--- Log opened Mon May 16 00:00:16 2016
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01:37 < fenn> surely i'm not the only one who sees the irony in denying people knowledge needed to automatically close captiopn video because the video isn't closed captioned already[C[C[C[C[C[C[C[C[C[C[C[C[C[C
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04:46 < pasky> kanzure: http://pasky.or.cz/argus-repl4nlp.pdf maybe you'll think of some applications for your huge transcripts / logs database
04:47 < pasky> the models are implemented in python to be real-world usable, we even have a REST API ( though it'd have to be tweaked for the HypEv task)
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05:24 < kanzure> i don't understand "it would definitely have to be a volunteer project"
05:29 < chris_99> http://www.bioo.tech/ - well this looks suspect ;)
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05:37 < kanzure> fenn: what knowledge am i denying others access to?
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05:42 < kanzure> oh that was probably about the "litigation" thing mentioned. nevermind.
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06:50 < JayDugger> Thank you for the link, pasky.
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06:55 < FourFire> Invited user <trudko>
06:57 < trudko> Hi kanzure , I was told that you might be able to point me to some interesting resources about how can software developers without much of understanding of biology and science help accelerating genomics research. Personally I found few bioinformatics  open source software , mostly for data visualization, then there are machine learning projects(outside of web development knowledge) and some API like 23 and me...
06:57 < kanzure> trudko: read everything http://diyhpl.us/~bryan/papers2/bio/ http://diyhpl.us/~bryan/papers2/bio/books/
06:59 < trudko> thanks but from quick view seems like most of that is for someone with some basics in biology and genetics
06:59 < kanzure> use the first link then
06:59 < trudko> and right now I am looking more for projects which I can show my cooworkers to get them interested in the field
07:00 < trudko> I am not looking at how I can personally learn more about this in depth(although I am planning to do that)
07:00 < kanzure> unfortunately bioinformatics requires you to learn some things before "help accelerating x research"
07:01 < trudko> it depends right? For example I dont have to know much to work on data visualization software which would be used by researchers
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07:02 < kanzure> there's lots of projects that can use extra programmers, but it wont advance any genomics knowledge
07:03 < kanzure> e.g. bioperl/biopython/lots of plasmid vector programs/benchlab web interface things/blast stuff/crossbow cloud things/vtk/mayavi
07:05 < kanzure> most of the advances in this field of science come from people who look at a traditional problem in biology, molecular biology, genetics, synthetic biology, protein design, etc. and then say "holy shit you guys are fucking idiots, this can be automated with a for-loop and some basic control structure".
07:05 < kanzure> (not always that simple, but yeah.)
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07:10 < trudko> kanzure:  heh I see, so what would you say would be low hanging fruit for web developers which would like to somehow help this field except maybe sending extra cash on the research?
07:12 < kanzure> trudko: juul has been looking for some people to help him out on a frontend project for biobricks foundation, for plasmid/lab management things
07:14 < trudko> kanzure: thanks will check it and if you are here juul ping me ;)
07:15 < kanzure> yes juul is in here
07:15 < kanzure> also bioperl/biopython probably does web development things.. go poke those people.
07:17 < trudko> great I think I got some good idea what to talk about. One more question maybe. My basic understanding about genome sequencing application comes from reading popular articles mostly about Craig Venter work and it seems that whole point is right now to get as much whole genomes as possible put machine learning on it and hope that something come up.
07:19 < kanzure> craig venter has been working on gene synthesis at the moment, not gene sequencing.
07:20 < kanzure> he was doing gene sequencing back in the early 2000s though.
07:20 < kanzure> i highly recommend never reading popular articles about anything ever. they are always wrong.
07:21 < kanzure> there are people working on bioinformatics with machine learning, sure.. like protein classification, metabolism optimization, phylogenetic sorting, etc.
07:24 < trudko> what about his company Human Longetivity, my understanding was that they want to get as much genomes plus additional data and  use something comes up from that.
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07:31 < kanzure> they might be doing something interesting, but iirc they never released any specific details, so it's hard to know.
07:31 < kanzure> "genomes! phenotypes!" yes these are some of the things you would need to do anything interesting... so what?
07:33 < kanzure> btw that company purchased a bunch of dna sequencing machines, it's really a stretch to say that venter is working on sequencing. i mean yes he's collecting data but so what? if you want to play with human genomes, go download the terabyte dataset off of aws....
07:34 < kanzure> ("1,000 human genomes")
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07:40 < trudko> yeah and what do you think about Jun Wang focusing on machine learning too? Seems like he his big name in genomics(http://www.nature.com/news/exclusive-genomics-pioneer-jun-wang-on-his-new-ai-venture-1.18091)
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07:54 < kanzure> i wonder how much human productivity is wasted by "news" like that
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07:57 < jessie22> hi
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08:12 < kanzure> http://www.wsj.com/articles/tech-savvy-families-use-home-built-diabetes-device-1462728637
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08:36 < maaku> fenn: doubly ironic given the subject matter of the class is "Deep Learning for Natural Language Processing"
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09:25 < mz_o__> kanzure: earlier, when I mentioned "volunteer project" I alluding to a coordinated effort of extracting/summarizing old logs
09:25 < kanzure> none of you have volunteered to do that, so i don't give a shit. i'll just pay someone.
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09:33 < mz_o__> Of course. Things cant come to a halt just because no one takes the initiative
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09:40 < kanzure> https://utopiaordystopia.com/2016/05/07/a-less-bleak-lesson-from-the-silent-universe/
09:40 < kanzure> "they estimate the chance that we’re the first and only is 1 in 10 billion trillion"
09:42 < kanzure> "It is IMHO not a very impressive paper. Basically their argument is "Look, the probability per star needed to get an empty universe is really low, so a priori we should expect it to be higher." My own upcoming paper shows that if you do the probabilities right you can easily get empty universes given what we know."
09:42 < kanzure> "(The quick of it: people assume some key Drake equation parameters must lie in a far smaller range than they are allowed to by our actual knowledge, and this produces over-optimistic estimates. When you update on the empty sky, it makes the past great filter more likely than a future great filter.)
09:42 < kanzure> "
09:43 < kanzure> ""Big" is the interesting term here: what is a big universe? If I tell you the universe may have 10^10, 10^20 , 10^50, 10^100, or 10^10^100 stars, when will you say "whoa, that sounds unlikely?" (assuming we are doing this from comfy armchairs without actually rushing off to a telescope to check). Presumably you will have some feeling that certain numbers are so large that they are a priori unlikely. Conversely, if I ask if you think the ...
09:43 < kanzure> ... probability of life on an earthlike planet is about 1, 0.01, 10^-6, 10^-30 or 10^-10^115, you will likely think some of the numbers sound unlikely. But why? How would you justify this from the armchair? Much of people's prior estimates have far too narrow ranges of likely numbers."
09:43 < kanzure> "The main point of the paper is that a reasonable range for the life probability easily runs from from 1 to 10^-100 given what we know (and this does not include the rather uncertain intelligence and tech probabilities). There are about 10^25 stars in the observable universe. So there is 25 orders of magnitude between the sun and the observable universe - but if you choose an exponent for the probability of life uniformly between -100 ...
09:44 < kanzure> ... and 0, that means that we have just one chance in four to get more life than us in the observable universe."
09:44 < kanzure> "Now, many of us think we know better. But if we think life has a chance in between 10^-6 to 10^-2, we need to give evidence for this range. If you think my above log-uniform distribution of probability is stupid, you need to have an argument for why something less spread out is reasonable. And my argument is not that the universe *must* be empty, just that armchair astrobiology, when properly done and taking actual uncertainty into ...
09:44 < kanzure> ... account, makes it look like the most likely possibility.
09:45 < kanzure> .wik KIC 8462852
09:45 < yoleaux> "KIC 8462852 (eponymously Tabby's Star after lead author Tabetha S. Boyajian, or WTF Star, formally for "Where's The Flux?", but also a reference to an expression of disbelief) is an F-type main-sequence star located in the constellation Cygnus approximately 454 parsecs (1,480 ly) from Earth." — https://en.wikipedia.org/wiki/KIC_8462852
09:47 < kanzure> "I largely agree with your analysis.  But it's possible we missed something, like a physics based reason for intelligent species to stay in their star system or even to stick to their home planet.  I have speculated about civilizations "collapsing" to 300 m spheres sunk in the deep ocean.  The small size gets the latency down and the cold water deals with the waste heat problem."
09:52 < kanzure> http://lists.extropy.org/pipermail/extropy-chat/2016-May/087925.html
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10:03 < mz_o__> 4
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13:08 < kanzure> target2 report released a few days ago, https://www.ecb.europa.eu/pub/pdf/other/targetar2015.en.pdf
13:08 < kanzure> "TARGET2 turnover in 2015 amounted to a total value of €469.8 trillion, corresponding to a daily average of €1.8 trillion."
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13:19 < kanzure> plastic maps from lidar data http://www.aeracode.org/2016/5/16/hello-london-rising/
13:23 < chris_99> heh cool
13:24 < chris_99> maybe they could use https://www.youtube.com/watch?v=YlUhPrAqiY0 (Computational Hydrographic Printing) to colour it
13:29 < kanzure> they could use CaptHindsight to color it, if he was still around in here
13:29 < kanzure> (he's in #linuxcnc)
13:35 < maaku> as with most anthropic or fermi arguments, does this in any way change my priorities?
13:37 < kanzure> maaku: getting better at observing and finding remote infrastructure is useful because you can gather knowledge about what physically doesn't work (or what does work)
13:38 < maaku> kanzure: sure, that's the one piece of astronomy work that actualy give useful, pragmatic results. if only people took SETI seriously :(
13:39 < kanzure> the most interesting drake equation work that i saw recently was one that did some rather clever math regarding shifting observable segments of the sky
13:40 < kanzure> oh maybe it was more about terrestrial planets, hm
13:41 < kanzure> ""Terrestrial planets across space and time" http://arxiv.org/abs/1602.00690v1
13:41 < kanzure> or this is the wrong paper
13:51 < kanzure> huh.. can't find it. weird.
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14:37 < kanzure> "High Throughput, High Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing" https://www.maxplanckflorida.org/news-and-media/news/the-new-slendr-technique-protein-labeling-in-the-developing-brain-by-genome-editing/
14:38 < kanzure> "SLENDR (single-cell labeling of endogenous proteins by CRISPRCas9-mediated homology-directed repair)"
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15:55 < kanzure> maaku: your quora thing finished
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16:01 < maaku> thanks for the reminder
16:19 < maaku> yay there's a new AIMA book in the works
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17:01 < kanzure> Cory: hi
17:03 < maaku> is that theuni Cory?
17:05 < Cory> Lol I'm mostly in Bitcoin channels so I expect the confusion there. But nowhere is safe!
17:06 < maaku> well yeah I saw you are in bitcoin-workshops. have we met?
17:06 < maaku> just trying to put a face to a nick :)
17:07 < ybit> https://vimeo.com/163751907
17:07 < ybit> .title
17:07 < yoleaux> 3D Printing Metal in Midair on Vimeo
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17:12 < superkuh> Very cool.
17:18 < Cory> I don't think so, maaku. I recognize you from Bitcoin stuff, but I haven't been too active on IRC since 2012 or so. I was mostly in -otc then.
17:19 < maaku> well good to see you here too
17:21 < Cory> You as well. :) Seems to be lots of crossover and I like the discussion here, so I added it to my collection of channels to idle in.
17:33 < kanzure> Cory: that's because we engineered some brain slugs and they made their way into the heads of bitcoin core developers
17:34 < jrayhawk> I named mine "Bitey".
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18:19 < justanotheruser> is that how you got them to come over here?
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18:33 < kanzure> justanotheruser: ask your slug and you'll know the answer
18:35  * justanotheruser came here before Bitconi
18:35 < justanotheruser> or at least that's what... my memory tells me
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19:00 < kanzure> aw crap i forgot about eric hunting
19:00 < kanzure> ooh actually he would be a good option for paying to review and summarize the logs..
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19:22 < JayDugger> Would these (as-yet-undone) log summaries appear on the wiki?
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19:34 < juul> hrm, does anyone have contact info for trudko?
19:34 < kanzure> FourFire does.
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21:26 < gwillen> So I asked this in another channel and got crickets, so let me ask here: what do people think about Metformin as a potential anti-aging drug (for practical use right now based on data already available)?
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21:41 < Jawmare> *crikets*
21:42 < Jawmare> gwillen, its going to wreck the economy
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23:30 < fenn> gwillen: metformin causes nausea and terrible feeling in a lot of people, or so i hear. that's probably enough to prevent its widespread use
23:34 < fenn> it might be easier to sell people on green coffee extract, which apparently has the same mechanism (?)
23:34 < fenn> chlorogenic acid
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23:41  * fenn reads http://www.nature.com/news/anti-ageing-pill-pushed-as-bona-fide-drug-1.17769
23:42 < fenn> "Plans call for the trial to enroll 3,000 people aged 70–80 years"
23:52 < gwillen> huh!
23:55 < gwillen> fenn: do you know if the nausea and terrible feelings are dose dependent
23:55 < gwillen> like, can you take a little metformin for a little benefit
23:55 < fenn> i got the impression it was related to how much sugar you ate, more sugar more nausea
23:55 < gwillen> ohhhhh, interesting
23:55 < fenn> but i could be misremembering
23:56 < gwillen> okay, I didn't understand before why diabetes would be associated with hypoglycemia, but it all makes sense if it's actually metformin taken for diabetes that causes it
23:57 < gwillen> (or injected insulin of course, but that would be acute rather than chronic)
23:58 < fenn> 2015-11-25.log:17:50 < ebowden> Also, berberine was as effective as metformin in a phase 3 clinical trial for type 2 diabetes for some reason.
--- Log closed Tue May 17 00:00:16 2016