--- Log opened Sat Apr 22 00:00:33 2017
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00:13  * nmz787_ sleeps so I can get up for this tomorrow https://sites.google.com/site/acsossf/2017-schedule
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05:13 < kanzure> is that about the FIB? i'll hvae to think about it some more.
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07:22 < kanzure> musics https://www.youtube.com/watch?v=y6XytmP5-O8
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08:58 < kanzure> hooray "Stopping work on the glowing plant project" https://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit/posts/1786250
09:00 < kanzure> https://groups.google.com/d/msg/diybio/x8QhyhnFdDU/ZhpflcgtCQAJ
09:16 < cluckj> hooray?
09:17 < kanzure> glowing plant was evil and so were the people involved
09:21 < cluckj> evil how?
09:21 < kanzure> it doesn't glow.
09:26 < cluckj> :/
09:26 < kanzure> also glowing is evil anyway, unless it's being used to extract information from neurons
09:30 < JayDugger> Glowing plants for low-power ecofriendly landscape lighting?
09:30 < JayDugger> Do I win Earth Day bingo with those buzzwords?
09:45 < satori_> haha
09:45 < satori_> throw in 'synergy' for double-points!
10:01 < JayDugger> Naw, I have some self-respect.
10:07 < nmz787_> kanzure: yeah for the FIB
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10:08 < kanzure> .title https://news.ycombinator.com/item?id=14173271
10:08 < yoleaux> "Users will only be able to view patents via HTTP. HTTPS will no longer work" | Hacker News
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12:27 < kanzure> bloop
12:54 < kanzure> both ZNF704 and ZNF562 seem to have longevity-impacting alleles
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13:09 < nmz787_> blop
13:09 < kanzure> "Copy number variation associates with mortality in long-lived individuals: a genome-wide assessment" http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.796.7335&rep=rep1&type=pdf (2015)
13:10 < nmz787_> kanzure: these guys might be interested in your bioinformatics quest: www.perlara.com
13:11 < nmz787_> supposedly their model is people with rare diseases who no other companies will invest $ into treatments, they will start investigations (basically doing big pharma's discovery work they might not be interested in )
13:11 < nmz787_> so idk, your case seems like a rare gift, but maybe it will be interesting, or maybe they have the techniques to deal with small datasets
13:13 < kanzure> neat.
13:13 < kanzure> i need to get the data first.
13:13 < kanzure> i only have some of the data, need to do genome sequencing next on the two people
13:16 < kanzure> musics https://www.youtube.com/watch?v=cRHvxM0uOMU&t=1m
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13:17 < kanzure> "Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum" https://www.nature.com/articles/ncomms10561
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13:21 < kanzure> that is a fun paper..
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13:24 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=e5c988ec Bryan Bishop: add a bunch of longevity SNPs >> http://diyhpl.us/diyhpluswiki/genetic-modifications/
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13:42 < nmz787_> kanzure: does your bioinformatic quest have a name? I mean something keyword searchable?
13:42 < nmz787_> (not your info, but industry/medical/etc)
13:42 < nmz787_> other reports of this?
13:43 < kanzure> no other known reports :(
13:44 < kanzure> yeah we need to come up with a name for this phenotype
13:44 < kanzure> andytoshi: any ideas?
13:46 < nmz787_> haha, this perlara guy said martin shkreli was the only investor that told him 'yes' at the end of a pitch (during the same meeting)
13:48 < kanzure> open to name suggestions, "bizarre anti-sleep deprivation syndrome"
13:48 < nmz787_> breakout labs mention
13:48 < nmz787_> BUZZ
13:49 < kanzure> "sleep deprivation absence syndrome"
13:49 < nmz787_> it has to have a good acronym too
13:49 < nmz787_> SDAS :/
13:50 < nmz787_> ASS (absence of sleep syndrome)
13:50 < nmz787_> etc
13:51 < nmz787_> "'no' is just a latent yes"
13:51 < nmz787_> re: investors and asking them for money a second time
13:57 < andytoshi> weirdly wakeful wizard syndrome
13:58 < kanzure> hah.  so it is.
13:59 < nmz787_> WWWS
13:59 < nmz787_> easy enough
13:59 < nmz787_> 3WS
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15:05 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=0b491a8d Bryan Bishop: add more radiation resistance notes >> http://diyhpl.us/diyhpluswiki/genetic-modifications/
15:07 < kanzure> .wik TOMM40
15:07 < yoleaux> "Translocase of outer mitochondrial membrane 40 homolog (yeast), also known as TOMM40, is a protein which in humans is encoded by the TOMM40 gene." -- https://en.wikipedia.org/wiki/TOMM40
15:15 < kanzure> 15:15 <@gwern> kanzure: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740882/ I don't see RIMS1 in your list so this might be interesting. when I first saw it in 2013 or so, no replications or releated work, perhaps for obvious reasons
15:38 < kanzure> "Genetic enhancement of cognition in a kindred with cone-rod dystrophy due to RIMS1 mutation"
15:38 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=ce894931 Bryan Bishop: also mention RIMS1 >> http://diyhpl.us/diyhpluswiki/genetic-modifications/
15:46 < kanzure> "Patri Friedman points out that people genetically engineered to have single copies of all the autosomal recessive IQ boosters could not mate with each other naturally."
15:46 < nmz787_> this is theory?
15:47 < kanzure> iirc patri had some genetic work done on his kiddos but i didn't tell you
15:48 < kanzure> it's quoted from http://www.futurepundit.com/archives/002812.html about ashkenazi intelligence hypothesis and neurodegenerative diseases and muscular dystrophy disease stuff
15:49 < kanzure> http://web.archive.org/web/20061007153056/http://catallarchy.net/blog/archives/2005/06/05/low-hanging-fruit-for-genetic-engineering/
15:51 < kanzure> cc yashgaroth
15:53 < yashgaroth> is this just the usual heterozygote advantage stuff?
15:55 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=6029e423 Bryan Bishop: add optogenetic control of methlytransferase >> http://diyhpl.us/diyhpluswiki/gene-editing/
15:55 < kanzure> uhh maybe. i'm not 100% clear on how to find cases of that.
15:56 < yashgaroth> stuff like if you have one copy of the allele for tay-sachs you're smarter, but get two and you actually get tay-sachs...same as sickle cell but for brains
15:57 < kanzure> where do i find these.
15:59 < yashgaroth> I don't know if there's evidence that e.g. the tay-sachs allele increases intelligence, vs just being from centuries of inbreeding
16:01 < yashgaroth> but people love to speculate
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16:55 < kanzure> kent suggests "fructose metabolism pathways like NMRs have for metabolism without oxygen" does anyone know what he is talking about
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17:05 < kanzure> "There's a SNP in mice that's responsible for 20% of the variance in penis bone size"
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17:25 < kanzure> nmz787_: "any idea what Yaniv's "DNA Fountain" is?"
17:39 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=572b133f Bryan Bishop: include references for a church talk transcript >> http://diyhpl.us/diyhpluswiki/transcripts/hgp-write/2016-05-10/from-recoli-to-1-million-genomes/
17:40 < kanzure> what is this doing on the wiki, where did it come from? "Also, programmatic DNA synthesis could be achieved with programmable recombination. Use a bead with attached DNA. Use recCas9 (guide RNA programmable recombinase) to extend each of the DNA molecules. Wash or flush any non-recombined reactants and byproducts. Insert guide RNA and recCas9 for next cycle, plus next DNA fragment."
17:41 < kanzure> from http://diyhpl.us/wiki/gene-editing/
17:42 < kanzure> "We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture"
18:22 < kanzure> cool, george church is in time's 2017 "100 most influential people in the world" list
18:25 < cluckj> make him pay for lunch then
18:28 < kanzure> you sure your priorities are straight?
18:30 < cluckj> :)
18:31 < cluckj> no
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20:36 < nmz787_> kanzure: dna fountain ref plz
20:37 < nmz787_> this ? http://science.sciencemag.org/content/355/6328/950
20:37 < nmz787_> .title
20:37 < yoleaux> DNA Fountain enables a robust and efficient storage architecture | Science
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20:40 < nmz787_> from the abstract alone, it seems like they simply confirmed that PCR does what it says, and that polymerase doesn't make many mistakes
20:40 < nmz787_> I can infer that maybe their encoding has some error correction built in based on polymerase error profile???
20:44 < nmz787_> "In a new study in Science, a pair of researchers at Columbia University and the New York Genome Center (NYGC) show that an algorithm designed for streaming video on a cellphone can unlock DNAs nearly full storage potential by squeezing more information into its four base nucleotides."
20:45 < nmz787_> http://datascience.columbia.edu/researchers-store-computer-operating-system-dna
20:45 < nmz787_> soo, uhh, h.264 or h.265 ???
20:45 < nmz787_> (I still haven't opened the full paper)
20:46 < nmz787_> "The success of our strategy lies in careful adaptation of recent developments in coding theory to the domain specific constraints of DNA storage."
20:46 < nmz787_> http://dnafountain.teamerlich.org/
20:48 < kanzure> ah right i remember this. yeah, not interesting.  error correction codes are well known.
20:49 < kanzure> synthesis is the bottleneck, not encoding schemes
20:50 < nmz787_> yeah, doesn't seem to impress Intel flks
20:50 < nmz787_> folks*
20:51 < nmz787_> I tried the whole "but we make SSDs, and the whole internet in a Nalgene!!! :O :O :O "
20:55 < nmz787_> well, at least we have the evidence now, so it isn't valueless...
20:57 < nmz787_> I was talking to a guy who does codon expansion to use weird amino acids for novel peptides
20:58 < nmz787_> down at OSU... I didn't know genehacker's real name or department... so that line of conversation went nowhere
20:58 < nmz787_> 'hey do you know this other grad student's IRC handle?'
20:59 < cluckj> lol
21:03 < kanzure> nmz787_: it's charlie. he's in mechanical engineering, though.
21:03 < kanzure> in this group http://design.engr.oregonstate.edu/campbell
21:05 < kanzure> https://github.com/DesignEngrLab
21:07 < kanzure> 'design repository' http://ftest.mime.oregonstate.edu/repo/browse/
21:09 < kanzure> http://designengrlab.github.io/
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21:16 < kanzure> "Effectiveness of motor practice in lucid dreams: a comparison with physical and mental practice" https://www.researchgate.net/profile/Tadas_Stumbrys/publication/274642510_Effectiveness_of_motor_practice_in_lucid_dreams_a_comparison_with_physical_and_mental_practice/links/55f1616d08ae199d47c24ff0.pdf
21:17 < kanzure> "Improvement of darts performance following lucid dream practice depends on the number of distractions while rehearsing within the dream - a sleep laboratory pilot study" http://www.tandfonline.com/doi/abs/10.1080/02640414.2016.1267387
21:21 < kanzure> "We recently showed that frontotemporal stimulation with transcranial alternating current stimulation (tACS) is able to increase 40 Hz resonance activity in the dorsolateral prefrontal cortex during REM sleep [3], strongly associated with induction of lucid dreaming [4]."
21:21 < kanzure> "[3] Voss U, Holzmann R, Hobson A, Paulus W, Koppehele-Gossel J, Klimke A, Nitsche MA. Induction of self-awareness in dreams through frontal low current stimulation of gamma activity. Nat Neurosci. 2014 Jun;17(6):810-2"
21:21 < kanzure> "[4] Voss U, Holzmann R, Tuin I, Hobson JA.Lucid dreaming: a state of consciousness with features of both waking and non-lucid dreaming. Sleep. 2009 Sep;32(9):1191-200."
21:26 < kanzure> that first one is https://pdfs.semanticscholar.org/a14f/d109f549a88b59d39a2326314aadd7d3a937.pdf
21:33 < kanzure> need me some lucid dreaming SNPs and dream recall SNPs
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--- Log closed Sun Apr 23 00:00:34 2017