--- Log opened Mon Jan 09 00:00:00 2017
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05:21 < archels_> "Over 10 generations, the population's mean fitness increased twofold. This evolution occurred in spite of an unintentional integer overflow problem in recurrent nodes in the hidden layer that caused outputs to oscillate."
05:21 < archels_> genetic algorithms
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05:46 < kanzure> ah, some recurrent network + selection stuff. did that do interesting things?
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08:24 < JayDugger> Good morning.
08:25 < kanzure> yesss?
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10:27 < kanzure> rebelbio thing "The conference will take place on February 9th in UCC's Devere Hall from 8am late with our launch party"
10:28 < kanzure> "Our keynote speaker is Cyprien Verseaux, an astrobiologist and astronaut who undertook the HI-SEAS IV mission, a one-year simulated Mars mission funded by NASA to address crew cohesion and performance issues expected during a trip to Mars. He will speak in depth about his research into how synthetic bacteria will one day become the answer to create a stable colony on Mars."
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15:01 < kanzure> http://www.rifters.com/real/Blindsight.htm
15:18 < kanzure> "They're back now, after all-- raised from the grave with the voodoo of paleogenetics, stitched together from junk genes and fossil marrow steeped in the blood of sociopaths and high-functioning autistics." wat
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17:15 < jcorgan> can't tell if BS or awesome:
17:15 < jcorgan> https://www.statnews.com/2017/01/09/illumina-ushering-in-the-100-genome/
17:15 < jcorgan> .title
17:15 < yoleaux> A new era for DNA research: An entire human genome sequenced in an hour
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17:59 < justanotheruser> How do I get two hours of work done in one hour
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18:25 < kanzure> justanotheruser: amphetamine
18:28 < kanzure> justanotheruser: also, an hour in the library saves ten hours in the lab, and such
18:28 < kanzure> "We had been assured that the body would remain intact--the muscles electrically exercised, the body flexed and fed, the corpus kept ready to return to active duty should Heaven experience some inconceivable and catastrophic meltdown. Everything was reversible, we were told. And yet--there were so many who had ascended, and not even the deepest catacombs go on forever. There were rumors of d...
18:29 < kanzure> ...ismemberment, of nonessential body parts hewn away over time according to some optimum-packing algorithm. Perhaps Helen would be a torso this time next year, a disembodied head the year after. Perhaps her chassis would be stripped down to the brain before we'd even left the building, awaiting only that final technological breakthrough that would herald the arrival of the Great Digital Upload.""
18:29 < kanzure> ehh a little literary i guess
18:31 < kanzure> "Methods for non-viral gene therapy include the injection of naked DNA, electroporation, the gene gun, sonoporation, magnetofection, the use of oligonucleotides, lipoplexes, dendrimers, and inorganic nanoparticles."
18:32 < kanzure> hey what happened to hydrodynamic injection, cell-penetrating peptides, polymerosomes, liposomes, DNA+plastic polyplexing
18:32 < kanzure> " Virosomes are one example; they combine liposomes with an inactivated HIV or influenza virus. This has been shown to have more efficient gene transfer in respiratory epithelial cells than either viral or liposomal methods alone. Other methods involve mixing other viral vectors with cationic lipids or hybridising viruses."
18:33 < kanzure> .wik virosoome
18:33 < yoleaux> kanzure: Sorry, that command (.wik) crashed.
18:33 < kanzure> .wik virosome
18:33 < yoleaux> "A virosome is a drug or vaccine delivery mechanism consisting of unilamellar phospholipid membrane (either a mono- or bi-layer) vesicle incorporating virus derived proteins to allow the virosomes to fuse with target cells. Virosomes are not able to replicate but are pure fusion-active vesicles." -- https://en.wikipedia.org/wiki/Virosome
18:35 < kanzure> .wik protofection
18:35 < yoleaux> "Protofection is the transfection of foreign mitochondrial DNA into the mitochondria of all cells in a tissue to supplement or replace the native mitochondrial DNA already present." -- https://en.wikipedia.org/wiki/Protofection
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18:38 < kanzure> yashgaroth: what was the ligandal mechanism of action?
18:41 < yashgaroth> well that's proprietary ~nanotechnology~, but some combination of liposomes, dendrimers, conjugation to peptides or some other stuff I'd wager
18:41 < kanzure> nanoparticle cage stuff, or mostly liposome/lipid stuff?
18:42 < yashgaroth> oh nm it's whatever the fuck a "polyplex" is https://patents.google.com/patent/CA2924535A1/en?assignee=andre+watson
18:43 < kanzure> damn i was just looking for a patent, didn't find anything
18:43 < kanzure> polyplex is DNA + plastic
18:45 < yashgaroth> so a conjugation of PEI for DNA binding, histone tail peptide for nuclear localization, poly-glutamic acid for...something, lemme see
18:47 < kanzure> .title https://patents.google.com/patent/CA2924535A1
18:47 < yoleaux> CA2924535A1 - Nanoparticle-mediated gene delivery, genomic editing and ligand-targeted modification in various cell populations - Google Patents
18:48 < yashgaroth> glutamic acid for stabilization and charge balancing or w/e I'm not a chemist, then you stick DNA to it, and silica coat the whole thing, then add even more cell-targeting shit to the outside of that...
18:49 < yashgaroth> it's some sort of nano-gobstopper
18:50 < kanzure> that makes you some kind of molecular willy wonka?
18:51 < kanzure> makes sense i suppose, random bits of plastic get into all kinds of cells anyway just from environmental contaminants
18:51 < yashgaroth> that's andre, I'm a vermicious knid
18:52 < yashgaroth> wait is it actual plastic? just seems like poly amino acids
18:52 < kanzure> ok just silica then
18:54 < yashgaroth> there's always the tradeoff of "ok we need to protect the DNA, then get it into the cell, then escape the lysosome, then traffic to the nucleus, then release the DNA" against, like, keeping it simple enough to work because biology
18:55 < yashgaroth> oh and targeting specific cells because you can just put a targeting ligand on there and they'll magically shoot straight to that tissue and totally not all get sequestered into the liver or lungs or wherever nanoparticles usually end up
18:55 < kanzure> yes the silica eating part... how to do that.
18:56 < kanzure> i don't recall that being a part of normal cell metabolism
18:56 < yashgaroth> I'd be more worried about the polyethyleneimine metabolism
18:57 < kanzure> why's that?
18:58 < yashgaroth> because I don't believe it exists
18:58 < kanzure> for binding DNA to the object?
18:59 < kanzure> perhaps it's just not a significant amount
19:00 < yashgaroth> oh it's great for transfection, it'll compact DNA and stick to cell membranes; I mean if your delivery is efficient enough you won't be introducing a huge amount but people don't really use it in vivo
19:02 < yashgaroth> anyway I'm happy to talk shit about them forever, but with only a vague knowledge of their tech it's a bit tricky
19:03 < kanzure> it does sound somewhat complex, compared to "make virus, load it up with DNA".
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19:04 < yashgaroth> if I had to guess I'd say their main problems are correctly assembling the functional nanoparticles, and getting correct delivery in vivo; admittedly, those are broad problems
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19:21 < yashgaroth> ah ok they have the pictures here https://patentscope.wipo.int/search/docservicepdf_pct/id00000028560781/PAMPH/WO2015042585.pdf ... seems like it's working ok in cell culture, better than normal transfection reagents, but the effort of making the nanoparticles outweighs any benefit
19:21 < yashgaroth> but yeah in vivo is a whole different animal, best of luck to 'em though
19:22 < kanzure> music based on NASA mission audio https://somafm.com/missioncontrol/
19:24 < kanzure> yashgaroth: which diagram were you looking at?
19:25 < yashgaroth> fig. 2A has the assembly of the nanoparticle, then they do a few comparisons to lipofectamine further down
19:26 < kanzure> .wik lipofectamine
19:26 < yoleaux> "Lipofectamine or Lipofectamine 2000 is a common transfection reagent, produced and sold by Invitrogen, used in molecular and cellular biology.  It is used to increase the transfection efficiency of RNA (including mRNA and siRNA) or plasmid DNA into in vitro cell cultures by lipofection." -- https://en.wikipedia.org/wiki/Lipofectamine
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19:30 < yashgaroth> of course there is new lipofectamine 3000, who knows if it's still better than that
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19:34 < justanotheruser> any other advice for working faster
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19:35 < kanzure> justanotheruser: well, if you type faster, you can write more things down?
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19:49 < kanzure> justanotheruser: in programming, generally the answer is that if you are working quickly, then you're writing redundant software. for example, you should not be relying on muscle memory (because that means you're writing redundant source code...).
19:50 < kanzure> having said that, i'll admit to being highly interested in optimization
19:55 < kanzure> .wik cranial electrotherapy stimulation
19:55 < yoleaux> "Cranial electrotherapy stimulation (CES) is a form of non-invasive brain stimulation that applies a small, pulsed electric current across a person's head with the intention of treating a variety of conditions such as anxiety, depression and insomnia." -- https://en.wikipedia.org/wiki/Cranial_electrotherapy_stimulation
19:55 < kanzure> so.. why is that not the same thing as direct current stimulation?
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20:32 < superkuh> Because it's AC.
20:33 < justanotheruser> kanzure: Or I'm slow at desiging software
20:33 < justanotheruser> designing
20:33 < justanotheruser> I do not think typing is a bottleneck at all in writing software, I probably would be 10% faster if I typed twice as fast
20:40 < justanotheruser> don't some people use CES for ADHD?
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20:45 < justanotheruser> oh I think I'm confusing this with neurofeedback
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--- Log closed Tue Jan 10 00:00:01 2017