--- Log opened Tue Oct 25 00:00:31 2016
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07:40 < kanzure> "A statistical definition for reproducibility and replicability" http://biorxiv.org/content/early/2016/07/29/066803
07:40 < kanzure> "The molecular mechanism of the type IVa pilus motors" http://biorxiv.org/content/early/2016/10/24/082750
07:41 < kanzure> "Type IVa pili are protein filaments essential for virulence in many bacterial pathogens; they extend and retract from the surface of bacterial cells to pull the bacteria forward with unprecedented force. They are used for attachment, swarming and twitching motility, biofilm formation, up-regulation of other virulence factors, and natural competence. The pilus is assembled by the motor subcomplex which consists of the inner membrane ...
07:41 < kanzure> ... protein PilC and the cytoplasmic ATPase PilB. ... Here we report the structure of the core ATPase domains of Geobacter metalloreducens PilB bound to ADP and the non-hydrolysable ATP analogue, AMP-PNP, at 3.4 and 2.3 Å, respectively ... Our data indicate a clockwise rotation of movement in PilB, which would support the assembly of a right-handed helical pilus. Conversely, our analysis suggests a counterclockwise rotation in PilT that ...
07:41 < kanzure> ... would enable right-handed pilus disassembly. The proposed model provides insight into how this family of ATPases can power pilus extension and retraction with extraordinary forces."
07:42 < kanzure> "The demise of the synapse as the locus of memory: A looming paradigm shift?" http://biorxiv.org/content/early/2016/10/24/082719
07:42 < kanzure> "This paper briefly considers the history and appeal of synaptic plasticity as a memory mechanism, followed by a summary of the cognitive scientists' objections regarding these assertions. Next, a variety of tentative neuroscientific evidence that appears to substantiate questioning the idea of the synapse as the locus of memory is presented. On this basis, a novel way of thinking about the role of synaptic plasticity in learning and ...
07:42 < kanzure> ... memory is proposed."
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08:07 < JayDugger> Thank you for dropping the previous link, kanzure.
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08:13 < kanzure> TODO: if mRNA display sucks so much, then we should make a less sucky version.
08:24 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/Directed%20evolution%20by%20in%20vitro%20compartmentalization%20-%202006.pdf
08:27 < kanzure> .wik peter watts (author)
08:27 < yoleaux> "Peter Watts (born 1958) is a Canadian science fiction author and former marine-mammal biologist." — https://en.wikipedia.org/wiki/Peter_Watts_(author)
08:30 < kanzure> pasky: there are good data sets for speech. lots of them. don't worry about the B2B part, that part is not as miserable as you might think...
08:30 < JayDugger> Watts, Peter. _The Things_. (2010) http://clarkesworldmagazine.com/watts_01_10/
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11:29 < kanzure> "laws of sane personal computing" http://www.loper-os.org/?p=284
11:32  * kanzure looks at https://github.com/camillescott?tab=repositories
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11:36 < kanzure> "A good candidate for a technology that should be banned globally would be a mind-reading technology that allows you to point the device at somebody's head and intrude on their privacy and read their thoughts without their consent or knowledge. That type of technology is an unmitigated evil, and nobody should be allowed to develop or use it." but then how am i going to remember
11:36 < chris_99> heh
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12:25 < fenn> yeah these people don't seem to understand that the human body doesn't come with a consent button
12:25 < fenn> there's no foolproof way to make a thing that only works when you want it to
12:29 < fenn> "All executable code visible during any kind of debugging session or accessible to the operator in any other way shall also be exclusively of [source code] form"  seems a little extreme. how do you debug your compiler then?
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12:30 < fenn> "no programmer need ever be made aware of just how it does it"  is OK i guess until it breaks, and then you're cursing whoever hermetically sealed this OS so you can't get to the internals
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12:35 < kanzure> fenn: no, you just clearly don't know about your consensus glands
12:35  * fenn farts
12:36 < fenn> surely we can all agree it smells like roses
12:38 < kanzure> dpk: you can just say so in here
12:38 < dpk> but it's all proven with Coq so it can't possibly be buggy
12:38 < dpk> </semitroll>
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15:09 < nmz787_i> http://static.sdu.dk/mediafiles/Files/Om_SDU/Institutter/Isse/Ilya/pt08_SPCircuitry.pdf
15:10 < nmz787_i> Surface-plasmon circuitry
15:10 < nmz787_i> http://www.optics.rochester.edu/workgroups/novotny/papers/history4.pdf
15:10 < nmz787_i> The History of Near-field Optics
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15:53 < nmz787_i> what about Coq? jules just gave me an intro to that a few days ago
16:14 < nmz787_i> I was just saying last night, why doesn't someone write a webbrowser in Coq so we can get over these browser exploits already
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16:36 < kanzure> well, there's servo, which is in rust.
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16:44 < Urchin> formal proofs of correctness of the software are not very popular among programmers
16:52 < Urchin> this may be of interest: https://en.wikipedia.org/wiki/List_of_tools_for_static_code_analysis#Formal_methods_tools
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17:41 < nmz787_> servo is interesting, didn't know about that
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17:48 < kanzure> me saying things about zcash announcements https://news.ycombinator.com/item?id=12792750
17:49 < maaku> Urchin: you'll find them more popular among the people here
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17:51 < kanzure> maaku: plz review my above comment. i might be missing things.
17:53 < maaku> The guy you're replying to is ignorant, but I'm not a fan of zcash either. I'm personally refraining from saying anything (positive or negative) about it in public.
17:53 < maaku> But your post is technically correct on each point, the best kind of correct.
17:54 < kanzure> i wanted to highlight why "financial link" is worth talking about; people are going to think i'm talkign about a certain other topic. sigh.
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17:55 < kanzure> i guess i'll add "It may not be clear to casual readers that in bitcoinland there are no protocol rules about paying developers. "
17:56 < maaku> zerocash does fail-open in one big sense though: unlike zerocoin if the init parameters are saved (or the crypto falls apart) you can do not just fraudulent spends, but infinite, undetectable inflation
17:57 < kanzure> right.. and if you were colluding to store some of those parameters from trusted setup, and a government adversary came knocking on your door threatening to take away your kids--- how much would it take to convince you to silently corrupt the system?
17:57 < maaku> me? hah "here you go!" i'm not an internet hero
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18:03 < nmz787_> here you go kids, or software tweaks??
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18:05 < kanzure> nmz787_: maaku is saying that his priority is his family, not protecting some lore about a cryptocurrency
18:07 < nmz787_> hehe, I figured, I was just trying to be funny
18:07 < nmz787_> I guess by parameters and setup I assumed something about a config file holding secret adjustment knobs
18:07 < nmz787_> rather than lore
18:08 < nmz787_> https://www.youtube.com/watch?v=YKuPQzhk8rY
18:08 < nmz787_> .title
18:08 < yoleaux> Sonic the Hedgehog 2 Full Soundtrack - YouTube
18:08 < maaku> kanzure: oh whoops I read the wrong HN comment. yes, you are offering appropriate skepticism
18:09 < kanzure> nmz787_: in some areas of cryptography, there is something called "trusted setup" which says that the system is cryptographically secure as long as 4 people (or whatever) all delete the initial data. after they set up the system, it's secure. but if one of them keeps the data..... then they have a backdoor and can seriously fuck with the system.
18:11 < kanzure> wow there is no wikipedia article on "trusted setup"
18:11 < kanzure> wtf
18:11 < nmz787_> ah
18:14 < maaku> Common Reference String / CRS is the technical term
18:14 < kanzure> there's one paragraph on "common reference string". wtf?
18:15 < kanzure> *only one
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18:17 < nmz787_> .wik common reference string
18:17 < yoleaux> "In cryptography, the common reference string (CRS) model captures the assumption that a trusted setup in which all involved parties get access to the same string crs taken from some distribution D exists. Schemes proven secure in the CRS model are secure given that the setup was performed correctly." — https://en.wikipedia.org/wiki/Common_reference_string
18:17 < maaku> nmz787_: the CRS is kinda like a skeleton key to the whole system
18:17 < nmz787_> did that wiki article define itself using the definition???
18:18 < kanzure> i was really expecting a much longer article, one that would explain how this is essentially "god mode" in some constructions, or otherwise endows its users with omnipotence
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18:19 < maaku> kanzure: ah, then you'll get an edit war from some nitpicker who will note that there are multi-party compute procols for generating the parameters using encrypted computation so that no one can have the CRS
18:19 < maaku> ...nevermind that those MPC schemes require a CRS ;)
18:19 < maaku> turtles all the way down
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18:25 < kanzure> i foresee endless wars between the yak shavers and the turtle hermits
18:25 < kanzure> also, i would like to formally register my objections to "super saiyan blue"
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18:53 < nmz787_> this could be great lounge music https://youtu.be/kAbL8NjoRhI?t=1116
18:53 < nmz787_> .title
18:53 < yoleaux> Donkey Kong Country - Soundtrack (SPC) - YouTube
18:57 < nmz787_> .wik skittlebrau
18:57 < yoleaux> nmz787_: Sorry, that command (.wik) crashed.
18:57 < nmz787_> .wik skittlebrau
18:57 < yoleaux> nmz787_: Sorry, that command (.wik) crashed.
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19:02 < fenn> "that beer that has candy floating in it, you know, Skittlebrau?"
19:03 < fenn> this seems quite do-able
19:04 < nmz787_> I tell foreigners it is a classic traditionally American drink
19:04 < nmz787_> loved by all in the land
19:05 < fenn> tequila with a gummy worm in it?
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19:05 < nmz787_> finally got something coded for monosat that is keeping the CPU at 100%
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19:06 < fenn> is it an ising model
19:07 < nmz787_> if anyone is interesting in looking at my ugly code https://gist.github.com/nmz787/10c60e76941a8e5de624454666ea65b3
19:07 < nmz787_> .title
19:07 < yoleaux> An attempt at making a point-to-point route solver for 3D grids, using graph reasoning through monosat · GitHub
19:08 < fenn> is it for packing tubes together?
19:08 < fenn> like microfluidic channels or wires
19:08 < nmz787_> sure
19:08 < nmz787_> yep
19:09 < nmz787_> that's my goal
19:10 < nmz787_> I have another approach that works OK, but won't scale well (where a net increases variables by number of grid locations)
19:11 < nmz787_> some 'light' background reading http://www.cs.tau.ac.il/research/alexander.nadel/RoutingUnderConstraintsFMCAD16.pdf
19:11 < fenn> aw looks like development on this has stopped https://sourceforge.net/projects/liquidpcb/
19:12 < nmz787_> huh, that PDF wasn't what I thought it was (I was expecting it to be the journal style article)
19:12 < nmz787_> that is a lot prettier though
19:13 < nmz787_> than this http://www.cs.tau.ac.il/research/alexander.nadel/fmcad16_profl.pdf
19:14 < kanzure> wasn't there also a generic open-source constraint solver thingy
19:16 < nmz787_> there are many of those, I guess you could say
19:16 < nmz787_> .g python-constraint
19:16 < yoleaux> http://ipv6.google.com/sorry/index?continue=http://www.google.com/search%3F%26q%3Dpython-constraint%26btnI%3D&q=CGMSECoBBPgCAXIwAAAAAAAIaucY7KPAwAUiGQDxp4NLnaGU-5QuKfisLxYEEdpAy41lNig
19:16 < nmz787_> super slow though: https://labix.org/python-constraint
19:16 < nmz787_> very nice to write code for...  but very slow performance, at least in my usage tests
19:17 < nmz787_> then there's stuff like z3, picosat, cryptominisat, this monosat... dReal, um, tons more I am not thinking of
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19:17 < kanzure> there's http://clp.dimi.uniud.it/sw/cudasat/
19:18 < nmz787_> whatever these are aren't really readable https://github.com/dreal/dreal/tree/master/benchmarks/microfluidics
19:18 < nmz787_> https://github.com/dreal/benchmarks/blob/master/smt2/microfluidics/README.md
19:19 < nmz787_> damn, wayback lacks https://ece.uwaterloo.ca/~drayside/microfluidics/
19:19 < kanzure> "(assert (<= w 0.0005))
19:19 < kanzure> "(assert (<= w 0.0005))" is just "assert w <= 0.0005"
19:19 < kanzure> similarly with "(* w1 (^ h1 3))"
19:20 < nmz787_> huh, I guess they took those files down :/
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19:22 < fenn> since we're sharing music: https://www.youtube.com/watch?v=Vb91HY28fZM&t=13m
19:24 < nmz787_> "ZS Genetics has an opening for a full-time electron microscopy scientist. This position is in support of technology development for EM-based DNA sequencing and analysis. The microscopist will be responsible for imaging activities in aberration corrected Scanning Transmission Electron Microscopy (AC-STEM) for research and development activities surrounding heavy atom labeled DNA imaging."
19:24 < fenn> lol good luck
19:25 < fenn> they're far too late to acqui-hire halcyon molecular
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19:26 < nmz787_> I haven't heard of any of these folks http://www.zsgenetics.com/our-team/
19:27 < nmz787_> they don't have George Church on-board, it must be real
19:27 < kanzure> yes the intersection of biotech people and the internet is still quite limited.
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19:33 < fenn> http://www.zsgenetics.com/third-generation-sequencing/  didn't they know the rest of the world is already _using_ fourth-gen sequencing
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19:41 < fenn> stupid universe stop shrinking! http://www.piclist.com/techref/postbot.asp?by=thread&id=%5BEE%5D+45+vs+90+degree+pcb+traces.&w=body&tgt=top#151559a
19:41 < fenn> (tldr peter todd appears recommending liquidpcb)
19:43 < fenn> apparently he was (is?) writing a EDA toolset with bezier curve capability
19:45 < kanzure> https://github.com/petertodd/tuke
19:48 < fenn> seems like a nice idea
19:48 < kanzure> have you been timestamping things
19:48 < fenn> no, should i be?
19:48 < kanzure> yes
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19:49 < fenn> er, why? and what should i be timestamping exactly?
19:49 < kanzure> also, with his git wrapper in opentimestamps-client.git, any signed commit you make is also timestamped
19:49 < kanzure> you can also timestamp arbitrary files that seem somewhat important or whatever
19:49 < kanzure> like wikipedia backups or "important hashes" of important things
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19:50 < kanzure> one of the main benefits of bitcoin-provable timestamps is that it shows that all of the various proof-of-work assumptions would need to be violated for you to backdate a new hash beyond some point in time
19:50 < fenn> ok, why are you excited about timestamps now? wasn't this always possible?
19:50 < kanzure> so while you can timestamp two versions of a file at the same time, you can't make an earlier timestamp of a third version. later you could reveal just one of the timestamp proofs to show that you (or er, someone) had timestamped that hash in the past.
19:51 < kanzure> it's just a highly usable interface. there were a few web services that offered to put timestamps into bitcoin blockchain or whatever, using OP_RETURN, but it was not scalable at all.
19:51 < kanzure> in petertodd's opentimestamps, he is operating a "calendar" server which aggregates all hashes from 1 second intervals, and then returning a proof to the client, which can later be upgraded (into a better/matured proof) once a "daily" aggregate transaction is committed into the bitcoin blockchain.
19:52 < kanzure> https://alice.btc.calendar.opentimestamps.org/
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19:53 < kanzure> for example, he has globbing that seems to correctly work-- if you do "ots stamp photos/*.jpg" it will only send a single hash to alice.btc.calendar.opentimestamps.org
19:53 < fenn> yeah but does that hash change if one of the photos besides the first one changes :P
19:54 < kanzure> no
19:54 < kanzure> "ots stamp photos/*.jpg" creates *.jpg.ots files
19:54 < fenn> ...
19:54 < fenn> this seems unnecessarily complicated
19:55 < fenn> why not just send the hash of each file?
19:55 < kanzure> "ots info whatever.ots" produces output like: http://pastebin.com/raw/E41EeMcP
19:55 < kanzure> it sends what's essentially a merkle tree
19:55 < nmz787_> fenn: my guess is that unless a PCB is routable without curves, it is less likely to be able to be routed with curves... just my gut feeling... or at least that the two are pretty well correllated
19:55 < kanzure> his server doesn't need to know all the details...
19:56 < nmz787_> so if I can make an autorouter that works well, then it should just be an optimization on top of that to elimate hard angles
19:56 < kanzure> sorry, i mean, it sends a merkle root, not the contents of the merkle tree
19:56 < nmz787_> fenn: have you seen this before? https://en.wikipedia.org/wiki/TopoR
19:57 < fenn> yes
19:57 < kanzure> in this example, 21622d718891131ed98191eb92f4be6b416409c4374e2886172ead84d1358215 is sha256 of http://gnusha.org/logs/hashes/loghashes.004.txt
19:57 < kanzure> TopoR just the name is giving me flashbacks to http://diyhpl.us/wiki/cad/opencascade/
19:58 < fenn> it means "axe" in russian
19:58 < kanzure> TopoDS TopoAbs Topo...
19:58 < kanzure> TopOpeBRepDS
19:58 < kanzure> wait really
19:58 < kanzure> i thought it was topology :| :|
19:58 < fenn> yes but also it's a topological router
19:59 < nmz787_> "топор"
19:59 < nmz787_> sounds more like tap-or
20:00 < kanzure> i have timestamped a number of interesting artifacts, such as wikipedia dumps and that one torrent that had all the magnet links from thepiratebay
20:00 < kanzure> (and magnet links include hashes too)
20:01 < fenn> yeh well i wish people would just make robust distributed systems instead of backing up things before they inevitably break
20:01 < kanzure> these are not backups of course
20:01 < kanzure> you're right that if you lose the file then having the hash isn't particularly useful
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20:03 < kanzure> this is only really helpful for things like data integrity over time, and pulling rabbits out of hats to defend against false allegations of backdating
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21:06 < nmz787_> how do I tell if page swapping is killing my performance? other than getting off my ass to boot up a server in another room
21:06 < nmz787_> (and running it there)
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21:37 < fenn> nmz787_: iotop shows disk activity
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22:03 < nmz787_> fenn: thanks, that isn't the culprit
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22:23 < nmz787_> so I recently asked in the freecad chatroom about thoughts on using a different CAD backend/core, instead of opencascade... didn't get any replies after the first ~5 mins of me asking, and they were all negative like "that doesn't sound like it will work"
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--- Log closed Wed Oct 26 00:00:32 2016