--- Log opened Thu May 25 00:00:03 2017
00:19 -!- jtimon [~quassel@117.29.134.37.dynamic.jazztel.es] has quit [Ping timeout: 260 seconds]
00:28 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
00:31 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 240 seconds]
00:38 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap
00:40 -!- nmz787_i [~ntmccork@134.134.139.82] has quit [Quit: Leaving.]
01:30 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 245 seconds]
01:52 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection]
01:54 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap
02:10 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection]
02:12 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap
02:32 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
02:38 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
02:43 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has joined ##hplusroadmap
02:43 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap
03:07 -!- jtimon [~quassel@117.29.134.37.dynamic.jazztel.es] has joined ##hplusroadmap
03:07 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has quit [Quit: Leaving.]
03:10 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has joined ##hplusroadmap
03:15 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
03:20 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 246 seconds]
03:21 -!- augur [~augur@2602:304:cdac:e260:4ce6:4c0d:97da:35a6] has joined ##hplusroadmap
03:42 -!- augur [~augur@2602:304:cdac:e260:4ce6:4c0d:97da:35a6] has quit [Remote host closed the connection]
03:53 -!- Jen [~Jen3@cpc76808-brmb10-2-0-cust571.1-3.cable.virginm.net] has quit [Ping timeout: 245 seconds]
04:11 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap
05:03 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection]
05:06 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap
05:20 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
05:35 -!- NikopolSohru [~NSohru@185.107.80.182] has quit [Ping timeout: 246 seconds]
05:46 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 255 seconds]
05:53 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
06:26 < kanzure> http://www.nature.com/news/lab-grown-blood-stem-cells-produced-at-last-1.22000
06:27 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection]
06:31 -!- nmz787_i [~ntmccork@134.134.139.83] has joined ##hplusroadmap
06:33 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
06:35 < kanzure> "T7RNAP variants have been engineered to recognize different promoter variants [32-35], which allow independent expression of multiple genes."
06:36 < kanzure> [32] Shis, D. L., and Bennett, M. R. (2013) Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc. Natl. Acad. Sci. U. S. A. 110, 5028-33.
06:36 < kanzure> [33] Temme, K., Hill, R., Segall-Shapiro, T. H., Moser, F., and Voigt, C. A. (2012) Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res. 40, 8773-8781
06:37 < kanzure> [34] Carlson, J. C., Badran, A. H., Guggiana-Nilo, D. A., and Liu, D. R. (2014) Negative selection and stringency modulation in phage-assisted continuous evolution. Nat Chem Biol 10, 216-222.
06:37 < kanzure> [35] Ellefson, J. W., Meyer, A. J., Hughes, R. a, Cannon, J. R., Brodbelt, J. S., and Ellington, A. D. (2014) Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat. Biotechnol. 32, 97-101.
06:39 < kanzure> .wik arabinose
06:39 < yoleaux> "Arabinose is an aldopentose - a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group." -- https://en.wikipedia.org/wiki/Arabinose
06:40 < kanzure> "In this work, we show that the T7RNAP can be made light-inducible by splitting the polymerase into two fragments, and fusing it to photo-activatable dimerization domains. Our protein engineering strategy was guided by previous studies showing that the T7RNAP can be split[26,32,43-45] and reconstituted  through dimerization to enhance and control its function[26], as well as structural informa...
06:40 < kanzure> ...tion about the T7RNAP[46]. We aimed to implement light-control using the heterodimeric "Magnet" domains[16]. Magnets were engineered from the small homodimerizing photoreceptor Vivid (VVD) from the filamentous fungus Neurospora crassa[47] and consist of the nMag and pMag heterodimerizing protein domains, which specifically bind each other. Magnets use flavin as a chromophore for blue light-ind...
06:40 < kanzure> ...uced binding of the two domains, which is abundant in bacterial and eukaryotic cells. A similar strategy to make T7RNAP light-inducible was recently reported[48]."
07:03 < nmz787_i> so flavins are how Magnets work!
07:03 < nmz787_i> .wik flavin
07:03 < yoleaux> "Disambiguation: Flavin" -- https://en.wikipedia.org/wiki/Flavin
07:03 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has quit [Ping timeout: 246 seconds]
07:03 < nmz787_i> .g flavin flave
07:03 < yoleaux> http://www.urbandictionary.com/define.php?term=flave
07:04 < nmz787_i> heh - "to be smooth, error free, visually outstanding, to appeal to the senses"
07:22 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has joined ##hplusroadmap
07:35 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 268 seconds]
07:36 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 240 seconds]
07:38 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
07:40 < nmz787_i> http://roningenetics.org/Sequencing.html  - "Just posting this because it was a surprise that the company could not synthesize this sequence."  "I sent it to Operon and they could not synthesize it due to some repetitive/simple sequence regions (these regions they noted are also pasted below). they tried for a month."
07:41 < kanzure> nmz787_i: do you have numbers on oligonucleotide synthesis cost minus all the sequencing and redoing?
07:42 < nmz787_i> "the gene sequence didn't seem to have that many regions of complexity to cause the failure observed, so it's difficult to pinpoint exactly how to improve upon the sequence. It is possible the presence of folding motifs or the GC rich portion interfered with the correct assembly of the gene (we were unable to obtain a clone with the correct gene sequence). Also, there were two ORFs for this gene sequence, so that could have factored in to the 
07:42 < nmz787_i> kanzure: nope
07:43 < nmz787_i> kanzure: I'm not sure that most companies that sell oligos, also seqeuence... usually its just a de-salting or HPLC maybe
07:44 < kanzure> i thought they are all sequencing these days? otherwise the errors pile up..
07:45 < nmz787_i> no I think that's only for gene-length stuff
07:45 < nmz787_i> I could be wrong
07:45 < kanzure> actually the error rate seems sort of low in general these days-- 1 error per 200 bp.  but this seems to be worse for repetitive sequences of course :).
07:45 < kanzure> yeah but almost everything interesting is at least gene length
07:45 < nmz787_i> right
07:45 < nmz787_i> I think the last time you asked that question, you asked re 'gene synthesis' not 'oligo'
07:46 -!- augur [~augur@2602:304:cdac:e260:4ce6:4c0d:97da:35a6] has joined ##hplusroadmap
07:50 -!- night [~Adifex@unaffiliated/adifex] has quit [Ping timeout: 246 seconds]
08:05 < kanzure> ah.
08:06 -!- augur [~augur@2602:304:cdac:e260:4ce6:4c0d:97da:35a6] has quit [Remote host closed the connection]
08:09 < nmz787_i> huh, igem seems to have had team pages get spammed
08:15 < kanzure> they use mediawiki so probably any mediawiki spambot will work
08:18 < nmz787_i> sucks
08:18 < nmz787_i> at least the history is still there
08:19 < kanzure> juul: does randy know?
08:23 < nmz787_i> my Gleaux plant is being shiped :)
08:23 < nmz787_i> shipped*
08:44 < kanzure> bioluminescence stuff?
08:47 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving]
08:47 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has quit [Quit: Leaving.]
08:48 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
08:52 < nmz787_i> yup
08:52 < nmz787_i> firefly genes in the tobacco
09:01 < kanzure> "the Cyberpunk PPRPG from R Talsorian ( https://en.m.wikipedia.org/wiki/Cyberpunk_2020 ) .. One of my favorite features was cyberpsychosis. As a gameplay element, it was an answer to "Why don't you just buy godlike cyber replacements for your body?""
09:01 < kanzure> that does not sound like a good answer
09:03 < nmz787_i> UC Davis reports "Pallet jacks aren't as dangerous as forklifts"
09:04 < nmz787_i> they also note "Loads can topple from uneven floors, inclines, excessive speed"
09:04 < kanzure> nmz787_i: sounds like you're preparing to get a top entry on https://alt.org/nethack/topdeaths.html
09:07 < nmz787_i> haha
09:21 < nmz787_i> hmm, preventing the loaded pallet jack from moving downhill is an interesting problem
09:21 < nmz787_i> like, presumably the parking lot has a slight slope from their garage/bay door
09:22 < nmz787_i> or if the trailer was right up next to that interface, the trailer might have a slight down-slope
09:22 < nmz787_i> winching the load up the ramp seems like it will work, but then it might crest and start rolling.... unless I have some movable wheel chocks
09:27 < juul> kanzure: don't know. biobricks foundation doesn't run igem and i don't talk to randy more than about once a year
09:27 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap
09:28  * juul just extracted a file from a virtualbox image from a dd image from an external harddrive from the back of my closet
09:29 < juul> to get at some bitcoin i stashed back in 2011
09:30 < juul> it's funny how backups age
09:32 < juul> also, Nerve Attenuation Syndrome
09:37 < kanzure> success?
09:38 < kanzure> juul: btw did you look at https://groups.google.com/d/msg/enzymaticsynthesis/WvDidIldm7c/q7aQTnmkAAAJ
09:43 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds]
09:47 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
09:50 < juul> no success :( i think they're in a safe in europe
09:51 < cluckj> are there enough coins there to pay for the flight to get them?
09:53 < cluckj> "free" vacation to europe :D
09:54 < juul> heh, well i'm going there anyway soon for battlemesh
09:56 < juul> kanzure: i like the ideas, but they all seem like the require some magic technology we don't have
09:57 < juul> what if we had a nucleotide analogue that gets picked up by e.g. a T7 polymerase but when it attaches it kills the polymerase
09:58 < juul> then we link that toxic nucleotide with a molecule that makes it unavailable unless light of a specific wavelength is present
09:58 -!- bsm1175321 [~mcelrath@135.84.167.210] has quit [Ping timeout: 255 seconds]
09:59 < juul> then we grow a shit ton of the transformed bacteria while blinking the light on and off
09:59 < juul> anything that doesn't learn to turn off the polymerase in the dark then dies
10:00 < juul> then once we have the light-sensitive polymerase we try to evolve a polymerase that can sense two different wavelengths
10:02 < juul> could we step by step fast-evolve something that has "learned" to convert light input to the correct DNA sequence?
10:14 < kanzure> well there was a light-sensitive polymerase published yesterday but it doesn't do what you think it does
10:15 < kanzure> "Dynamic blue light-inducible T7 RNA polymerases (Opto-T7RNAPs) for precise spatiotemporal gene expression control" http://biorxiv.org/content/early/2017/05/23/140871
10:26 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has joined ##hplusroadmap
10:29 < kanzure> juul: ^
10:32 -!- augur [~augur@76-218-206-38.lightspeed.sntcca.sbcglobal.net] has quit [Remote host closed the connection]
10:47 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds]
11:22 -!- emeraldgreen [~user@ppp91-122-183-181.pppoe.avangarddsl.ru] has quit [Quit: Leaving.]
11:24 < archels> .title https://arxiv.org/pdf/1705.03394.pdf
11:24 < yoleaux> archels: Sorry, that doesn't appear to be an HTML page.
11:25 < archels> "That is not dead which can eternal lie: the aestivation hypothesis for resolving Fermi's paradox"
11:25 < archels> Sandberg et al
11:28 < kanzure> "opportunity cost: advanced civilizations have mainly "seen it all" in the present universe and do not gain much more information utility from hanging around in the early era"
11:28 < kanzure> ehh..
11:29 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
11:40 < archels> the early universe was such a boring place, yo
11:41 < archels> they hadn't even invented music yet
11:41 < cluckj> still is
11:41 < chris_99> heh
11:42 < archels> at least there is music
12:04 -!- adlai [~adlai@unaffiliated/adlai] has quit [Ping timeout: 246 seconds]
12:05 -!- ExeciN [ExeciN@91.121.238.185] has quit [Disconnected by services]
12:17 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
12:31 -!- nicexe [ExeciN@bnc.stormbit.net] has joined ##hplusroadmap
12:41 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
12:44 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
12:47 < kanzure> "Even if only the resources available in a galactic supercluster are exploited, later-era exploitation produces a payoff far greater than any attempt to colonize the rest of the accessible universe and use the resources early. In fact, the mass-energy of just the Earth itself (5.9 ? 10^24 kg) would be more than enough to power more computations than could currently be done by burning the pres...
12:47 < kanzure> ...ent observable universe! (6 ? 10^52 kg)."
12:47 < juul> archels: if you get bored i guess you just lower your clock speed. like when you get bored in sim city and sped it up.
12:50 < thesnark> fermi's paradox doesn't seem so hard to me honestly. not sure why alien species would gaf about us in the first place
12:50 < thesnark> not sure why we're surprised that organisms who are not at all like us and probably more intelligent than us don't find us so fascinating that they want to talk to us
12:51 < thesnark> or use the same technology as us? like that's just such a huge assumption
12:53 < thesnark> fermi's paradox is really just humans wondering why they aren't as important as they thought they were IMO
13:06 < juul> i was just asked this question: RegEx is to byte strings as _what_ is to genetic sequences?
13:07 < juul> any better answer than "BLAST or Smith-Waterman" ?
13:14 < kanzure> thesnark: fermi paradox isn't explicitly about aliens talking with humans
13:15 < kanzure> juul: yea i would have said BLAST
13:18 < kanzure> thesnark: i think hypertelescopes would be helpful like these 10,000 kilometer-wide easily-deployable megastructures http://diyhpl.us/~bryan/papers2/space/Self-deployed%20extremely%20large%20low%20mass%20space%20structures%20-%202007.pdf
13:18 -!- up_dn [~up_dn@2601:4a:c300:2676:94a3:94a8:9c45:fa8] has joined ##hplusroadmap
13:19 -!- NikopolSohru [~NSohru@185.143.230.239] has joined ##hplusroadmap
13:28 < thesnark> kanzure: agree, better telescopes would likely help
13:28 < thesnark> kanzure: also you had me at easily deployable megastructure
13:50 -!- up_dn [~up_dn@2601:4a:c300:2676:94a3:94a8:9c45:fa8] has quit [Quit: up_dn]
13:57 < kanzure> .wik hylauranic acid
13:57 < yoleaux> "Hyaluronic acid (HA; conjugate base hyaluronate), also called hyaluronan, is an anionic, nonsulfated glycosaminoglycan distributed widely throughout connective, epithelial, and neural tissues." -- https://en.wikipedia.org/wiki/Hyaluronic_acid
14:22 -!- preview [~preview@2407:7000:842d:4000::3] has quit [Remote host closed the connection]
14:22 -!- preview [~preview@2407:7000:842d:4078:ab39:1b65:59a7:cd65] has joined ##hplusroadmap
14:24 -!- NikopolSohru [~NSohru@185.143.230.239] has quit [Quit: Leaving]
14:44 -!- Reventlov [~reventlov@unaffiliated/reventlov] has quit [Quit: WeeChat 1.7.1]
14:44 -!- strages [uid11297@gateway/web/irccloud.com/x-jjveioboqropokno] has joined ##hplusroadmap
14:50 -!- Reventlov [~reventlov@unaffiliated/reventlov] has joined ##hplusroadmap
15:33 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
15:33 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
15:34 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
15:35 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
15:47 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 255 seconds]
15:57 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving]
16:07 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
16:20 -!- thesnark [~mike@unaffiliated/thesnark] has quit [Quit: leaving]
17:01 -!- Burnin8 [~Burn@pool-108-18-203-134.washdc.fios.verizon.net] has joined ##hplusroadmap
17:03 -!- Burninate [~Burn@pool-108-18-203-134.washdc.fios.verizon.net] has quit [Ping timeout: 268 seconds]
17:04 < nmz787_i> heading to meet friend with the trailer... then to home depot for crating lumber and screws.... then hitting the road south
17:04 -!- nmz787_i [~ntmccork@134.134.139.83] has left ##hplusroadmap []
17:07 -!- strages [uid11297@gateway/web/irccloud.com/x-jjveioboqropokno] has quit [Quit: Connection closed for inactivity]
17:19 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap
17:21 < kanzure> that was the last i've ever heard from nmz787.
18:20 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds]
18:39 -!- thesnark [~mike@unaffiliated/thesnark] has joined ##hplusroadmap
18:54 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds]
19:22 -!- thesnark [~mike@unaffiliated/thesnark] has quit [Ping timeout: 246 seconds]
19:24 -!- thesnark [~mike@unaffiliated/thesnark] has joined ##hplusroadmap
19:29 < kanzure> "The reciprocal of this is that here in Oklahoma we've got animal breeders turning saltwater runoff from reinjection wells into mini seas so as they claim... to breed tiny pet whales. The goal is to have teacup size whales that fit into purses in a hundred years or so. Idk internet cuteness combined with the desire to eat them in a sustained way or something, I guess." wizardforhire https://ne...
19:29 < kanzure> ...ws.ycombinator.com/item?id=14421644
19:31 -!- thesnark [~mike@unaffiliated/thesnark] has quit [Ping timeout: 240 seconds]
19:33 -!- thesnark [~mike@unaffiliated/thesnark] has joined ##hplusroadmap
19:39 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 268 seconds]
20:21 -!- jtimon [~quassel@117.29.134.37.dynamic.jazztel.es] has quit [Ping timeout: 240 seconds]
22:22 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap
22:22 -!- TC is now known as Guest54793
22:26 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 260 seconds]
23:40 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
--- Log closed Fri May 26 00:00:04 2017