--- Log opened Wed Jul 15 00:00:11 2015
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01:49 < fenn> ugh i am STILL awake so i guess i will dump my reconaissance report here
01:50 < fenn> counterculture labs looked very early in the startup phase of a hackerspace and i don't think they're really ready to either house the dna synthesizer or make good use of it
01:51 < fenn> currently the lab has no plumbing, and despite the copious quantities of stuff everywhere, nothing quite seems to work
01:52 < fenn> the majority of their recurring income is from classes and workshops, and they seem worried about getting a sustainable membership base to support the space with dues
01:53 < fenn> it seemed like there were not very many members at all, and most of them part of the vegan cheese iGEM project (?) which will end soon ish
01:53 < fenn> lab activities mostly confined to fermentations of various sorts, mushroom growing, and construction
01:57 < fenn> i don't know if all biohackerspaces are like this or what
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02:28 < fenn> also there was in fact pizza and beer, and there was also a meeting
02:28 < fenn> everybody wins?
03:32 < kanzure> oh right they probably have the same terrible membership model as everyone else
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03:39 < kanzure> well, maybe i should just ship the whole thing to my mom's shop and tell her to deal with it :P
03:40 < fenn> it would be less than useless there
03:41 < kanzure> :-)
03:41 < fenn> i think everyone is seriously underestimating the amount of tweaking and fiddling that will be necessary to get good dna out
03:41 < kanzure> right
03:42 < kanzure> worst case scenario is, i could hire an organic chemist to fix all our mistakes
03:46 < fenn> that would be a best case scenario
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04:08 < kanzure> oh, well then let's go find a chemist
04:23 < kanzure> i've been meaning to see if we could recruit the dude who sold me the abi 391 synthesizer
04:23 < kanzure> although he seemed a little hilariously strong on the conservative axis
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04:27 < kanzure> http://tronclub.com/ electronic-circuit-kit-per-month thingy.
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04:52 < kanzure> also, are the reaction conditions for phosphoramidite oligonucleotide synthesis really incompatible with enzymes? enzymes would really make a lot of this better.
04:52 < kanzure> thermostable ligase can probably be mutated to hell and back to be more selective about which strands it combines, which you would add to the cycling ligase reaction depending on which strands you know need to be combined on each cycle, perhaps
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05:39 < kanzure> "Ligation of 5' dna overhangs to 3' dna overhangs using short single-stranded oligonucleotide linkers" (1997) http://www.biotechniques.com/multimedia/archive/00011/97233bm14_11730a.pdf
05:44 < kanzure> .title http://www.nature.com/nature/journal/v391/n6664/abs/391288a0.html
05:44 < yoleaux> DNA shuffling of a family of genes from diverse species accelerates directed evolution : Abstract : Nature
05:46 < kanzure> .title http://nar.oxfordjournals.org/content/19/15/4247.short
05:46 < yoleaux> Chemical ligation of DNA: the first non-enzymatic assembly of a biologically active gene
05:48 < kanzure> selenium-mediated autoligation of dna strands http://pubs.acs.org/doi/abs/10.1021/ja994019h?journalCode=jacsat
05:49 < kanzure> "Non-polymerase-cycling-assembly-based chemical gene synthesis: strategies, methods, and progress" http://www.sciencedirect.com/science/article/pii/S0734975007001164
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05:49 < kanzure> "Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides" http://nar.oxfordjournals.org/content/early/2009/09/10/nar.gkp687.abstract
05:49 < kanzure> "Here it is demonstrated that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp, and can be as long as 200 nucleotides in length. This straightforward scheme for assembling chemically-synthesized oligonucleotides could be a useful tool for building ...
05:49 < kanzure> ... synthetic DNA molecules."
05:51 < kanzure> huh i wonder where this came from http://diyhpl.us/~bryan/papers2/bio/dna-assembly/
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05:54 < kanzure> "Combimatrix, which uses the electrochemical platform developed by Egeland and Southern (17)" Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication (2005)
05:54 < kanzure> huh, the inkjet dna synthesis method was apparently pioneered by the hood lab (which built posam). apparently they were the first?
05:55 < kanzure> http://www.synbuild.com/High-quality%20gene%20assembly%20Borovkov%20NAR%202010.pdf
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06:01 < kanzure> "Nonenzymatic plasmid ligation mediated by minor groove-binding molecules" http://pubs.acs.org/doi/abs/10.1021/bi00192a017
06:02 < kanzure> "Electrochemically induced DNA cleavage by copper-bipyridyl complex" http://www.sciencedirect.com/science/article/pii/S1388248103003217
06:07 < kanzure> .title ligation assembly gene
06:07 < yoleaux> kanzure: Sorry, that command (.title) crashed.
06:07 < kanzure> whoops
06:07 < kanzure> "It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly." http://www.nature.com/ncomms/2015/150310/ncomms7424/full/ncomms7424.html?hc_location=ufi
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06:13 < kanzure> huh, we don't have a chemical ligation method for dna really.
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07:15 < CaptHindsight> Beer Church was proven to be successful. Hold brewing classes on brewing starting from the atomic level
07:21 < nmz787_i> I think L.A. biohackers is more 'together', from the sound of things I've heard... I also think biocurious is pretty together... but apparently they don't like us (or do they not like kanzure???)?
07:21 < nmz787_i> together at least in terms of funding for the space and equipment and plumbing and such
07:22 < nmz787_i> having someone in those places who is willing to hop on here for reporting or debugging would be good though
07:22 < nmz787_i> I think keoni could be persuaded to get on here
07:22 < nmz787_i> maybe
07:26 < kanzure> i thought biocurious is perpetually underfunded and on the verge of closing
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07:58 < juri_> again, i can reach out to BUGS. I have visited their wetlab, and can confirm educated people, plumbing, a working vent hood, and rigorous contamination prevention procedures. they clone any plant there.
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08:06 < kanzure> yes but it's an hour trip for you
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08:06 < kanzure> that's wrong in all sorts of evil ways
08:08 < juri_> just offering what i can.
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09:07 < kanzure> well there's always brmlab
09:09 < pasky> what about brmlab?
09:09 < kanzure> well we are building an inkjet dna synthesizer
09:09 < kanzure> and we need a home for it
09:10 < kanzure> somewhere it will be loved and maintained and used
09:10 < pasky> hmm, sounds cool, but tbh i don't think the biolab at brmlab is very active, we never got a critical mass going; the other trouble is that making GMOs is illegal in europe
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09:11 < kanzure> unrelated,
09:11 < kanzure> https://www.washingtonpost.com/news/volokh-conspiracy/wp/2015/07/14/if-it-becomes-possible-to-safely-genetically-increase-babies-iq-it-will-become-inevitable/
09:11 < kanzure> pasky: ok understood. got any other places?
09:15 < pasky> kanzure: la paillase or w/ever it's spelled? also a large biohackerspace in london afaik; legal problems may be the same, though
09:16 < kanzure> hmph
09:16 < kanzure> https://hackaday.com/2015/07/14/vintage-vinyl-laser-etched-on-a-tortilla/
09:17 < kanzure> yeah it seems like most of the bio groups suffer from the exact same problems
09:18 < kanzure> absolutely no learning is happening
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09:24 < juri_> that happens in hackerspaces, as well.
09:25 < juri_> hense, why i like the freegeek model. too bad i'm running a hackerspace. ;)
09:26 < nottimschmidt> hackerspaces are extraordinarily difficult beasts
09:26 < kanzure> they are broken by design
09:26 < kanzure> needs better design
09:27 < nottimschmidt> Having founded one with which I am now disenchanted, I have to agree.
09:27 < kanzure> i think a consulting firm model would work better
09:27 < kanzure> where the consulting firm has paying projects (various mechanical things)
09:27 < kanzure> then the income pays for the toys and for the people to come in and break everything regularly
09:28 < nottimschmidt> an income stream outside the membership's dues and the not-for-profit industrial complex would be helpful
09:28 < juri_> freegeek arkansas ran off of public donations.
09:28 < kanzure> if the members had money then they wouldn't be using a hackerspace anyway
09:29 < juri_> tip jar next to the door.
09:29 < nottimschmidt> we have some members with money, and some of them are involved in running the hackerspace, and still nothing gets done, for the politics and hurt feels
09:30 < nottimschmidt> leadership with a vision is a necessary component
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09:30 < nottimschmidt> strong communication is a necessary component
09:32 < nottimschmidt> and the people exercising those things have to feel empowered and supported
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10:07 < archels_> .suggest our aim is *
10:07 < yoleaux> Perhaps our aim is *: ~ to keep this bathroom clean ~, ~ to satisfy red snapper ~, our aim is, ~ to provide ~, ~ true ~, ~ to keep this bathroom clean poster ~, ~ wakefulness ~, ~ to keep this bathroom clean wall decor ~, ~ too high and we miss it ~, ~ not to do away with corporations ~
10:08 < archels_> .suggest our aim is to promote *
10:08 < yoleaux> No suggestions for our aim is to promote *.
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10:09 < archels_> wait, never mind
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11:09 < juul> i may have talked to them last night
11:09 < juul> unfortunately i had to be part of the mesh weekly meeting and had not slept for 48 hours
11:09 < juul> so i may have been a little short and weird
11:10 < juul> here's a ukulele duet of hotel california to make up for it https://www.youtube.com/watch?v=r6BYgBnyDQs
11:12 < kanzure> them==?
11:12 < kanzure> oh, probably people
11:18 < kanzure> https://en.wikipedia.org/wiki/Phosphite_ester
11:18 < kanzure> https://en.wikipedia.org/wiki/Organophosphorus_compound
11:21 < kanzure> "The absence of physical dividers between the sites occupied by individual oligonucleotides, a very limited space on the surface of the microarray (one oligonucleotide sequence occupies a square 25×25 μm)[114] and the requirement of high fidelity of oligonucleotide synthesis dictate the use of site-selective 5'-deprotection techniques. In one approach, the removal of the 5'-O-DMT group is effected by electrochemical generation of the ...
11:21 < kanzure> ... acid at the required site(s).[115] Another approach uses 5'-O-(α-methyl-6-nitropiperonyloxycarbonyl) (MeNPOC) protecting group, which can be removed by irradiation with UV light of 365 nm wavelength.[114]"
11:21 < kanzure> strange how all of this seems to be biochemists or molecular biologists, and not any chemistry people?
11:23 < kanzure> (last year) http://www.northwestern.edu/newscenter/stories/2014/06/pioneer-in-dna-synthesis-dies-at-age-92.html
11:26 < kanzure> ok history page http://www.trilinkbiotech.com/tech/oligo_history.asp
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11:48 < justanotheruser> kanzure: it appears ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/Haloferax_elongans/latest_assembly_versions/ was just a symbolic link and it works fine
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12:25 < kanzure> justanotheruser: tricky
12:25 < kanzure> .title https://news.ycombinator.com/item?id=9892810
12:25 < yoleaux> Vim's 400 line function to wait for keyboard input | Hacker News
12:34 < CaptHindsight> kanzure: I've been finding similar with bio not really working together with chemists
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13:15 < kanzure> CaptHindsight: i know almost zero chemists.
13:15 < kanzure> i think the one chemist that i know is..... eleitl.
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13:15 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Photoremovable%20protecting%20groups%20in%20chemistry%20and%20biology%20-%20reaction%20mechanisms%20and%20efficiency.pdf
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13:21 < pasky> I think hackerspaces work fine, e.g. brmlab is; the thing is, about 1/3 of the founding members gradually left (not on bad terms, just lost interest) because it didn't live up to their dreams, but I think it was the dreams that were completely unrealistic; there's limited amount of brainpower you can gather at such a place, and it's fundamentally limited in that it doesn't pay the bills
13:22 < pasky> I don't think a consulting firm model would work better, at least I've never seen a company like that which could find the balance to keep its "employees" at say 50% utilization
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13:24 < pasky> in the end, citizen science, hackerspaces etc. are just a post-work activity which you do in your limited spare time, much less than you spend working; with that time allocation and budget, there's only one ingredient that could compensate, and that's incredible statistically unlikely luck
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13:38 < CaptHindsight> kanzure: I know several chemists and they look at radcure as some kind of voodoo
13:38 < CaptHindsight> it seems to come down to what area of chemistry they are interested in
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14:25 < nmz787_i> CaptHindsight: radcure?
14:26 < nmz787_i> radical cures?
14:26 < nmz787_i> UV curable resins?
14:26 < nmz787_i> CaptHindsight: so are you a polymer chemist?
14:27 < nmz787_i> CaptHindsight: have you head of .wik atrp ?
14:27 < nmz787_i> .wik atrp
14:27 < yoleaux> "Disambiguation: ATRP" — https://en.wikipedia.org/wiki/ATRP
14:27 < nmz787_i> .wik Atom-transfer radical-polymerization
14:27 < yoleaux> "Atom transfer radical polymerization (ATRP) is an example of a reversible-deactivation radical polymerization. Like its counterpart, ATRA or atom transfer radical addition, it is a means of forming a carbon-carbon bond through a transition metal catalyst." — https://en.wikipedia.org/wiki/Atom-transfer_radical-polymerization
14:31 < kanzure> i think it should be possible to make a linker chemistry that ligates two oligos together, which should be able to discriminate from itself. surely this should be a thing that people do...
14:32 < kanzure> for example: two sets of oligos, first set has A acceptor and B donor linker types on opposite ends, second set has B acceptor and C donor linker types on opposite ends
14:36 < CaptHindsight> this is more what I work with just about daily
14:37 < CaptHindsight> nmz787_i: I've had to become one since I make all sorts of photopolymers, resins, paints, inks, coatings etc
14:51 < CaptHindsight> I just finished a UV radical cured resin that is reverseable post cure to a liquid
14:52 < CaptHindsight> I skimmed over the ATRP
14:53 < CaptHindsight> I'll have to see how it can work with the bases
14:56 < CaptHindsight> ATRP is also used to make many of the oligomers I use
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15:56 < kanzure> nmz787_i: whatever happened to http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png
16:08 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/oligonucleotide-synthesis-by-phosphoramidite-method-cycle-diagram.png
16:09 < kanzure> couldn't you use the base protection/deprotection scheme to combine an oligo with another oligo? you would cap the other end so that it does not react with itself. i guess that wouldn't work unless you only had 1 new oligo molecule in the pot. too bad....
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16:19 < kanzure> hmm
16:19 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Toward%20an%20Ideal%20Synthesis%20of%20Oligonucleotides%20-%20Development%20of%20a%20Novel%20Phosphoramidite%20Method%20with%20High%20Capability.pdf
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16:42 < nmz787_i> .gc 4^6
16:42 < yoleaux> 25,270,000,000 (site), 2,700,000,000 (api)
16:43 < nmz787_i> err
16:43 < nmz787_i> .wa 4^6
16:43 < yoleaux> 4⁶: 4096; Number name: 4 thousand 96; Number line: http://is.gd/GBpXLT
16:43 < kanzure> nucleic acid chemistry research group https://www.mpibpc.mpg.de/hoebartner
16:44 < nmz787_i> kanzure: it might have been something about the efficiency of hybridization or the ligase sitting down on such a short sequence... or maybe the whole handling even 4096 items
16:45 < kanzure> why were we okay with a 4096 library? did we have a working ligation protocol.
16:46 < kanzure> "Synthesis and properties of DNA oligonucleotides with a zwitterionic backbone structure" http://pubs.rsc.org/en/Content/ArticleLanding/2014/CC/C4CC06371F
16:46 < kanzure> "The nucleosyl amino acid (NAA)-modification of oligonucleotides is introduced, which enables the preparation of oligonucleotides with zwitterionic backbone structures. It is demonstrated that partially zwitterionic NAA-modified DNA oligonucleotides are capable of duplex formation with native polyanionic counterstrands and show retained sensitivity towards base-pairing mismatches."
16:47 < kanzure> ""The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides.""
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17:11 < nmz787_i> kanzure: I had some paper about minimally-viable PCR primers, and I think they showed some action down to 6bp
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17:13 < nmz787_i> kanzure: can you grep the logs for my name and the word nucleotide... there is some modified nucleotide that I've mentioned before, but I can't remember the prefix/suffix
17:14 < kanzure> nmz787_i: http://diyhpl.us/~bryan/irc/nmz787-nucleotide.log.txt
17:20 < kanzure> .title https://www.youtube.com/watch?v=ddtkszic4II
17:20 < yoleaux> Andy James - Progressive Marathon - YouTube
17:20 < kanzure> (music)
17:23 < ParahSailin> a nucleotide that idt will do?
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17:31 < nmz787_i> i think it was a succinate
17:32 < ParahSailin> what does it do
17:34 < nmz787_i> I think it was something about increasing efficiency in liquid-phase synthesis
17:35 < nmz787_i> "To introduce dA, dC, and dG into the 3-terminal site, their 3 derivatives or other equivalents are required. Because succinic anhydride reacts with the nucleobases (Kume et al., 1984), the amino functions of these deoxyribonucleosides should be protected to avoid such side reactions."
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17:41 < nmz787_i> how can I easily upload a file using python?
17:42 < nmz787_i> hmm, someone says this works for <1.5MB r = requests.post('http://httpbin.org/post', files={'report.xls': open('report.xls', 'rb')})
17:44 < ParahSailin> yeah def use requests
17:45 < kanzure> lesswrong says this might be acceptable scifi "the fall of doc future" http://docfuture.tumblr.com/post/82363551272/fall-of-doc-future-contents
17:49 < kanzure> 17:47 < feep> kanzure: it's like if alan moore wrote watchmen while an extrapolation of a bonobo CEV looked over his shoulder every few seconds and was like "you know, I bet your characters would have way fewer issues if they made out more"
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21:15 < kanzure> "Optogenetic vision restoration using rhodopsin for enhanced sensitivity" http://www.ncbi.nlm.nih.gov/pubmed/26137852
21:15 < kanzure> "Optogenetic gene therapies are in development, but, to date, have suffered from the low light sensitivity of microbial opsins, such as channelrhodopsin and halorhodopsin, and azobenzene-based photoswitches. Several groups have shown that photoreceptive G protein coupled receptors (GPCRs) can be expressed heterologously, and photoactivate endogenous Gi/o signaling. We hypothesized such a GPCR could increase sensitivity due to endogenous ...
21:15 < kanzure> ... signal amplification. .... Importantly, both the light responses of the retinal explants and the visually-guided behavior occurred reliably at light levels that were 2-3 orders of magnitude dimmer than required for channelrhodopsin."
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21:35 < ParahSailin> bay area real estate in bubble?
21:35 < ParahSailin> considering whether to buy
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21:50 < justanotheruser> ParahSailin: if a silicon valley bubble exists, then probably
21:50 < justanotheruser> not a VC expert or anything, but I think "Yo" getting $10M in funding indicates a bubble
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22:47 < rigel> justanotheruser: yo bought zynga, so now they own AOL
22:47 < rigel> after zynga bought AOL last year
22:48 < night> whoa
22:48 < night> the plot thickens
22:49 < rigel> oh, steve case. oh how the mighty have fallen.
22:49 < night> is this reddit stuff?
22:52 < night> Oh, that's another Steve
22:53 < night> too many goddamn steves in silicon valley
22:53 < night> I read a line about "how the mighty have fallen" in reference to reddit steve yesterday
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--- Log closed Thu Jul 16 00:00:12 2015