run by diabetics - i.e. they're building a device they themselves want to use / are using 09:11 < kanzure> here is a good overview of SELEX things http://www.medicinal-chemistry.org/files/harki/The%20Discovery%20of%20Protein-Targeting%20Aptamers%20by%20SELEX.pdf 09:13 < kanzure> "cell-SELEX" i wonder if this is for cell surface property selection, or if this is something else.. 09:17 < kanzure> another overview http://www.trilinkbiotech.com/tech/selex.asp 09:21 < kanzure> peptide sequencing still works, right? we could modify a ribosome to print random amino acid chains instead of looking at RNA. the goal would be to select for ribosomes that print really long proteins. and then later the goal would be to select for ribosomes that are more controllable by human influence or human-generated signals. (this is an alternative to the idea of using a library of 64 synthetases and an evolved ribosome that binds ... 09:21 < kanzure> ... to whatever synthetase we give it). 09:23 < CaptHindsight> kanzure: for some reason the inkjet DNA printer is suddenly getting interest yet the paper is from 2004 09:24 < kanzure> https://www.google.com/search?q=site%3Aigem.org+SELEX 09:24 < kanzure> CaptHindsight: POSAM? yeah i think it has always been popular :). 09:24 < CaptHindsight> kanzure: maybe in here but not outside 09:25 < CaptHindsight> the ChinaCo flatbad inkjets are made too crappy, like most reprap style printers... 09:26 < CaptHindsight> so I can't start with those and expand, cheap bastards 09:28 < kanzure> there's probably an inkjet manufacturer that would be interested in getting into biotech or having their system at the heart of a biotech revolution, who's in your rolodex? :P 09:28 < CaptHindsight> I hope that they don't cheap out copying the design I give them 09:28 < CaptHindsight> me 09:29 < CaptHindsight> I know them all. They are clueless when it comes to materials deposition 09:29 < CaptHindsight> they all want the graphics arts applications with $5/L inks that sell for $4k/L 09:30 < kanzure> do they recognize their relevance to industrial applications? 09:30 < CaptHindsight> they are money driven, if they made a POSAM it would be $100K and the fluids would be $10K/g vs $1k/g 09:31 < CaptHindsight> there are the greediest and most controlling types that you have met 09:32 < CaptHindsight> that's why the inkjet industry is so secretive 09:32 < kanzure> "Gilead currently holds the patent rights to the SELEX technology and has licensed it to Archemix, who is using the technology to develop pharmaceutical applications for aptamers. Archemix has sublicensed this technology to NOXXON, who is using it for the development of their Spiegelmer® technology." 09:33 < CaptHindsight> NDA's for everything 09:33 < kanzure> hah someone patented SELEX. wonderful.... sigh. 09:34 < CaptHindsight> kanzure: which countries advertise medical tourism and not enforce the US patent system? 09:34 < CaptHindsight> or maybe do so less than others 09:34 < kanzure> US patent system is worldwide enforced through an evil organization called WIPO 09:34 < CaptHindsight> tell that to China 09:34 < kanzure> https://en.wikipedia.org/wiki/World_Intellectual_Property_Organization 09:35 < kanzure> china uses WIPO for their own patents 09:35 < CaptHindsight> heh 09:35 < CaptHindsight> well grasshopper, you have much to discover 09:35 < kanzure> fightaging.org was organizing a medical tourism initiative, he had picked a number of candidate countries 09:35 < CaptHindsight> it's selective enforcement 09:35 < kanzure> china can turn a blindeye to some things but i get the sense that it's more related to paying off the right people, rather than china being OK with things. 09:36 < kanzure> anyway, reason@fightaging.org would be the person to ask regarding medical tourism 09:36 < CaptHindsight> or if your project/company is guberment funded 09:36 < kanzure> apparently he moved to austin, texas but we've never met each other. he is trying to remain anonymous. i think i'll get him eventually. 09:37 < CaptHindsight> believe me they are OK with some things 09:38 < CaptHindsight> most authors apply for the patent right before publishing their papers 09:39 < CaptHindsight> why I often see the patent awarded <1 year after publishing 09:39 < CaptHindsight> "hey here's what we found, loo at this" but "F-You we patented it" 09:40 < CaptHindsight> loo/look 09:40 < streety> the patents on SELEX look to be over 20 years old 09:41 < CaptHindsight> have any open source not for profit projects ever been sued for patent infringement? 09:42 < kanzure> where is mindspillage, she would have good answers 09:45 < CaptHindsight> I'd focus on getting things to actually work 09:46 < CaptHindsight> negotiate later 09:47 < CaptHindsight> it's easy to talk about something for several years without getting anything done 10:15 < chris_99> .title http://www.bbc.co.uk/news/technology-36711994 10:15 < yoleaux> The DIY diabetes kit that's keeping us alive - BBC News 10:17 < CaptHindsight> yeah #wearenotwaiting, I thought we'd be way ahead of where we are now by 2000 10:19 < CaptHindsight> I need to patent the nano-usb connector 10:20 < CaptHindsight> what's a good com port for a nanoscale device to connect to a PC? 10:22 < CaptHindsight> what are the most efficient ways to get data in and out of a hybrid nanoscale oligo factory? 10:23 < CaptHindsight> say we drop an 8-bit micro into a cell with a few K or RAM, what's the best way to communicate with it using a PC? 10:24 < CaptHindsight> or/of 10:24 < kanzure> probably radio, light, stuff like that 10:25 < kanzure> long-term, the biologists seem to think that we will be using DNA to send messages from cells 10:25 < kanzure> for example, the other day in here i mentioned someone's proposal to have an array of nanopore dna sequencing devices at the human heart to read any dna messages directly from the bloodstream 10:26 < CaptHindsight> yes, but making it practical 10:26 < CaptHindsight> the heart is a good central point but the cells are rushing through it pretty quickly 10:26 < CaptHindsight> and how do you read a ton of them at once? 10:27 < kanzure> huge array of nanopores for sequencing 10:27 < kanzure> if you don't capture the molecule no big deal, it will come back around eventually 10:28 < CaptHindsight> I guess I'll have to work on the practical end 10:30 -!- ArturSha1 [~ArturShai@37.218.162.107] has quit [Ping timeout: 246 seconds] 10:32 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has quit [Ping timeout: 252 seconds] 10:35 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 10:41 < xentrac> CaptHindsight: one of the things the Berkeley Motes folks did was modulate a retroreflector for communication 10:42 < xentrac> so you would shine a light at a mote with, say, 1mW of light, and get back something like a 100μW signal from the mote, which was spending nW power levels moving a mirror back and forth to make and break a corner reflector 10:59 < kanzure> another dna synthesis proposal https://groups.google.com/d/msg/enzymaticsynthesis/8Upr8bPY-7I/R9X08u-oBwAJ 11:13 < fenn> kanzure: i guess you missed the point of FISSEQ/aptamer idea - it's not for sequencing, it's so you can do a whole lot of different stains in a single image. arbitrarily many, instead of just two or three 11:18 < fenn> IRDA for nanobot comms lol 11:18 < fenn> i knew i was saving that PDA for something 11:18 < CaptHindsight> xentrac: recall the data rate? 11:18 < fenn> it's just a serial port 11:19 < kanzure> FISSEQ was about sequencing, not staining :) 11:20 < fenn> 20 kbit 11:20 < kanzure> without FISSEQ you can already do lots of cycles of antibody staining, imaging and washing 11:20 < fenn> .title info.iet.unipi.it/~anastasi/papers/mswim04.pdf 11:20 < fenn> bah 11:20 < yoleaux> fenn: Sorry, that doesn't appear to be an HTML page. 11:21 < fenn> "Performance Measurements of Motes Sensor Networks" 11:21 < xentrac> no 11:21 < fenn> oh maybe 250 kbit 11:23 < kanzure> if you are doing in situ sequencing with FISSEQ then you have tissue in front of a microscope, you might as well do protein expression labeling and imaging since you have the microscope there anyway. i guess you could argue "just collect all the DNA that stuck around, and sequence it later" which is nice i guess, or you could argue "nobody's got time for multiple rounds of staining and washing" and "multiple rounds is too damaging to ... 11:23 < kanzure> ... tissue" which are true things... 11:24 < fenn> kanzure the protein and RNA are not going to be in the same place 11:24 < kanzure> hm? the aptamer is supposed to find the protein and attach to the protein. 11:25 < fenn> yes 11:25 < fenn> uh, nevermind, i thought you meant something else by "expression" 11:26 < kanzure> "expressed proteins" 11:26 < kanzure> (rather than "gene expression", which is apparently what lots of other people are interested in) 11:28 < fenn> CaptHindsight: "CCR reflectivity can be modulated at bit rates up to 10 kbps" 11:28 < fenn> from http://robotics.eecs.berkeley.edu/~pister/publications/1998/smartdust_comm_memo.pdf 11:29 < kanzure> marblestone did an okay writeup of a lot of potential "chips in cells" stuff 11:30 < fenn> corner cube retroreflector is for long distance communication though, you could do a lot faster with just an LED 11:31 < fenn> assuming you have the power to run it 11:44 < xentrac> the retroreflector thing is for avoiding the need to have the power to run it 11:45 < xentrac> I imagine you could modulate a mechanical mirror at several MHz with enough power too 11:45 < xentrac> although of course you can modulate many LEDs at hundreds of MHz 12:02 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 252 seconds] 12:06 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 12:23 -!- mabel [~mabel@97-126-107-80.tukw.qwest.net] has joined ##hplusroadmap 12:23 -!- mabel [~mabel@97-126-107-80.tukw.qwest.net] has quit [Changing host] 12:23 -!- mabel [~mabel@unaffiliated/jacco] has joined ##hplusroadmap 12:32 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:49 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 12:53 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 13:07 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 13:10 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 13:18 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 13:19 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 13:26 -!- mabel [~mabel@unaffiliated/jacco] has quit [Ping timeout: 260 seconds] 13:27 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 13:43 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 13:45 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 13:50 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 13:59 -!- jaboja [~jaboja@2a00:f41:38f3:6e3:de85:deff:fe55:967a] has joined ##hplusroadmap 13:59 < kanzure> http://biology.stackexchange.com/questions/19316/first-rna-polymerase-mrna 14:01 < kanzure> "Johnston et al. (2001) took this experiment even further: starting with a pool of slightly mutated ribozyme ligases developed in a previous SELEX experiment, they were able to generate a ribozyme polymerase. This polymerase was able to catalyze the addition of nucleotides to a growing oligonucleotide chain up to 14 bases long and based off of an RNA template. The polymerase was also quite accurate." 14:13 -!- Joshchamp [sid159459@gateway/web/irccloud.com/x-dxswkhtsixvqcdix] has quit [Ping timeout: 264 seconds] 14:16 < kanzure> "RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension" http://fab.cba.mit.edu/classes/S62.12/docs/Bartel_RNA.pdf 14:16 -!- Joshchamp [sid159459@gateway/web/irccloud.com/x-emtvnzohgkknnkbo] has joined ##hplusroadmap 14:29 < kanzure> .wik polynucleotide phosphorylase 14:29 < yoleaux> "Polynucleotide Phosphorylase (PNPase) is a bifunctional enzyme with a phosphorolytic 3' to 5' exoribonuclease activity and a 3'-terminal oligonucleotide polymerase activity. That is, it dismantles the RNA chain starting at the 3' end and working toward the 5' end. It also synthesizes long, highly heteropolymeric tails in vivo." — https://en.wikipedia.org/wiki/Polynucleotide_phosphorylase 14:29 < kanzure> "Discovered by Ochoa in 1951, the RNA-polymerization activity of PNPase was initially believed to be responsible for DNA-dependent synthesis of messenger RNA, a notion that got disproved by the late 1950s (http://www.jbc.org/content/281/15/e12.full.pdf). 14:29 < kanzure> " 14:30 < kanzure> "The same abbreviation (PNPase) is also used for another, otherwise unrelated enzyme, Purine nucleoside phosphorylase." 14:30 < kanzure> ugh 14:33 < kanzure> "Polyribonucleotide phosphorylase is a double-stranded DNA-binding protein." http://www.ncbi.nlm.nih.gov/pubmed/9502433 14:33 < kanzure> "[...] The PNPase possesses two enzymatic activities, namely 3'-5' processive exoribonuclease activity and 5'-3' RNA polymerase activity" 14:37 < kanzure> "plastid-encoded polymerase" "nucleus-encoded polymerase" "... Given that DNA and RNA polymerases both carry out template-dependent nucleotide polymerization, it might be expected that the two types of enzymes would be structurally related. However, x-ray crystallographic studies of both types of enzymes reveal that, other than containing a critical Mg2+ ion at the catalytic site, they are virtually unrelated to each other; indeed ... 14:37 < kanzure> ... template-dependent nucleotide polymerizing enzymes seem to have arisen independently twice during the early evolution of cells. One lineage led to the modern DNA Polymerases and reverse transcriptases, as well as to a few single-subunit RNA polymerases from viruses. The other lineage formed all of the modern cellular RNA polymerases." 14:50 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has joined ##hplusroadmap 14:53 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 15:08 -!- Filosofem [~Jawmare@unaffiliated/jawmare] has joined ##hplusroadmap 15:11 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has quit [Ping timeout: 272 seconds] 15:16 -!- Burnin8 [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has joined ##hplusroadmap 15:18 -!- jron [~okok@54.161.129.226] has quit [Ping timeout: 246 seconds] 15:19 -!- Burninate [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has quit [Ping timeout: 276 seconds] 15:19 -!- balrog [~balrog@unaffiliated/balrog] has quit [Ping timeout: 244 seconds] 15:19 -!- jron [~okok@ec2-54-161-129-226.compute-1.amazonaws.com] has joined ##hplusroadmap 15:20 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 15:47 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 15:53 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 15:55 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 16:09 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 16:09 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has quit [Ping timeout: 260 seconds] 16:10 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 276 seconds] 16:13 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 16:23 < kanzure> "New Nonnucleoside Substrates for Terminal Deoxynucleotidyl Transferase: Synthesis and Dependence of Substrate Properties on Structure" (2005) 16:23 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 16:28 < kanzure> church writes perl :\ some of his scripts are included in various patents 16:28 < ebowden_> Church is love, Church is life. 16:38 < kanzure> "Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051619/ (2015) 16:39 < kanzure> "In situ formation of an azo bridge on proteins controllable by visible light" http://pubs.acs.org/doi/abs/10.1021/jacs.5b06234?journalCode=jacsat 16:40 < kanzure> "Small molecule photoswitches could complement protein-based switches by mitigating potential interference and affording high specificity for modulation sites. However, genetic encodability and responsiveness to nonultraviolet light, two desired properties possessed by protein photoswitches, are challenging to be engineered into small molecule photoswitches. Here we developed a small molecule photoswitch that can be genetically installed ... 16:40 < kanzure> ... onto proteins in situ and controlled by visible light. A pentafluoro azobenzene-based photoswitchable click amino acid (F-PSCaa) was designed to isomerize in response to visible light. After genetic incorporation into proteins via the expansion of the genetic code, F-PSCaa reacts with a nearby cysteine within the protein generating an azo bridge in situ. The resultant bridge is switchable by visible light and allows conformation and ... 16:40 < kanzure> ... binding of CaM to be regulated by such light. This photoswitch should prove valuable in optobiology for its minimal interference, site flexibility, genetic encodability, and response to the more biocompatible visible light." 16:41 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-tdupvvwwbyczymmp] has joined ##hplusroadmap 16:48 < kanzure> and here is one that uses spiropyran instead of azobenzene https://www.weizmann.ac.il/Organic_Chemistry/Rafal/pub/Noncovalent_Interactions_with_Proteins_Modify%20_the_Physicochemical_Properties_of_a_Molecular_Switch.pdf 16:48 < kanzure> although this one does not seem to use artificial amino acids 16:49 < kanzure> "Photosensitive GFP mutants containing an azobenzene unnatural amino acid" http://www.sciencedirect.com/science/article/pii/S0960894X14013432 16:50 < kanzure> using an artificial amino acid seems like a much better technique compared to using spiropyran or azobenzene in a dnazyme or ribozyme like from "Light-driven DNA nanomachine with a photoresponsive molecular engine" http://pubs.acs.org/doi/abs/10.1021/ar400308f 16:50 < kanzure> or like from "Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supraphotoswitch" http://pubs.acs.org/doi/abs/10.1021/sb300120n 16:52 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-tdupvvwwbyczymmp] has quit [Read error: Connection timed out] 16:53 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-xukqyjbyzupwvojm] has joined ##hplusroadmap 16:54 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 264 seconds] 16:58 < kanzure> "Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn2+ Sensor into a Light-Responsive Zn2+ Binding Protein" (ligand activity modulated by photoswitching, or er, binding activity only functional under illumination, rather) 17:07 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 17:12 < kanzure> "Azobenzene photoswitching without ultraviolet light" http://2014.igem.org/wiki/images/0/0e/Technion-Israel-Azobenzene.pdf (2011) (supplementary info) 17:12 < kanzure> "Most azobenzene-based photoswitches use UV light for photoisomerization. This can limit their application in biological systems, where UV light can trigger unwanted responses, including cellular apoptosis. We have found that substitution of all four ortho positions with methoxy groups in an amidoazobenzene derivative leads to a substantial (~35 nm) red shift of the n-π* band of the trans isomer, separating it from the cis n-π* ... 17:12 < kanzure> ... transition. This red shift makes trans-to-cis photoswitching possible using green light (530-560 nm). The cis state is thermally stable with a half-life of ~2.4 days in the dark in aqueous solution. Reverse (cis-to-trans) photoswitching can be accomplished with blue light (460 nm), so bidirectional photoswitching between thermally stable isomers is possible without using UV light at all." 17:16 -!- jaboja [~jaboja@2a00:f41:38f3:6e3:de85:deff:fe55:967a] has quit [Remote host closed the connection] 17:27 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 17:29 < CaptHindsight> hhmmm no open source CGM Continuous Glucose Monitor 17:33 < CaptHindsight> need an open biosensor project 17:36 < CaptHindsight> jesus , everything needs to be built 17:37 < CaptHindsight> has anyone actually built anything other than some software for an Rpi? 17:51 < kanzure> lots of people use the gpio pins 18:05 < kanzure> "A general method for regulating protein stability with light" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906921/ (2013) 18:05 < kanzure> "We here describe a novel genetically encoded protein domain that is degraded upon exposure to non-toxic blue light. We demonstrate that fusion proteins containing this domain are rapidly degraded in cultured cells and in zebrafish upon illumination." 18:05 < kanzure> degradation is a little bit overkill but i guess that's better than nothing. and it's a protein domain so that's nice.. 18:06 < kanzure> "Blue-Light Inducible Degradation (B-LID) domain" 18:08 < yashgaroth> only works intracellularly, mediated by the proteasome 18:10 < kanzure> oh. 18:10 < kanzure> and the azobenzene unnatural amino acid? are you going to tell me santa claus isn't real, next? 18:11 < yashgaroth> nah that's probably fine 18:14 < CaptHindsight> benzos are often used in radiation/light reactive applications 18:15 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 18:15 < kanzure> yex the reason why it's useful here is because someone put it into an amino acid and an expanded genetic alphabet 18:16 < kanzure> so a genome can specify, through genetics, that a certain amino acid in a certain protein should be responsive to light, or be light-switchable 18:16 < kanzure> which is useful for an optically controlled polymerase 18:16 < CaptHindsight> there's a shitload of photoreactive things you can do to oligos 18:17 < CaptHindsight> I don't think the bio people spend much time looking into what they do in industrial applications 18:17 < kanzure> yes yesterday i pointed out a few papers where they use azobenzene and spiropyran and friends to make dnazymes and ribozymes that undergo movement in response to optical stimulation 18:17 < CaptHindsight> they should probably have lunch with the industrial chemists some time :) 18:20 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Ping timeout: 260 seconds] 18:22 < kanzure> yeah the photopolymer/photoresin materials people seem to get involved in lots of deeply weird thngs 18:22 < kanzure> and then there's dye stuff... 18:44 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 272 seconds] 19:03 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 19:08 < kanzure> non-covalently bound light-controlled inhibitor of a protein's catalytic activity domain http://onlinelibrary.wiley.com/doi/10.1002/anie.201307207/full (this seems to be a free-floating inhibitor) 19:11 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-xukqyjbyzupwvojm] has quit [Quit: Connection closed for inactivity] 19:14 < kanzure> "Methods of storing information using nucleic acids" https://patents.google.com/patent/US20150269313A1/en 19:16 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 19:21 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Ping timeout: 260 seconds] 19:27 < kanzure> some sort of academic paper recommendation engine thing https://github.com/titipata/science_concierge 19:27 < kanzure> from kording lab 19:27 < kanzure> "sciencestein" 19:28 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 19:35 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 276 seconds] 19:51 < nildicit> any thoughts on http://www.transhumanpolitics.com/ ? 20:00 -!- Filosofem is now known as Jawmare 20:07 < kanzure> waste of time; better to build things. 20:10 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 20:14 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 20:14 -!- ebowden_ [~ebowden@147.69.137.125] has joined ##hplusroadmap 20:15 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 20:16 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 20:17 -!- SolG is now known as _sol_ 20:20 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Ping timeout: 260 seconds] 20:32 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 20:39 -!- ebowden_ [~ebowden@147.69.137.125] has quit [Remote host closed the connection] 20:43 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 20:45 < nmz787> damn, for half a second I read PMPase and heard it in my head as 'pimp-ase'... but then re-read and saw it was PNPase :( 20:56 -!- ebowden_ [~ebowden@2001:8003:100e:c500:3d9c:1cd6:342e:50f6] has joined ##hplusroadmap 20:57 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 21:01 < nildicit> kanzure, how are the political motives injected into the creation of things a waste of time tho 21:06 < nmz787> nildicit: I don't think kanzure gets how many people out there are easily swayed by a free meal to ensue violence and/or property destruction 21:07 < nmz787> and thus the need to educate them and get them on 'our side' 21:07 < nmz787> (even though it seems damn obvious to us) 21:07 < nmz787> nildicit: in general politics is basically salesmanship and communications between tribes... and being a salesman sucks 21:08 < nmz787> I work in a tech company and was just recently told I need to sell ideas to higher-ups... because even though we're all tech folks, they need sold to because shit isn't obvious 21:09 < nildicit> I remember an immortallife article questioning whether or not "deathism" is a meme. 21:09 < nildicit> Those were dark times 21:09 < nmz787> knowledge in humans doesn't seem to be able to be wide and deep for many people 21:10 < nildicit> engineers don't like politics, I know. 21:10 < nildicit> I've been reading into the history of the transhumanist political landscape and it's weird 21:11 < nildicit> things have definitely changed in the past four/five years too 21:13 < nildicit> The Transhumanist National Commitee was formed in response to the Zoltan Istvan's illegitimate party and campaign for instance 21:13 < kanzure> i am going to ban you 21:13 < kanzure> this is an immense waste of time 21:13 < nildicit> I'm not even trolling, kanzure 21:14 < nildicit> You still haven't answered my question 21:14 < kanzure> i know. i don't care. it's still a waste of time. get the fuck out. 21:15 * nildicit goes back to idling 21:15 < kanzure> only reason why this place is still around is because i keep murdering anyone who even hints at politicizing any of this shit; i will absolutely disembowel you and drown you in a mixture of your own blood vomit piss. 21:15 < kanzure> thanks. 21:16 < nildicit> No wonder this place is pretty dead. 21:16 < ebowden_> Not really. 21:17 < ebowden_> Lots of technical discussion. 21:17 < ebowden_> Oh, wait, nevermind. 21:17 < ebowden_> Not lots. 21:17 < nildicit> My logs consist of more kanzure link/quoting than anything else tbh 21:17 < nildicit> Not like that's a bad thing 21:17 < nildicit> it's not 21:19 < ebowden_> kanzure, did that vetinary oncologist and complete troll, Lando-SpacePimp, get banned from this channel? 21:20 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Read error: Connection reset by peer] 21:22 < kanzure> that was probably another channel 21:22 < ebowden_> Ah, ok. 21:22 < ebowden_> Yeah, I remember they were banned in a channel, just not which one it was. 21:24 < ebowden_> That one is actually a scientist, just also a troll. Apparently they earned a reputation of sorts, brought Surströmming to Food Friday at vet school. 21:37 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-eahkdezqbpeezcvl] has joined ##hplusroadmap 21:42 -!- ArturSha1 [~ArturShai@37.218.162.107] has joined ##hplusroadmap 21:45 < kanzure> http://www.aptagen.com/aptamer-index/aptamer-list.aspx 21:56 < kanzure> fenn: you shoud have argued "the wash cycles probably don't work", it's a good reason to do aptamers + sequencing rather than microscopy imaging of colors. 22:20 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 260 seconds] 22:26 -!- ebowden_ [~ebowden@2001:8003:100e:c500:3d9c:1cd6:342e:50f6] has quit [Remote host closed the connection] 22:27 -!- joshcryer [~g@unaffiliated/joshcryer] has joined ##hplusroadmap 22:28 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Read error: Connection reset by peer] 22:28 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 22:30 -!- ebowden_ [~ebowden@2001:8003:100e:c500:53e:a7e2:58b8:cd6f] has joined ##hplusroadmap 22:48 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 22:48 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 22:52 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 22:56 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:07 -!- drewbot [~cinch@ec2-54-224-81-1.compute-1.amazonaws.com] has quit [Remote host closed the connection] 23:07 -!- drewbot [~cinch@ec2-54-162-141-64.compute-1.amazonaws.com] has joined ##hplusroadmap 23:33 -!- Orpheon [~Orpheon@68.168.62.81.dynamic.wline.res.cust.swisscom.ch] has joined ##hplusroadmap 23:36 -!- Th3_Prince [~b3nszy@132.147.10.243] has joined ##hplusroadmap 23:36 < Th3_Prince> hey 23:36 < Th3_Prince> what should i major in if I want to go into agi 23:39 < chris_99> hmm not sure, but you could look into computational neuroscience 23:39 < Th3_Prince> eh 23:39 < Th3_Prince> between physics 23:39 < Th3_Prince> math 23:39 < Th3_Prince> and compsci 23:42 -!- augur [~augur@2602:304:cdac:e260:6993:788e:ad5c:fb4d] has joined ##hplusroadmap 23:52 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-tclkfcxkwfetpwxu] has quit [Quit: Connection closed for inactivity] --- Log closed Sun Jul 17 00:00:59 2016