--- Log opened Thu Oct 22 00:00:03 2015
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05:21 < kanzure> hrmph
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05:29 < justanotheruser> hello #hackernews
05:29 < justanotheruser> I'm here to complain about the fact that every day there is a new intro tutorial on deep learning. That is all
05:32 < kanzure> i think you mean #startups
05:33 < justanotheruser> are there a lot of startups in this channel
05:33 < justanotheruser> I thought this was just your blog
05:34 < kanzure> #hackernews is an actual channel that was created by people who didn't know about #startups
05:34 < kanzure> #startups is also an actual channel
05:35 < justanotheruser> yeah, I'm just talking about the website, which features a deep learning/neural network tutorial on the front page daily
05:40 < kanzure> https://www.fightaging.org/archives/2015/10/methuselah-foundation-podcast-an-interview-with-david-gobel.php
05:40 < kanzure> https://www.fightaging.org/archives/2015/10/reporting-from-a-comparative-biology-of-aging-conference.php
05:41 < kanzure> https://www.fightaging.org/archives/2015/10/rejuvenation-biotechnology-2015-keynote-videos.php
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06:59 < eudoxia> has anyone had this problem with sci-hub where it just presents an endless sequence of captchas
06:59 < Aurelius_Work> I read that as cats
06:59 < Aurelius_Work> I'm tired
07:06 < eudoxia> false alarm, i found a way around it
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08:08 < kanzure_> https://www.indiegogo.com/projects/help-end-viral-diseases-with-dracos#/
08:08 < kanzure_> https://www.lifespan.io/campaigns/sens-mitochondrial-repair-project/
08:08 < kanzure_> "SENS research has had a banner year this year. Oisin Biotechnology has been seed funded to develop a means of senescent cell clearance, another group demonstrated proof of principle senescent cell clearance and corresponding health improvements in mice, Human Rejuvenation Technologies was founded to develop lysosomal aggregate clearing enzymes as a therapy, a method of synthesizing glucosepane was published in Science, Gensight has ...
08:08 < kanzure_> ... raised a boatload of money for their allotopic expression work"
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08:16 < fenn> it's too bad senescence isn't the cause of aging
08:17 < maaku> well there isn't one specific cause of aging
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08:38 < kanzure_> http://www.nytimes.com/2015/10/20/science/editing-of-pig-dna-may-lead-to-more-organs-for-people.html
08:38 < kanzure_> oh wait we saw this already. nevermind.
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08:45 < CaptHindsight> maaku: time
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10:14 < maaku> touché
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10:33 < kanzure_> bad programming is the cause
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10:36 < kanzure_> well, incomplete selection is the cause
10:36 < fenn> 23andme still has some interesting things to say, even though they haven't rolled out the new health-related info
10:37 < kanzure_> what's the plan for long-term astronomy?
10:37 < kanzure_> recording the entire universe at high-fidelity resolution over all wavelengths for the next million years will require a very large amount of storage space
10:38 < kanzure_> presumably you can get rid of a lot of the data because it will just match expectations or predictions
10:38 < kanzure_> and maybe you can do the same from multiple sources, so that you don't have to store complete astronomical data from n observatories
10:39 < kanzure_> and even if you do have 100k years of data, how the shit are you going to search that efficiently or run algorithms against that data set?
10:39 < fenn> ohnoes data
10:39 < kanzure_> query speed might be zero
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10:45 < maaku> kanzure_: opinions on DRACOS?
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10:46 < maaku> i.e. am I throwing money away if I donate?
10:46 < kanzure_> donations are a bad plan
10:46 < kanzure_> 11:58 < yashgaroth> DRACO won't work for HIV, or any other virus with latency
10:46 < kanzure_> venturecommunist was working on DRACO things, i wonder where he went
10:47 < maaku> ok but for the things it does claim, e.g. cold, flu, herpes?
10:47 < kanzure_> 15:39 < venturecommunist> if it's really non-toxic in-vivo in humans presumably it's a cure for AIDs, HPV, HSV, Hep A/B/C/D/E Ebola, Influenza and the Common Cold
10:47 < kanzure_> 15:40 < ParahSailin> the draco antiviral drugs are the simple fusion protein you described?
10:47 < kanzure_> 15:40 < venturecommunist> right
10:47 < kanzure_> 15:42 < ParahSailin> hm good catch on the paper
10:47 < kanzure_> 15:36 < ParahSailin> what would pkr and adaf1 do in e coli?
10:47 < kanzure_> 15:37 < venturecommunist> the genes would produce the proteins, if they're expressed in e coli
10:47 < kanzure_> 15:37 < venturecommunist> the protein being a chimera of TAT, PKR and ADAF1
10:48 < kanzure_> http://gnusha.org/logs/2014-01-13.log
10:48 < maaku> call me names, but I care more about eliminating the common cold and flu than HIV
10:50 < kanzure_> why would that be bad ?
10:58 < fenn> eliminating any of those would be huge
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11:12 < fenn> oh my bad about 23andme, "Customers who received their health information prior to November 22, 2013 will still be able to see their health reports, but those who purchased after that time will only receive their ancestry information as well as access to their uninterpreted raw data."
11:20 < kanzure_> not clear whether they update the raw data as long as you have a subscription
11:20 < delinquentme> when talking about real time system + interfaces to non-real time code ... how does one typically refer to the non-real-time code?
11:21 < kanzure_> some of their text i saw yesterday indicated that they might re-run their snp arrays and give better data. but never seen any evidence of this.
11:21 < kanzure_> delinquentme: batch, offline, blocking, delayed, job, work, task
11:21 < kanzure_> queued.
11:22 < kanzure_> should clarify that i haven't seen any evidence, but i also haven't looked
11:32 < kanzure_> exercise form recognition http://www.dilpreetsingh.me/activity-recognition
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11:59 < maaku> fenn: they just got FDA approval, no? I presume that means everyone will have access to the health info again
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12:01 < maaku> oh n/m. "The revamped reports of genetic tendencies, plucked from spit samples, will not offer customers insights on their risks of developing a range medical conditions, such as Alzheimer’s disease, as previous testing did. Instead, the new test focuses on informing customers about their ancestry, the mutations that could pose disease risks to their children, and traits such as their reaction to alcohol and potential for hair loss."
12:01 < maaku> .title http://arstechnica.com/science/2015/10/23andme-reboots-genetic-health-testing-now-with-fda-approval/
12:01 < yoleaux> 23andMe reboots genetic health testing, now with FDA approval | Ars Technica
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12:07 < superkuh> I deleted my 23andMe account a few days ago. Right before this announcement. Right after the news about cops dipping in to their databases.
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12:13 < kuudes> the cops-23andme seems really straightforward to me. that was what has so far prevented me from sampling myself and my relatives
12:14 < kuudes> like, given they wiretap everyone all the time, why wouldn't they invade genetic fingerprint db?
12:14 < superkuh> In retrospect, yes. But I didn't want to believe because I wanted the data. Which... I still have on disk.
12:15 < kuudes> I have considered a german company, which only sends the data to you, and does not store it on their servers
12:15 < maaku> kuudes: it's a bigger deal than you are making. yes the NSA listens on everyone, but they generally haven't been sharing info with local cops
12:16 < maaku> the issue here is that genetic evidence is -way- less reliable than the justice system believes
12:16 < maaku> it works in a homicide investigation because the chances of a false positive with a sample size of just the suspects you had anyway is rather small
12:17 < maaku> but you cast such a broad net, you'll get 10k false positives for every search
12:17 < maaku> i'm innocent, but chances are my DNA 'matches' evidence for a crime somewhere
12:17 < kuudes> well but if you combine that to cell tower records to also close out those who have not been anywhere near the location etc
12:17 < kanzure_> hey at least they aren't looking at bite marks
12:18 < kanzure_> oh wait they are looking at bite marks
12:19 < kuudes> locally we have the problem that the passports have fingerprints, which specifically were said will not be used for crime investigation when it was done some 5 years ago, and now they want to include that to crime investigation (and donate that to NSA probably for their weird bonuspoint credit system)
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12:53 < ryankarason> i am also interested in gettting a DNA sampling.. but i haven't looked it to it long enough to know how the data works.. does 23andme own your DNA data?
12:54 < TMA> hmm, I shall use my fingerprintless password while it is still valid.
12:54 < ryankarason> i'd prefer my data to be free.. so it would be nice to just find a way to sample it myself and just publish it on git..
12:54 < kanzure> lots of people have uploaded their 23andme snp data as a csv file to various places
12:54 < kanzure> like snpedia
12:54 < ryankarason> kanzure: ok.. but do i have all rights to this data?
12:54 < ryankarason> or does 23andme own it?
12:54 < kanzure> what??
12:55 < kanzure> that's for a judge to decide
12:55 < ryankarason> my thought would be.. that 23andme owns everything in their database
12:55 < TMA> kuudes: if they have the data, assume they store it. No auditor would ever find otherwise
12:55 < ryankarason> and theirfor has the right to sell off my data or even lock me out of it.
12:55 < ryankarason> it would be what i would guess.. but i haven't researched enough to know.
12:56 < kanzure> you should download the data before they "lock you out"
12:56 < ryankarason> i am OK with my data being open.. i just don't like the idea of someone else /owning/ it.. i need to research.
12:56 < ryankarason> kanzure: aye aye.
12:57 < ryankarason> how much $ worth of equiptment would i need to sample it myself?
12:57 < kanzure> uh depends on how much you want to do on your own. make your own snp probe array? buy one?
12:57 < kanzure> why not just sequence your gneome?
12:58 < kanzure> *genome
12:58 < TMA> ryankarason: if you take a photograph of someone, you are the copyright owner of the photograph. the photographee has some rights (right to be used in nondefamatory manner) but not the copyright to the photo
12:58 < ryankarason> right.. i am interesting in sequencing my genome.. but i don't know enoug habout it
12:58 < ryankarason> was thinking about reading Mullis's PCR book
12:58 < kuudes> TMA, yeah, tends that way. though that is *germany*, where such is veery baad, because of Stasi and the Nazis.
12:59 < kanzure> well, these days you go pay a core lab facility to read your genome
12:59 < kuudes> "been there, done that, didn't like it."
12:59 < kanzure> use scienceexchange.com
12:59 < ryankarason> TMA: ah .. OK.. good way to look at it.. i usually don't study copyright stuff because it just makes me sad
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12:59 < TMA> ryankarason: I think the same argument is with DNA data
13:00 < ryankarason> good to know.
13:00 < ryankarason> i was afraid such was the case.
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13:01 < ryankarason> i want to then find some "photographer" that will sell me all rights to the photograph (DNA) of myself.
13:01 < TMA> ryankarason: ultimately it depends on who wins the lawsuit.
13:01 < ryankarason> right.. but i don't have money or influence to  win such
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13:03 < maaku> TMA: things aren't so clear when you are paying for a service
13:03 < kuudes> well, photographs are not that good of an analogy, as they have their own, special class of copyright, which requires less of achievement than other classes
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13:04 < ryankarason> is there any precedence yet with DNA stuffs?
13:05 < TMA> maaku: yep. if it is work for hire, then the copyright is transferred; however, if it is a commodity service, the copyright is not transferred by default
13:05 < kuudes> ie. over here copyright requires the work to be as a whole an "artistic work", where the creator has made some non-obvious presentation in the work - for instance things like diagrams, charts etc usually are not under copyright here
13:06 < ryankarason> copyright law is so strange=P
13:07 < kuudes> but photographs are in a special class of photograph, which can be artistic work, but even if it is not, is still considered a photograph, which grants some monopoly to the photographer over that specific photograph, even if the work as a whole is not an artistic work
13:07 < TMA> the burden of proof lies with the party claiming noncopyrightable status (unless the party is the author)
13:07 < kuudes> mainly the latter is to prevent newspapers from not paying to the photographers, I have understood
13:07 < kuudes> the interesting bit is that this is dependent on the technology - drawings and videos are not legally photographs
13:08 < kuudes> so anyones holiday shots are photographs, and thereby protected as such, but their holiday videos are not artistic works likely, because usually such are of such quality, that most anyone would make a similar creation, which makes it not-a-work
13:09 < kuudes> over here in finland of course, such laws have much local nuances
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13:55 < kanzure> http://www.zerohedge.com/news/2015-10-22/abbvie-stock-plunges-after-fda-warns-serious-liver-injury-risk-companys-hep-c-treatm
13:55 < poppingtonic> .title http://bioengineer.org/bioengineering-breakthrough-scientists-create-a-working-animal-limb-in-a-lab/
13:55 < yoleaux> Bioengineering breakthrough: Scientists create a working animal limb in a lab
13:56 < kanzure> nah see quote in logs from yesterday
13:57 < poppingtonic> you discussed this yesterday?
13:59 < poppingtonic> I only see the beagle story, which I remember.
13:59 < kanzure> uh, maybe day before
13:59 < kanzure> ah maybe i was thinking of epibone
14:00 < kanzure> .title https://www.youtube.com/watch?v=p143bISuEJk
14:00 < yoleaux> Rat Tissue Decellularization - YouTube
14:00 < poppingtonic> yeah I've grepped to 18th, no related animal mentions
14:01 < poppingtonic> Well, Ctrl+F'd
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14:03 < kanzure> .title http://circres.ahajournals.org/content/early/2015/10/21/CIRCRESAHA.115.307521.abstract
14:03 < yoleaux> Circulating Growth Differentiation Factor 11/8 Levels Decline with Age
14:04 < kanzure> popularized: http://news.sciencemag.org/biology/2015/10/antiaging-protein-real-deal-harvard-team-claims
14:04 < kanzure> (more "young blood")
14:30 < kanzure> 14:26 < Daeken> kanzure: so, i saw you were trying to reverse-engineer solidworks files a couple years ago ... well, i can successfully parse (the bulk of) solidworks 2015 files >:)
14:30 < kanzure> 14:27 < Daeken> kanzure: turns out that they're primarily parasolid files wrapped in zlib ... found an old spec from siemens (who apparently owns it now), and managed to write a parser
14:30 < kanzure> 14:27 < kanzure> yes, it's zlib
14:30 < kanzure> 14:27 < kanzure> xt spec was helpful yes/no?
14:30 < kanzure> 14:27 < Daeken> very
14:30 < kanzure> 14:27 < kanzure> parasolid xt spec
14:30 < kanzure> 14:27 < Daeken> https://gist.github.com/daeken/cf412009224a6770d6dc
14:30 < kanzure> 14:27 < kanzure> DisplayList is just zlib + what?
14:30 < kanzure> 14:28 < Daeken> hm, not familiar with displaylist.  i've just been looking purely at sldprt files
14:30 < kanzure> 14:28 < kanzure> https://groups.google.com/forum/#!topic/openmanufacturing/Fv2Ovmxnfyw
14:30 < kanzure> 14:28 < kanzure> Contents/DisplayLists__ZLB
14:30 < kanzure> 14:28 < Daeken> there are a bunch of uncompressed blobs that i don't understand, but all of the compressed data is just pure parasolid xt.
14:30 < kanzure> 14:29 < kanzure> it's OLE data, and then the "DisplayLists__ZLB" stuff is one of the components
14:30 < kanzure> 14:29 < Daeken> ahhh, that's right -- you were looking at an older format.  they totally changed it with 2015.
14:30 < kanzure> 14:29 < Daeken> no more OLE stuff
14:31 < kanzure> welp that's one way to solve a problem... "wait for solidworks to screw up their own file format"
14:31 < maaku> wait for disgruntled solidworks employee to switch to throw out the legacy in favor of sqlite
14:32 < maaku> (one can hope)
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14:33 < kanzure> http://demoseen.com/sldprt.zip
14:44 < fenn> i bet the displaylist is just a preview or precomputed result of the actual data structure
14:45 < kanzure> daeken claims no preview in solidworks 2015 format
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14:45 < Daeken> yo.
14:45 < kanzure> was just showing him the cantor dust presentation https://www.youtube.com/watch?v=4bM3Gut1hIk&t=19m40s
14:45 < fenn> oh i wasn't really trying to make intelligent comments on the solidworks format right now
14:46 < kanzure> yeah but makes sense to say those things in here instead of other dead channel
14:46 < Daeken> https://gist.github.com/daeken/d593592694e022269724 <-- those are the three parasolid files inside of 10043-1.sldprt
14:46 < poppingtonic> how did you do that?
14:46 < kanzure> since previous solidworks file format info has happened in here
14:46 < kanzure> daeken says gsf no go for solidworks 2015 files
14:46 < Daeken> (that file is really just a box.  you can see the drawing and STL at http://curtawiki.com/10143
14:47 < Daeken> figure it's a good place to start testing from.
14:47 < kanzure> wonder if it's just parasolid or anything extra
14:48 < Daeken> the compressed chunks are absolutely 100% valid parasolid files.
14:48 < Daeken> the uncompressed data -- your guess is as good as mine.
14:49 < kanzure> well, there's often some metadata
14:49 < Daeken> yeah.  i'm assuming it's all the 2d-specific and general solidworks bullshit.
14:49 < kanzure> parasolid format supports some metadata, but i doubt solidworks would be using that
14:49 < kanzure> maybe undo history tee data
14:49 < kanzure> *tree
14:49 < Daeken> ah hah! history is very possible.
14:49 < Daeken> but why wouldn't they compress that?  weird decision.
14:49 < kanzure> not sure if history data is preserved on persist
14:49 < kanzure> well there's a lot of history....
14:50 < maaku> history would be highly compressable
14:50 < Daeken> i know, but history usually compresses very well.
14:50 < Daeken> so them not having it in zlib is weird.
14:50 < Daeken> (and it's very, very clearly not compressed in any other way ... tons of nulls all around.)
14:51 < kanzure> Daeken: http://diyhpl.us/~bryan/irc/solidworks/ some random stuff
14:51 < kanzure> and http://diyhpl.us/~bryan/irc/step/alvarestech.com/temp/0steptools/www.isd.mel.nist.gov/personnel/kramer/pubs/parasolid-to-step2.pdf
14:52 < kanzure> and for STEP itself there is http://stepcode.org/ of course (brlcad uses this)
14:53 < Daeken> "In order to use Parasolid-to-STEP, it is necessary to have the Parasolid system, which"
14:53 < Daeken> is available for licensing from Shape Data, Limited.
14:53 < Daeken> i was hopeful there. haha
14:53 < Daeken> damn
14:53 < kanzure> available from siemens now :-/
14:53 < Daeken> indeed
14:54 < kanzure> so.. i have pskernel.lib
14:54 < kanzure> and parasolid_kernel.h
14:54 < kanzure> and pskernel.dll psxttoolkit.dll
14:55 < Daeken> unless you just want to use it straight out, i don't think it'll get you anything that the spec does, honestly.  that is, i don't think you need to reverse-engineer any of it.
14:55 < Daeken> the spec is ... remarkably sane.
14:58 < kanzure> fwiw again i'm too excited by http://verbnurbs.com/ to care about solidworks these days
14:58 < Daeken> haha, well, i've got a CAD dude redoing all these ancient Curta calculator engineering drawings in solidworks for me ... i want to be able to read these files and do what i want with them
14:59 < Daeken> so clearly, implementing an insane-ass file format is the way to go, instead of just buying some software.
14:59 < kanzure> have him redo something useful like drawings of buran
14:59 < Daeken> eh, not my thing :P
15:00 < poppingtonic> kanzure are blender
15:00 < kanzure> blender no good for engineering cad
15:00 < poppingtonic> sorry.. are blender's nurbs surfaces programmable enough for cad?
15:01 < poppingtonic> hmm..
15:01  * poppingtonic looks at verbnurbs
15:07 < nmz787_i> brlcad doesn't seem to get enough lovin
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17:08 < delinquentme> about to take a phone interview
17:08 < delinquentme> just had a massive sake
17:08 < delinquentme> shake*
17:09 < delinquentme> and now I need to shit
17:09 < delinquentme> fuck sorry. OT.
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17:13 < c0rw1n> delinquentme: "biology, still works. check"
17:16  * heath likes to imagine delinquentme had a massive sake before the interview
17:31 < kuudes> that could work or then not, I suppose
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18:29 < nmz787_i> hmm http://www.isparktoys.com/product/strain-the-bioengineering-game/
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18:59 < kanzure> to push towards fixing career-related impact factor metrics for scholars, all academic papers should use delayed release/reveal of closed-access references
19:00 < kanzure> or use doi-style id numbers (without author names or titles) that can be resolved by some site that reveals no information until the paper is public
19:00 < kanzure> unfortunately this is too inconveniencing for other scholars i think...
19:01 < kanzure> also, since most academic publishers are supposed to honor revocation requests, maybe we can convince all the scientists to revoke **everything** and all historical content not out of copyright yet
19:03 < cluckj> why are impact factor metrics important?
19:03 < yoleaux> 13 Oct 2015 11:15Z <kanzure> cluckj: anthropology stuff about bitcoin, tor, debian http://feedproxy.google.com/~r/TheDailyBitcoinShow/~5/DQ0MjIHWTmA/1395.mp3 (from scalingbitcoin)
19:03 < kanzure> cluckj: those are still used in many cases to decide career progression things and hiring decisions :-(
19:03 < kanzure> reputation is one of the primary reasons that science is still stuck in shithell
19:04 < kanzure> impact factor can't be computed if all of the references are hidden
19:04 < cluckj> so gross
19:04 < kanzure> but surely you knew this?
19:04 < cluckj> yes :)
19:04 < cluckj> references are important for like...other reasons tho
19:05 < kanzure> like sitting on your desk for 8 months?
19:05 < cluckj> lol
19:05 < kanzure> peer reviewers would be given access to the actual references immediately
19:07 < kanzure> a reference that nobody is able to access is almost useless
19:07 < kanzure> and there's no real reason to have that contribute to people's career metrics
19:07 < kanzure> or to journal metrics
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19:09 < cluckj> wouldn't you have to get the people that profit from using those metrics to do the things that would break them?
19:10 < kanzure> well, they would be publishing open-access papers i think
19:10 < kanzure> and maybe some closed-access, but perhaps they would still do that anyway
19:11 < kanzure> admittedly, the effect of doing this would probably be quite minimal at first... and for a while... because people still physically read nature.com for stuffs. so they will cite that stuff anyway.
19:15 < cluckj> yeah...would it just delay the metric calculation until the data was released?
19:19 < cluckj> haha, shit, the debian access control system that biella is talking about :(
19:20 < cluckj> I need to go find a citation for that
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19:44 < cluckj> that sucks that there is nobody doing bitcoin anthropology
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20:32 < JayDugger> Good evening, everyone.
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20:45 < lake_> http://www.lifeextension.com/magazine/2015/10    another good information site
20:48 < kanzure> cluckj: oh you listened
20:48 < kanzure> ?
20:49 < kanzure> i believe the presenter is contractually obligated by the handbook of ethics to provide you a citation if you ask
20:49 < kanzure> about the debian access control system
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21:23 < kanzure> hmph
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--- Log closed Fri Oct 23 00:00:04 2015