--- Log opened Tue Nov 11 00:00:47 2014
00:01 < delinquentme> FWIW ... instancing VMs on google cloud ...
00:01 < delinquentme> im going to say 10x faster than rackspace.
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00:03 < fenn> not synchrotron, just X-ray tomography of creepy crawlies: https://www.youtube.com/watch?v=OJxT8N99HkM
00:03 < fenn> techno remix
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00:11 < fenn> i imagine x-ray tomography/microscopy would work a lot better for chip reverse engineering than laboriously grinding away nanometer by nanometer and putting in and out of SEM chamber
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00:27 < fenn> commercial xradia 3d x-ray microscope/tomography claims to go to <50nm with 16nm voxel size
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00:32 < fenn> nmz787: making x-ray zone plates could be a viable use for your FIB
00:34 < fenn> paperbot: http://spie.org/Publications/Proceedings/Paper/10.1117/12.411652
00:34 < fenn> .title
00:34 < yoleaux> X-ray zone plate fabrication using a focused ion beam | (2001) | Ilinski | Publications | Spie
00:37 < fenn> ok i am dome rambling about x-ray microscopy now
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00:51 < fenn> wow the R-7 (soyuz) rocket has over 1700 launches
00:57 < fenn> they are still doing film-return reconnaissance satellites!
00:58 < fenn> so much for crypto
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01:17 < fenn> "One of our competitors, Orbital Sciences, has a contract to resupply the International Space Station, and their rocket honestly sounds like the punch line to a joke. It uses Russian rocket engines that were made in the '60s. I don’t mean their design is from the '60s -- I mean they start with engines that were literally made in the '60s and, like, packed away in Siberia somewhere."
01:18 < ebowden> Was it the engines that failed?
01:19 < fenn> considering how much pressure there has been on orbital sciences to develop a replacement motor i find the coincidental failure at this time to be highly dubious
01:19 < fenn> ebowden: yes it's the same engine
01:19 < fenn> it wouldnt take much sabotage to cause the engine to blow up
01:19  * fenn puts on tin foil hat
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01:23 < fenn> "They were intended for the ill-fated Soviet N-1 rocket moon shot."
01:24 < fenn> considering the soyuz launchers normally have a 97% success rate, i find the 22% success rate for the moon program (using the same launcher) to be suspicious as well
01:25 < fenn> to be clear, the soyuz uses a different engine
01:25 < ebowden> Are you getting all conspiratorial about the "coincidental failure"?
01:25 < NilsHitze> the .git link on the hpluswiki is wrong - anyone knows the correct one to clone the wiki?
01:28 < ebowden> *Are you getting all conspiratorial about the coincidental failure?
01:28 < ebowden> fenn, ^
01:28 < fenn> NilsHitze: hum you are right, git clone git://diyhpl.us/diyhpluswiki does not work, but git clone git+ssh://diyhpl.us/srv/git/diyhpluswiki  does
01:29 < fenn> ebowden: yes but it's all in the past and who cares
01:29 < fenn> oh, but for orbital sciences being sabotaged would be a blessing
01:30 < fenn> stock price to the contrary
01:32 < ebowden> "Well, I think that sandy hook was government hoax, but it's all in the past and who cares."
01:33 < fenn> ebowden: i thought you were talking about the soviet failures during the moon race
01:34 < ebowden> *was a government
01:34 < ebowden> Oh, right.
01:34 < ebowden> So you weren't saying you thought that the orbital sciences one was sabotage?
01:36 < NilsHitze> @fenn thx :)
01:36 < fenn> i haven't looked at any evidence, i'm just saying it's suspicious given the timing and the tensions with russia and this engine specifically being called out as an affront to american ideals or whatever
01:36 < fenn> and then it explodes?
01:36 < NilsHitze> why try and error when you can annoy folks on IRC
01:36 < fenn> NilsHitze i'm looking into why the link doesn't work
01:36 < fenn> it used to work
01:38 < NilsHitze> thx - also the certificate for ssh is crap and the register user link doesn't work
01:38 < NilsHitze> tam tam tam
01:38 < NilsHitze> sorry for being a pita
01:39 < fenn> register user has been disabled because "a botnet is nailing this and we may as well drop it for now."
01:39 < NilsHitze> uhhhhh hate it
01:44 < fenn> jrayhawk knows more about this *poke*
01:51 < NilsHitze> btw Hi, my name is Nils, i'm interested in living for another 150 years or more if possible
01:51 < jrayhawk> oh, git urls broke?
01:51 < jrayhawk> wait, what certificate for ssh
01:51 < jrayhawk> what's being certified
01:51 < fenn> secure.diyhpl.us certificate expired
01:52 < jrayhawk> that's https, but okay, i will go nab a new one
01:52 < fenn> NilsHitze: is that what you meant by "certificate for ssh is crap"?
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01:58 < NilsHitze> nah - if you try to register Chrome tells you the certificate expired
01:58 < NilsHitze> which isn't interesting right now because you've told me registration is disabled anyway
01:59 < jrayhawk> still works over ssh
01:59 < jrayhawk> ssh newuser@diyhpl.us
01:59 < NilsHitze> ah thx
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02:10 < jrayhawk> the git url should work better now
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02:24 < jrayhawk> cert stuff is waiting on some manual auditing step from startcom
02:24 < jrayhawk> which i guess i will look into further in the morning
02:35 < jrayhawk> re: "01:38 < NilsHitze> sorry for being a pita" thank you for being a pita
02:38 < fenn> jrayhawk: so what happened to cause the url to break?
02:38 < jrayhawk> someone said "yes" when dpkg offered to overwrite /etc/default/git-daemon on an upgrade
02:39 < fenn> how did you figure that out? :P
02:40 < fenn> i assume there was /etc/...conf.bak
02:40 < jrayhawk> Yeah. The command line arguments were wrong (defaults) and there was an /etc/default/git-daemon.dpkg-old
02:41 < fenn> i guess i don't understand how git:// works
02:43 < jrayhawk> jrayhawk@gnusha:~$ grep ^git /etc/services
02:43 < jrayhawk> git		9418/tcp			# Git Version Control System
02:43 < jrayhawk> jrayhawk@gnusha:~$ sudo netstat -lpn | grep 9418
02:43 < jrayhawk> tcp        0      0 0.0.0.0:9418            0.0.0.0:*               LISTEN      29708/git-daemon
02:43 < jrayhawk> the protocol is a pretty simple binary protocol
02:44 < fenn> ok i was poking around in apache config thinking it went over http, even though i should have known better
02:45 < jrayhawk> as long as you're dealing with a language than handles binary data reasonably gracefully (i.e. not bash) you can generally write a basic implementation in under an hour
02:46 < fenn> why is git over http such a pain to do right?
02:49 < jrayhawk> there are a lot of operations HTTP doesn't have by default, most notably the only "list directory contents" method is only in DAV
02:50 < jrayhawk> so things like retrieving a list of refs would be out unless DAV or the git-http-backend CGI
02:50 < jrayhawk> are used
02:51 < jrayhawk> or you specially prepare the repository to have a packed refs file and furthermore precomputed lists for commit deltas stored somewhere
02:52 < fenn> i've done that and it tends to break after a while
02:52 < jrayhawk> ayup, you have to keep re-running those
02:53 < jrayhawk> i forget what the command is
02:54 < jrayhawk> 'git update-server-info' apparently
02:56 < jrayhawk> i kinda think it's dumb that the git client doesn't, by default, at least attempt to walk backwards down the commit list and grab objects in the hope that they haven't been packed yet
02:56 < fenn> so when a user pushes to git:// how does the server know they have access to that specific repo?
02:56 < fenn> or pulls for that matter
02:57 < fenn> is it all based on unix groups?
02:58 < jrayhawk> there's no real access control on git://; you can either do authenticated ssl (which is probably still broken in gnutls compiles of curl, which i think is most of them now), or you can think of something elaborate and clever with the update hook.
02:59 < jrayhawk> for diyhpl.us and other piny instances, the gitdaemon user is just unable to read some repositories due to unix permissions.
03:01 < jrayhawk> I don't think I allow writes over git://, but I am told there are no git protocol spammer bots, yet.
03:01 < jrayhawk> so i could if you really wanted
03:01 < fenn> groups gitdaemon
03:01 < fenn> gitdaemon : nogroup
03:02 < fenn> so as long as your repo isnt world-writable you shouldnt be able to push anonymously
03:02 < jrayhawk> joey hess has a wacky update hook for ikiwiki.info that allows anonymous object writes over git:// and ref updates if and only if the updated objects are under doc/
03:03 < jrayhawk> but the entire point of a wiki is that it's world-writable
03:04 < fenn> yeah i guess
03:04 < fenn> in spirit at least
03:04 < jrayhawk> and literally
03:04 < jrayhawk> jrayhawk@gnusha:~$ stat /srv/git/diyhpluswiki.git/objects/
03:04 < jrayhawk> Access: (2777/drwxrwsrwx)  Uid: ( 1000/   bryan)   Gid: ( 1007/git-diyhpluswiki)
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03:05 < fenn> that's only the directory.. is that all you need?
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03:05 < jrayhawk> the objects are immutable
03:05 < jrayhawk> i mean, the files themselves
03:06 < fenn> i have no idea how git keeps track of where HEAD is
03:06 < jrayhawk> that's in refs/
03:06 < fenn> refs/ is empty
03:07 < jrayhawk> packed-refs is a special efficient-and-or-dumb version of refs/
03:10 < fenn> so an anonymous user could set HEAD to whatever they want?
03:10 < jrayhawk> no, you don't get direct filesystem access over git, and shell access is, by default, heavily restricted to the same ends.
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03:12 < jrayhawk> you can ask git to update the ref, but there are configurable restrictions such as receive.denynonfastforwards and receive.denydeletes that keep logically destructive ref-update operations from happening.
03:13 < jrayhawk> And, regardless, Ikiwiki maintains a separate checkout and will choke on a non-fastforward merge, so even if a user goes nuts, we still have the refs.
03:13 < jrayhawk> a user with a real shell
03:14 < fenn> attack of the enraged user
03:15 < fenn> do you have a preferred way to visualize/untangle git messes?
03:17 < fenn> i've tried gitk but it seems worse than the basic command line tools
03:17 < jrayhawk> gitk is reasonably nice for seeing what's already happened; i don't have strong opinions on UIs for doing complex merges in the actual untangling process, but there are quite a few of them to choose from.
03:18 < jrayhawk> Presumably you should use whatever merge interface is native to your text editor of choice.
03:18 < jrayhawk> e.g. vimdiff
03:20 < jrayhawk> you can google around for 'mergetool'
03:20 < jrayhawk> and get stuff like http://stackoverflow.com/questions/137102/whats-the-best-visual-merge-tool-for-git
03:21 < fenn> it's usually something like, i am trying to remove a commit from history in my private repo before pushing
03:22 < jrayhawk> oh, yeah, that'll involve cherry picking and/or rebasing
03:23 < jrayhawk> git-filter-branch is also handy
03:26 < jrayhawk> re: packed-refs being efficient-and-or-dumb: efficient in the case of having thousands of refs (or, in the case of libreoffice, hundreds of thousands due to gerrit), dumb in the case of http not, by default, having a way of doing a directory listing
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03:29 < pi_> re
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03:31 < jrayhawk> like, one read() on an existing filehandle returning 4 to 16kiB saves 69 to 277 loops of getdents()/open()/read()/close()
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03:36 < fenn> yes fetching hundreds of thousands of files over http would be bad
03:37 < fenn> is gerrit a collaborative editor like etherpad?
03:38 < fenn> i don't really see any reason to generate hundreds of thousands of commits
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03:44 < jrayhawk> gerrit stores merges to review as refs (presumably so they don't get garbage collected)
03:45 < jrayhawk> annoyingly, it continues to do this even after the refs have been merged
03:52 < fenn> for some stupid reason i never learned how to use git rebase -i
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05:49 < kanzure> because rebasing is rude to others
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06:21 < NilsHitze> Hey @kanzure
06:25 < fenn> i thought you were supposed to mess around on your own repo, get it to do what you want and test it a little, then go back through and separate out bits of functionality as patches for consideration, and do a pull request
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06:26 < fenn> so upstream doesn't have to sift through piles of "oh forgot to capitalize FooBar" commits
06:26 -!- pizza is now known as snuffeluffegus
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06:28 < kanzure> in general the rule is that if other people in this world already have your commits, it is usually rude to rebase because it will fuck them over
06:28 < kanzure> if you have never sent your commits out into the world, rebasing is pretty okay
06:29 < fenn> i agree, but it'd also polite to fix up your stuff before publishing them
06:29 < kanzure> i really don't like projects that force all pull requests to be a single commit. fuckers, that's why i made atomic feature-based commits in the first place.
06:30 < fenn> what's "atomic feature-based commits" if not a single commit?
06:30 < kanzure> some features are composed of multiple other features that can be independently reverted
06:30 < fenn> how is it atomic and multiple simultaneously?
06:31 < kanzure> no philosophy
06:32 < kanzure> i'm sure it could be argued that many pull requests that have multiple commits for independently revertable changes could probably be split up into multiple pull requests
06:33 < fenn> meh i can see ways people would abuse either policy
06:34 < fenn> it's probably best not to be perfectionist about revision history
06:34 < kanzure> oh how conenient a religion that doesn't require you to do any work
06:35 < fenn> perfectionism would be something like "all pull requests must be a single commit"
06:35 < fenn> i dunno
06:35 < fenn> i havent written any code in years
06:36 < fenn> there is only one ralph merkle
06:36 < kanzure> *convenient
06:37 < kanzure> still looking for evidence about ralph
06:37 < kanzure> you should write more code
06:37 < fenn> see http://www.computerhistory.org/fellowawards/hall/bios/Ralph,Merkle/  for photo evidence
06:38 < kanzure> they may have just used the other ralph image
06:38 < fenn> you want like a picture of him receiving the turing award?
06:38 < kanzure> i am not sure what would qualify as evidence
06:39 < kanzure> oh there was that thing by hellman that said when he first met ralph that he aspieblabbed about nanotechnology
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06:39 < fenn> but wait, what if a superintelligent time traveller impersonated merkle using nanotechnology
06:40 < fenn> what happened to believing in internet anomalies
06:41 < justanotheruser> fenn: they became an anomalie
06:41 < fenn> if you do the math there are literally millions of geniuses in the world
06:42 < kanzure> "Hellman: I smile when you say Merkle, I mean Merkle is just someone who makes you smile. He’s a comic. He comes and plops down in your office—have you met Ralph?"
06:42 < kanzure> "Hellman: He plops down in your chair and says, ‘Hi!’ I remember, this was after the discovery of public key cryptography, maybe fifteen years ago, he comes into my office and plops down and says, ‘Hi, I’m building a human brain.’ He’s one of the stars in nanotechnology. Building human brains and repairing human brains on dead people so you can bring them back to life some time in the distant future is ...
06:42 < kanzure> ... one of his passions."
06:42 < justanotheruser> if you define genius as being someone in the top few million people on earth in terms of intelligence
06:43 < fenn> it's usually defined as being three standard deviations above the norm; earth just has a large population atm
06:43 < kanzure> genius is just some factor of inertia or momentum or something
06:44 < kanzure> so that hellman quote sounds an awful lot like it's talking about the same ralph merkle to me
06:44 < kanzure> but google says the only place that text shows up on the web is in hplusroadmap logs
06:44 < fenn> huh. who said it?
06:44 < justanotheruser> fenn: unfortunately many of those geniuses don't have the resources to apply themselves
06:45 < superkuh> paperbot, http://link.springer.com/article/10.1007%2Fs11207-014-0586-7
06:45 < kanzure> fenn: well, it was me
06:45 < justanotheruser> divide the number of geniuses by 6 and you have the number that can apply themselves
06:45 < kanzure> that sounds like pop psychology crap
06:45 < justanotheruser> and then divide that by maybe 2 and get the number that actually do apply themselves
06:45 < kanzure> "apply themselves" what does that even mean
06:46 < justanotheruser> kanzure: It means they use their brain for things other than putting stuff together in a factory or farming land
06:46 < justanotheruser> or aren't too busy as a foot soldier
06:47 < kanzure> "Sometimes I sit here doing nothing, but on the inside my body is full of science and awesome. You nerds know what I mean."
06:47 < kanzure> farmers can still think, yo
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06:47 < justanotheruser> they can think, but they're not going to do much for the world another person with an 80 IQ couldn't
06:47 < fenn> sorry 4 standard deviations (iq 160 w/s.d. 15)
06:48 < justanotheruser> -o only 430k
06:48 < justanotheruser> *so
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06:52 < fenn> ya
06:53 < fenn> still a large number
06:54 < justanotheruser> I wonder what % of -wizards is geniuses
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06:54 < fenn> there's a lot of lurkers in there
06:54 < justanotheruser> true
06:55 < justanotheruser> I wonder what the % of messages in there are written by geniuses
06:55 < fenn> heh
06:55 < justanotheruser> I'd guess ~5-50%
06:56 < justanotheruser> That 45% difference is dependent on whether gmaxwell is 2 std dev or 3+
06:56 < fenn> why don't you ask and find out
06:56 < justanotheruser> s/2/3/ s/3/4/
06:56 < justanotheruser> Ask what his IQ is?
06:56 < fenn> he probably has taken an iq test at some point in his life
06:57 < justanotheruser> fenn: what is your IQ?
06:57 < fenn> aw shucks *bats eyelashes*
06:57 < fenn> a genius never tells
06:57 < justanotheruser> is that why you aren't telling?
06:58 < fenn> last time i took an iq test it said 167
06:58 < justanotheruser> was it a legit IQ test, or an online one?
06:58 < fenn> but they say they aren't really accurate that far out unless you take a special test
06:58 < justanotheruser> oh
06:58 < justanotheruser> well congrats on the large penisIQ
06:58 < fenn> woo
06:59 < fenn> i definitely fall into the "not applying self" category
06:59 < fenn> regardless of scores on tests
07:00 < justanotheruser> I've been convinced that IQ doesn't matter much in terms of your success level, contributions to society and technological/scientific contributions to society
07:00 < fenn> i'm convinced it does matter in terms of your scientific contributions
07:01 < fenn> but yeah a lot of measures of success have more to do with perseverance
07:01 < justanotheruser> fenn: I think you can work hard and have a medium IQ and contribute
07:01 < kanzure> wow, what the fuck is cc-by-nd? https://www.jamendo.com/en/track/1129271/energy
07:01 < kanzure> no-derivatives? wtf
07:02 < yorick> non-disclosure? :D
07:02 < yorick> yeah, no-derivatives
07:02 < kanzure> what's the point
07:02 < kanzure> that breaks everything
07:02 < yorick> https://creativecommons.org/licenses/by-nd/2.0/
07:02 < yorick> sharing!
07:02 < yorick> but you can't change anything
07:02  * justanotheruser changes a random bit
07:02 < yorick> or like, tar it.
07:03 < justanotheruser> wait, so can I convert it to a lossy format?
07:03 < yorick> that's building upon, isn't it?
07:03 < justanotheruser> I'd consider it a derivative, but no idea what a judge would or has though
07:03 < kanzure> license compatibility matrix -_- https://wiki.creativecommons.org/Frequently_Asked_Questions#When_is_my_use_considered_an_adaptation.3F
07:03 < justanotheruser> *thought
07:04 < justanotheruser> "Note that merely converting material into a different format that is difficult to access or is only available for certain platforms does not violate the restriction; you may do this without violating the license terms. "
07:04 < yorick> oh, if it's uncreative modification you're okay
07:04 < justanotheruser> ok
07:04 < fenn> just make sure to be really uncreative with your trolling then
07:04 < yorick> except when you're synchingmusic in timed relation with a moving image
07:05 < justanotheruser> well I have a program that defines a new format that "loses" information in the way I want and converts it to these new formats thousands of times until it is modified in the way I want it to be modified.
07:06 < justanotheruser> However, it was just a very lossy algorithm and cause certain segments of the song to lose and others not.
07:06 < fenn> is it called "autotune the news"
07:06 < justanotheruser> its called fruityloopholes
07:09 < fenn> kanzure: the merkle/hellman quote appears to be from http://conservancy.umn.edu/bitstream/107353/1/oh375mh.pdf
07:09 < fenn> .title
07:09 < yoleaux> fenn: Sorry, that doesn't appear to be an HTML page.
07:10 < fenn> "an interview with martin hellman"
07:11 < fenn> bbl
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07:35 < kragenjaviersita> 15:02 < kanzure> what's the point
07:35 < kragenjaviersita> 15:02 < kanzure> that breaks everything
07:35 < kragenjaviersita> you can give it to your friends or make a mixtape without breaking the law
07:37 < justanotheruser> kragenjaviersita: you can make a derivative you don't distribute?
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07:39 < kragenjaviersita> justanotheruser: not legally
07:40 < justanotheruser> well if you're ignoring the law then this license discussion is irrelevant
07:40 < kragenjaviersita> no
07:41 < kragenjaviersita> I mean people have a variety of relationships with the law beyond just "ignoring" and "obeying completely"
07:41 < kragenjaviersita> many people only obey the law when it's enforced, for example
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07:42 < justanotheruser> his claim that the license breaks everything meant it breaks everything for people who follow the whole license. It doesn't apply to people who ignore the part of the licencse that breaks everything.
07:43 < kragenjaviersita> you can share https://www.jamendo.com/en/track/1129271/energy via BitTorrent without fear of repercussions
07:44 < kragenjaviersita> you just can't remix it without fear of repercussions
07:46 < kanzure> i'm just surprised that it's a creative commons licensing term
07:47 < kragenjaviersita> creative commons started out with a very broad goal
07:48 < kragenjaviersita> if -ND surprises you, you will probably be shocked by Creative Commons Founders' Copyright, the Creative Commons Sampling License, and the Creative Commons Developing Nations License
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07:51 < kragenjaviersita> https://creativecommons.org/retiredlicenses
07:51 < kanzure> hrm
07:51 < kanzure> what's the point
07:51 < kanzure> how did this happen
07:52 < kragenjaviersita> you may not remembe rthis
07:52 < kragenjaviersita> but at the launch party for Creative Commons
07:52 < kragenjaviersita> Jack Valenti spoke via a video link endorsing it
07:53 < kragenjaviersita> I was blown away by Larry's virtuosity in pulling that off
07:53 < kragenjaviersita> it completely neutralized one of our biggest potential opponents
07:54 < kragenjaviersita> There's been a substantial amount of opposition to CC over the years
07:54 < kragenjaviersita> but it could have been MUCH worse
07:56 < kragenjaviersita> getting Valenti on our side necessitated a very "empowering creators" stance, not a "protecting users' freedoms" stance
07:56 < kragenjaviersita> and it wasn't just an act.  it was sincere.
07:58 < kragenjaviersita> so, if empowering creators is your purpose, you naturally want to offer a wide range of choices of license terms, covering the entire spectrum outside of the traditional "keep out!" endpoint
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08:38 < ParahSailin_> biologist sloppiness as a function of time, pipetting through a 384 well plate http://i.imgur.com/VhNTTZf.png
08:39 < ParahSailin_> as you can see, as they get towards the right-bottom corner, excited at the prospect of getting to go home, the aerosol effects markedly increase
08:43 < justanotheruser> Okay, so this is a bit of a crazy idea, but I want to mechanically evaluate a round of sha2. Has anyone here done any mechanical computing?
08:46 < kanzure> bug kragenjaviersita
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08:51 < ParahSailin_> i am a champion abacist
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09:01 < delinquentme> awww yeahhh
09:01 < JayDugger> I'd hold out for a professional dactylonomist.
09:01 < delinquentme> sunnyvalé
09:02 < JayDugger> Simultaneously mechanical and digital.
09:04 < delinquentme> kanzure, on that developernomics.
09:04 < delinquentme> SO sure. crypto currency is blooming
09:04 < delinquentme> but do we think the USD will tank?
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09:09 < kanzure> delinquentme: http://nakamotoinstitute.org/mempool/speculative-attack/
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09:09 < delinquentme> Forced, as in "compelled by economic reality"
09:09 < delinquentme> this sounds right
09:10 < delinquentme> I think theres some subtlety to the long term investing in software devs as using a product down the road
09:10 < delinquentme> also this is really REALLY  good https://www.youtube.com/watch?v=aRl6Xc209L8&list=PLcghjaDFUHglje0wiMUDMTrUV6z5wGGQq&index=57
09:24 < kanzure> .title
09:24 < yoleaux> Electro - Hatty Keane - No One Loves You (Kairo Kingdom Remix) - YouTube
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09:59 < nmz787_i1> this might be interesting to read:
09:59 < nmz787_i1> .wik The Soul of a New Machine
09:59 < yoleaux> "The Soul of a New Machine is a non-fiction book written by Tracy Kidder and published in 1981. It chronicles the experiences of a computer engineering team racing to design a next-generation computer at a blistering pace under tremendous pressure. The machine was launched in 1980 as the Data General Eclipse MV/8000." — http://en.wikipedia.org/wiki/The_Soul_of_a_New_Machine
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10:01 < nmz787_i1> which leads to:
10:01 < nmz787_i1> .wik Mushroom management
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10:01 < yoleaux> "Mushroom management, also known as Pseudo-Analysis or Blind Development, is a term used to mockingly refer to a way of running a company where the communication channels between the managers and the employees do not work properly." — http://en.wikipedia.org/wiki/Mushroom_management
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10:12 < paperlooker> paperbot: http://www.sciencedirect.com/science/article/pii/S000398611300307X
10:12 < heath> this is neat
10:13 < heath> http://www.otonomos.com/
10:13 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/%0A%20Enzymology%20of%20the%20carotenoid%20cleavage%20dioxygenases%3A%20Reaction%20mechanisms%2C%20inhibition%20and%20biochemical%20roles%0A%20.pdf
10:13 < heath> create a non US based company in minutes :)
10:13 < heath> s/minutes/hours
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10:49 < justanotheruser> kragenjaviersita: hello?
10:57 < streety> heath: interesting, is $300 standard for a US company?
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11:12 < heath> streety: i think they focus strictly on creating non-US based companies
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11:13 < heath> streety: about 6 years ago, i paid something like $500 to start a company
11:14 < streety> From a quick search it seems like the actual filing costs are lower but with add on services that $300-500 range seems common
11:15 < streety> It's interesting how cheap the UK fee is
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12:10 < kragenjaviersita> justanotheruser: hello?
12:11 < kragenjaviersita> I haven't done any mechanical computing.
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12:13 < kanzure> nice denial
12:18 < fenn> we all know about your babbage fetish
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12:45 < nmz787_i1> 'the babage-patch kids' -- latest Nick Jr. t.v. show in an alternate universe
12:45 < chris_99> haha
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12:50 < heath> who needs s-expressions, http://dogeon.org/
12:51 < fenn> yo doge i heard u like doges so i made an s-expression of doges?
12:52 < heath> it's taking on json instead of s-expressions, so maybe that was misleading
12:53 < fenn> EBNF is a totally different thing, ya
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13:06 < heath> yeah
13:07 < heath> related, https://en.wikipedia.org/wiki/Comparison_of_data_serialization_formats
13:09 < heath> neat: http://bfxdata.com/combined/btc.php charting swaps on bitfinex
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14:13 < nmz787_i1> few android apps, they just won $50k from Intel or someone http://lab4u.cl/lets-experiment/
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15:17 < nmz787_i1> http://spectrum.ieee.org/tech-talk/computing/hardware/bendable-sound-waves-can-skirt-objects-trap-particles
15:17 < nmz787_i1> paperbot: http://www.nature.com/ncomms/2014/140703/ncomms5316/full/ncomms5316.html#discussion
15:17 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fncomms5316
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15:38 < fenn> real life tractor beam
15:39 < fenn> oh this is something else
15:40 < fenn> weird stuff man
15:41 < nmz787_i1> if camels are ungulates, and camel-case naming exists... what would ungulate-case naming look like?
15:41 < nmz787_i1> it would have to be a superset, so just normal lower-case?
15:42 < delinquentme> cool. google just gave me 1k cores
15:42 < delinquentme> erm. 1k cpus. and 10 petabytes of persistent storage
15:42 < nmz787_i1> how many minutes of using the cores though?
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15:43 < delinquentme> i've got $800 in the account
15:44 < delinquentme> and its .0042 /10min  per CPU
15:44 < delinquentme> and its $0.0042 /10min  per CPU
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15:44 < fenn> .wik ungulate
15:44 < yoleaux> "Ungulates (pronounced /ˈʌŋɡjʊleɪts/) are a diverse group of large mammals that includes horses, cattle, pigs, giraffes, camels, deer, hippopotamuses, whales and dolphins. Most of them use the tips of their toes, usually hoofed, to sustain their whole body weight while moving. The term means, roughly, "being hoofed" or "hoofed animal"." — http://en.wikipedia.org/wiki/Ungulate
15:45 < fenn> dolphins
15:45 < fenn> bwaaaaa
15:45 < kanzure> andytoshi: igem is a competition of schools doing synthetic biology/genetic engineering things http://igem.org/Main_Page
15:45 < andytoshi> oh, cool
15:45 < kanzure> sort of
15:46 < kanzure> here are some particularly interesting igem projects i like http://diyhpl.us/wiki/dna/projects
15:46 < andytoshi> so many things to read :)
15:46 < andytoshi> i've got 600 tabs open because the tx legislature came into session
15:46 < fenn> igem is like a hackathon where people propose lots of cool ideas and then don't know how to finish them in the 2 days you get to work on it
15:46 < andytoshi> and my brain is fuzzing over for the day
15:46 < nmz787_i1> hah
15:46 < nmz787_i1> damn
15:47 < nmz787_i1> that surpasses my max tab count ever for sure
15:47 < andytoshi> hmm, i'm not sure how to count them
15:47 < kanzure> "many" is the current counting unit
15:47 < andytoshi> i don't have 600 open right now, but i've gone through 600 for the day bc that's how many mails i got
15:47 < kanzure> *correct counting
15:48 < fenn> andytoshi: are you a legal eagle? or an illegal eagle?
15:48 < nmz787_i1> or a beagle
15:48 < andytoshi> fenn: legal while i'm in the US :) these feds scare me
15:48 < andytoshi> i just like to keep an eye on the legislature
15:49 < nmz787_i1> giraffe-case. must be preceeded by 50 underscores
15:50 < fenn> dolphin-case. contains random cl!icks and p.ops
15:50 < nmz787_i1> :)
15:51 < kanzure> nutcase. nuff said.
15:52 < kanzure> igem needs to enforce nasa technical readyness indicators on all of the web pages or projects
15:52 < kanzure> technical readiness levels, i mean
15:52 < kanzure> http://esto.nasa.gov/files/trl_definitions.pdf
15:52 < kanzure> technology readiness levels
15:52 < kanzure> man i am a bad nerd
15:55 < fenn> i like imagining that this is the same person http://andytoshi.tumblr.com/
15:55 < fenn> evil crypto hacker with a j-pop crush
15:56 < kanzure> you want https://www.wpsoftware.net/projects/ and https://www.wpsoftware.net/andrew/
15:58 < nmz787_i1> hmm, how does a polish-sounding last name get transformed to a japanese sounding name on IRC
15:58 < andytoshi> nmz787_i1: it was a joke based on an american tv show
15:58 < andytoshi> (and my name is dutch fwiw)
15:59 < fenn> i figured it was some general purpose pseudonymous name suffix
16:00 < andytoshi> nmz787_i1: actually it was a bad joke .. on the bitcoin episode of "the good wife" in jan 2011(?) they changed satoshi's name to "mr bitcoin" we guess because satoshi was too foreign sounding, so on #bitcoin we all added toshi to our names
16:00 < andytoshi> and i just kept mine for years
16:01 < nmz787_i1> ah
16:01 < nmz787_i1> cool
16:01 < nmz787_i1> all internet-based moving-images are 'american'?
16:02 < nmz787_i1> blah
16:02 < fenn> dude, the internet is american
16:02 < nmz787_i1> yup
16:02 < nmz787_i1> al gore all the way
16:02 < nmz787_i1> back in 1969, right kanzure
16:02 < fenn> inventing the internetters since 1969
16:03 < fenn> i have a file somewhere of all the awesome stuff that seemingly randomly happened in 1969
16:05 < nmz787_i1> must have been lots of random stuff happening back then
16:06 < kanzure> sure, random
16:06 < fenn> kanzure did you type in all those igem links by hand?
16:07 < kanzure> yeah
16:07 < kanzure> someone has to look at this stuff
16:08 < kanzure> i was just bookmarking some of them. now that i have a functional bookmarking system and stuff.
16:09 < kanzure> heh the count is 1968 at the moment
16:09 < fenn> time traveling machine elves from the singularity, man
16:10 < kanzure> gnomes. elves are festive, gnomes don't have to be.
16:10 < fenn> gnomes are trademarked
16:10 < fenn> .wik machine elves
16:10 < yoleaux> "Terence Kemp McKenna (November 16, 1946 – April 3, 2000) was an American philosopher, psychonaut, ethnobotanist, lecturer, and author." — http://en.wikipedia.org/wiki/Machine_elves
16:10 < delinquentme> reall like this regex tool http://www.regexr.com/
16:11 < nmz787_i1> delinquentme: more than regex101.com ?
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16:14 < delinquentme> Values must match the following regular expression: '[a-z](?:[-a-z0-9]{0,61}[a-z0-9])?'
16:15 < delinquentme> trying to match black-00 black-01 black-02 ... black-nn
16:15 < delinquentme> seems like black-[0-9]{2} hsould do it ...
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16:17 < fenn> is it a game?
16:17 < fenn> match the regex before the machine elves get you
16:17 < kanzure> yes it's called "complete delinquentme's job interview"
16:18 < fenn> same thing
16:18 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Ex-Chat]
16:18 < fenn> ok delinquentme write the regex for a URL
16:19 < fenn> only valid URLs no hufflepuff
16:19 < fenn> also there are now unicode top level domains
16:20 < fenn> i thought for sure we'd get ipv6 first
16:20 < jrayhawk> we got ipv6 an eternity ago
16:20 < delinquentme> kanzure, nice try
16:20 < kanzure> i guessed
16:21 < delinquentme> " write a regex that matches things you want in this format " .. never seen this before
16:21 < jrayhawk> http://www.ex-parrot.com/pdw/Mail-RFC822-Address.html also nothing beats Mail::RFC822:Address
16:22 < delinquentme> you guys will like the fact that a number of the servers were named hubris
16:22 < delinquentme> 50 of them
16:22 < fenn> you can have comments in email addresses?
16:22 < jrayhawk> you can also have different inline character encodings in email addresses
16:25 < jrayhawk> domain literals are also a little-known feature
16:27 < fenn> Domain-literals which refer to domains within the ARPA  Internet  specify  32-bit  Internet addresses, in four 8-bit fields noted in decimal,... For example: [10.0.3.19]
16:28 -!- maaku_ is now known as maaku
16:28 < fenn> To: fenn@[127.0.0.1] it works!
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16:30 < Boscop> any channels about NIBS (tDCS, TMS, etc)?
16:30 < kanzure> you're in it
16:30 < delinquentme> kanzure, you're such a bastard
16:31 -!- nmz787_i1 [~nmccorkx@134.134.139.72] has quit [Remote host closed the connection]
16:31 < delinquentme> now Im like actually learning regex
16:31 < delinquentme> this is where psychology / pride goes awry
16:32 < fenn> probably the most useful thing you've ever learned
16:33 < fenn> except for the five hundred ways to kill a man
16:33 < kanzure> .title https://github.com/bitcoin/bitcoin/pull/4906
16:33 < yoleaux> Issue#1643: Coinselection prunes extraneous inputs from ApproximateBestSubset by AlSzacrel · Pull Request #4906 · bitcoin/bitcoin · GitHub
16:36 < jrayhawk> huh, the regex for IRIs is about as bad as the one for emails
16:38 < jrayhawk> http://www.omgwallhack.org/home/jrayhawk/tmp/rfc3987-pcre.txt
16:39 < jrayhawk> i guess parsing ip addresses is pretty hard, what else is in there?
16:39 < fenn> is there an RFC for RFC format?
16:40 < jrayhawk> http://www.rfc-editor.org/rfc-editor/instructions2authors.txt
16:40 < jrayhawk> http://www.rfc-editor.org/formatting.html
16:40 < fenn> i was looking at https://www.rfc-editor.org/rfc/rfc5385.txt
16:41 < fenn> https://www.rfc-editor.org/rfc/rfc2629.txt is even worse tho
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16:50 < fenn> it would be cool to have a game like those typing games where you have to type the words before they fall to the bottom of the screen, but there's so many you have to use regexes to possibly get them all
16:51 < fenn> and also they pile up on top so thick you can't actually read all the characters
16:52 < kanzure> wouldn't that just be lots of or statements
16:52 < kanzure> https://play.google.com/store/apps/details?id=edu.swarthmore.cs.cs71.regexreptiles&hl=en
16:52 < fenn> well there would be "good" blorbs that you have to work around
16:53 < fenn> like the stupid hostage in those first person shooter arcade games
16:53 < kanzure> https://play.google.com/store/apps/details?id=com.ilit.regexxword&hl=en
16:53 < kanzure> "Inspired by the MIT 2013 Mystery Hunt, this is the geek version of Sudoku-meet-crossword. Each clue on the grid represents a regular expression. The row of cells it points to must match this expression exactly."
16:54 < fenn> the snakes just make it harder to read the letters
16:54 < kanzure> yes
17:00 < fenn> Boscop: tDCS works by signalling glial cells to increase nutrient/waste circulation via calcium ion flows, yes/no/maybe?
17:02 < Boscop> i only know that it increases the frequency of spontaneous neuron firings
17:02 < fenn> we can actualy answer these questions by chopping up mice
17:02 < Boscop> fenn: how much voltage should i use with tDCS?
17:02 < fenn> if you're asking that, you shouldn't be
17:03 < Boscop> fenn: i couldn't find much info about voltage, only current
17:03 < fenn> because skull thickness is variable
17:04 < fenn> V=IR   in this equation your skull is the R
17:05 < fenn> and your skin and other electrical components like resistors
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17:05 < fenn> basically you should use a voltage that's safe even when your electronics malfunction
17:05 < fenn> also you should use passive electronics that can't malfunction
17:06 < fenn> also if you need to ask this question you shouldn't be building your own device from scratch
17:07 < fenn> most devices use a circuit that self-tunes its resistance to give a particular current, regardless of the resistance in series with it
17:08 < fenn> (yeah i know this isn't really how BJTs work)
17:08 < nmz787_i> hrmm, there must be a good joke about 'your skull makes a better resistor than a [insert funniness]'
17:11 < fenn> ungulate
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17:13  * fenn snores self to death
17:13 < kragenjaviersita> night
17:15 < maaku> is AGI on topic for here?
17:15 < nmz787_i> .wik agi
17:15 < yoleaux> "AGI may refer to:" — http://en.wikipedia.org/wiki/Agi
17:16 < maaku> artificial general intelligence
17:16 < nmz787_i> probably
17:16 < nmz787_i> we talk about getting uploaded
17:16 < nmz787_i> somehow, someday
17:19 < maaku> i'm very meh on uploading
17:19 < maaku> I'd rather see the other side of the singularity, thank you
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17:23 < nmz787_i> as long as the machinery is/seems as good/better than a human body, I think I'd be OK, or maybe not even notice
17:34 < kanzure> maaku: more this side of agi http://diyhpl.us/~bryan/papers2/brain-emulation-roadmap-report.pdf
17:34 < kanzure> so far the brain is the only thing that we know that does this
17:34 < kanzure> although pasky and fenn are more agi non-brain interested
17:34 < kanzure> the problem with ai is that most ai discussions go nowhere
17:35 < pasky> ah, right
17:35 < pasky> I really liked yesterday's Hinton's AMA
17:35 < pasky> he seemed like really having the right ideas about taking inspiration from the brain, but not get lost in the details
17:36 < pasky> (I know, we had this argument about whether "details" matter before :)
17:37 < maaku> kanzure: i'm very much non-brain interested
17:37 < maaku> WBE is too far away
17:37 < kanzure> how do you figure?
17:38 < kanzure> like, how much data have you looked at regarding the current biologically-accurate neuron simulators etc?
17:38 < maaku> well assuming moore's law, we're talking late 2030's, 2040's for WBE
17:38 < kanzure> and is the timeline your main objection?
17:38 < kanzure> maaku: wei dai used to write emails on the subject of cryptography, cryptocurrency and brain emulation/simulations
17:38 < kanzure> this is a fun thing to read and watch http://diyhpl.us/wiki/transcripts/markram-2006/
17:39 < kanzure> and regarding timeline of whole-brain emulation and other singularity events you might be interested in http://theuncertainfuture.com/ufHelp/GoryMath.html http://theuncertainfuture.com/
17:39 < kanzure> paper re: those last two links, http://diyhpl.us/~bryan/papers2/futurism/Changing%20the%20frame%20of%20AI%20futurism:%20From%20storytelling%20to%20heavy-tailed,%20high-dimensional%20probability%20distributions.pdf
17:39 < maaku> whereas de novo agi could be as close as 5 years away
17:40 < kanzure> er, i mean, he was using cryptography as a tool to protect simulations
17:40 < kanzure> er, i guess i am still being too vague
17:40 < maaku> and yes timeline is a chief objection
17:40 < maaku> but i'm also interested in problems humans are notoriously bad at
17:40 < kanzure> wei dai cryptography and ai/whatever simulations http://extropians.weidai.com/extropians.3Q97/4356.html
17:41 < maaku> yeah wei dai seems to have been subsumed into the MIRI any-practical-work-will-destroy-the-world meme :(
17:41 < kanzure> oh, i hadn't noticed that. i mean, i agree that he mentally hangs out with that crowd.
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17:43 < maaku> my interest is chiefly transhumanism, nanotechnology, space exploration, etc. which i gather to be mostly on topic here
17:43 < kanzure> right
17:43 < kanzure> this channel was originally about strategic engineering coordination for those types of projects
17:43 < kanzure> but it turns out that it is hard for me to shame others into doing meaningful work
17:43 < maaku> but some years ago I did my own weak inside view analysis and determined that AGI was the fastest path
17:44 < maaku> to enabling all three
17:44 < kanzure> there's a lot broken in the world of agi research
17:45 < maaku> so, e.g., my current hobby activities involve constructing an AGI capable of answering queries like "build me a nanofactory (a la freitas, merkle) starting with existing tools"
17:45 < kanzure> most of the time i find myself reading crazy theories of mind that reflect more on the author than anything that might actually work
17:45 < maaku> kanzure: right, unfortunately :(
17:46 < kanzure> any approach should not depend on the author having a good theory of mind, since it seems obvious that everyone is fucking bad at that particular route
17:46 < kanzure> re: starting with existing tools... so we were working on this bootstrapping open-source hardware package system for a while. (the incentives were all wrong and broken though.)
17:46 < maaku> yeah definitely
17:46 < kanzure> http://gnusha.org/skdb/
17:47 < kanzure> you can imagine at least in theory some method of engineering planning based on "installed machines"
17:47 < kanzure> (or packages)
17:49 < kanzure> there's lots of dependency graph stuff that has to happen to get to "build me a nanofactory" from "existing tools"
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17:49 < kanzure> technology is weird because the definition of "existing" really varies... if one research lab in the world has some implementation, does that mean it exists? doesn't seem to in any practical way for the purposes of serving as a step in a 100-step project.
17:50 < kanzure> i should really be rewriting SelectCoins right now heh
17:52 < kanzure> on the nanofactory side you may be interested in http://diyhpl.us/~bryan/papers2/nanotech/ https://github.com/kanzure/nanoengineer
18:00 < maaku> kanzure: right that's why I say 5+ years, not tomorrow ;)
18:00 < maaku> but for example what I'm working on is the language for representing both existing and requested capability
18:01 < maaku> but in terms of the actual AGI tech, I hold the contrary opinion that this is a mostly solved problem in theory
18:01 < maaku> at least for a problem of this scale
18:01 < kanzure> dependency graph analysis stuff and generative grammar stuff is totally solved, but that's not the hard part there
18:01 < kanzure> the problem of "existing and requested capability" verges on both philosophy but also very nuanced engineering.. where does the data come from?
18:02 < kanzure> or even s/data/knowledge
18:03 < maaku> kanzure: you have to approximate at a certain level. but for example the ability to do stochastic chemistry by traditional means, e.g. for vapor deposition
18:04 < maaku> and representing an AFM tip as an unknown, deformable shape
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18:04 < kanzure> well what are you proposing for the representation/approximation
18:04 < kanzure> i mean, you can approximate anything if your resolution is extremely bad :)
18:04 -!- bbrittain [~bbrittain@172.245.212.12] has quit [Quit: ZNC - http://znc.in]
18:05 < maaku> it's a datalog-derived (Dyna actually) language with strong typing and a notion of causality
18:05 < kanzure> .to fenn you are bad at picking okay times to sleep
18:05 < yoleaux> kanzure: I'll pass your message to fenn.
18:05 < delinquentme> OK sooooo the conclusion of the regex excercise was that the given regex was only to match strings
18:05 < kanzure> dynamol?
18:05 < kanzure> or is it modelica
18:05 < delinquentme> and the confusion arose when I thought I could send regexes to select instance names
18:05 < delinquentme> this isnt the case.
18:06 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has joined ##hplusroadmap
18:06 < bbrittain> yo
18:06 < bbrittain> long time no be here
18:06 < kanzure> hello bbrittain have you created grey goo yet
18:06 < maaku> kanzure: http://www.cs.jhu.edu/~jason/papers/eisner.nipsw08.pdf
18:06 < bbrittain> not yet, not yet
18:07 < bbrittain> just been furthering my disdain for the traditional biologist
18:07 < kanzure> er, did you start at the job?
18:07 < bbrittain> ja, been there for about 2 months now
18:07 < bbrittain> I like most everyone
18:07 < bbrittain> and they are way more enlightened than most bio people
18:08 < kanzure> maaku: my former advisor had a slightly different approach to things, http://diyhpl.us/~bryan/papers2/campbell/The%20A-Design%20approach%20to%20managing%20automated%20design%20synthesis.pdf
18:08 < bbrittain> but you still get weird sorta "post-doc"-syndrome shit from them sometimes
18:08 < kanzure> that's to be expected i think
18:08 < bbrittain> tk's been tutoring me in bio, which has been awesome
18:09 < kanzure> does he still hat eme
18:09 < kanzure> *hate me
18:09 < bbrittain> no mention, I can drop your name though
18:09 < kanzure> nah whatever
18:09 < bbrittain> he hates... a lot of people
18:09 < kanzure> hehe
18:09 < kanzure> good
18:09 < maaku> kanzure: yeah automated design is really what i'm trying to do
18:09 < bbrittain> kurzweil? zomg. he will go on about "that asshole"
18:10 < kanzure> maaku: so i jumped ship from that lab, but genehacker (who shows up here from time to time) is still with him and moved on to molecular nanotechnology things
18:10 < maaku> the AGI part just comes from the fact that it is faster (in my analysis) to have the computer teach itself to design
18:10 < kanzure> bbrittain: kurzweil is totally an asshole
18:10 < bbrittain> truth
18:10 < maaku> i'll look out for genehacker, thanks
18:10 < kanzure> maaku: so again i think the problem is the design knowledge there... i mean.. random data is not useful as a starting point.
18:10 < bbrittain> but, rarely do you here that from someone who went to school with him
18:11 < kanzure> when's the last time you actually saw any of his ocr software or his midi synthesizer software anyway. meh.
18:11 < kanzure> s/midi/keyboard
18:11 < maaku> kanzure: well in testing i plan on solving problems in my engineering textbooks
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18:11 < maaku> molecular nanotech is more the end goal, not a good place to start :)
18:11 < bbrittain> maaku: dream big
18:12 < kanzure> genehacker: maaku has a strong interest in molecular nanotechnology and automated design. he wants to go down an ai route.
18:12 < genehacker> an ai route for what?
18:12  * bbrittain just wants to work with mesoplasma florum
18:12 < kanzure> automated engineering
18:12 < kanzure> like "figure out how to build me a nanofactory" and "figure out how to build me a 200,000-part space station. on jupiter."
18:13 < maaku> genehacker: automated design/engineering capible of "design me a nanofactory and instructions for building starting from present capability"
18:13 < bbrittain> 0_o
18:13 < kanzure> "build me a dyson sphere starting from this dirt in my pocket"
18:13 < maaku> yup!
18:13 < kanzure> "and my belly button lint"
18:13 < genehacker> we aren't there yet
18:14 < kanzure> oh i didn't mean to imply he's waiting for it, he wants to implement it
18:14 < bbrittain> uhhh
18:14 < kanzure> bbrittain: you stumbled into a different conversation heh
18:14 < kanzure> bbrittain: in case context is not obvious...
18:14 < bbrittain> I got that
18:14 < genehacker> simulating nanosystems is really hard
18:15 < maaku> genehacker: right, i know. one of the instrumental goals would be, e.g. build better molecular dynamic simulators
18:15 < kanzure> maaku: so i think the actual route planning stuff is not hard, in fact i would even say it's trivial in this context
18:16 < genehacker> route planning? no that's very hard
18:16 < kanzure> maaku: so all of your attention should be focused on the other problems, like knowledge representation or how to get all that information available for the planning algorithms
18:16 < kanzure> route planning like path planning through a graph
18:16 < kanzure> e.g. graph search
18:16 < kanzure> sorry, i forgot that route planning means something else too
18:16 < maaku> the branching factor when you generalize makes it uncomputable very fast, which i assume is what genehacker is getting at
18:17 < genehacker> so how do you do that for molecular design?
18:17 < genehacker> *not molecular design, I mean for designing a molecular assembler
18:17 < bbrittain> so, a bunch of people from de shaw recently came to work. They are building custom computers to individually simulate molecules to find binding locations. I think we might be several orders of magnitude off this sorta level of even computational power, much less algos
18:17 < bbrittain> maaku: ^
18:17 < kanzure> tallakahath: see bbrittain's comment
18:17 < kanzure> oh tallakahath is not around. boo.
18:18 < genehacker> what do you mean by binding locations?
18:18 < maaku> hierarchical planning. ive got the basis of a design from some work my uncle did on hierarchical go programs in the 80's
18:18 < kanzure> (tallakahath does ab initio chemistry simulation stuff as a day job)
18:18 < genehacker> oh drug design
18:18 < genehacker> what really?
18:18 < bbrittain> ja, it was some cool shit
18:18 < genehacker> I've been meaning to talk to someone who does that
18:18 < bbrittain> looking for temporal non-traditional binding sites
18:19 < genehacker> wonder if anyone here know about de novo design
18:19 < kanzure> i know some rational protein design stuff because of my obsession with polymerase
18:19 < kanzure> not quite de novo
18:20 < bbrittain> uhh.. I've been trying to learn about that stuff :P
18:20 < bbrittain> polymerase is the shit.
18:20 < bbrittain> but really coolest enzyme is cas9
18:20 < maaku> bbrittain: designing mechanical nano stuff is actually far easier than drug analysis. the mechanical stuff you can constrain to be chemically and structually stable structures, resulting in easier molecular dynamics simulations
18:20 < kanzure> bbrittain: http://diyhpl.us/~bryan/papers2/polymerase
18:21 < kanzure> bbrittain: especially these things http://diyhpl.us/~bryan/papers2/polymerase/Light-dependent%20RNA%20polymerase%20-%20proposal%20-%20Tom%20Hargreaves.pdf
18:21 < genehacker> but mechanically constrained stuff is hard to synthesize
18:21 < bbrittain> kanzure: really, more than anything over the last couple months if I've learned I wasted three years studying CS. like... systems bio/chem is so much cooler
18:21 < bbrittain> but really only if you look at it a particular way...
18:22 < kanzure> you were already good at comp sci stuff weren't you? so why were you schooling for that..
18:22 < bbrittain> 'cause I was stupid
18:22 < kanzure> k
18:22 < bbrittain> I mean, I learned a bunch of type theory stuff and ML stuff I never would have... but damn if I could go back
18:22 < maaku> genehacker: you read the technology roadmap for prod. nanosys (http://www.foresight.org/roadmaps/) or freitas, merkle's minimal toolset (http://www.molecularassembler.com/Papers/MinToolset.pdf) ?
18:22 < kanzure> haha
18:23 < kanzure> genehacker has those memorized by heart
18:23 < genehacker> well not quite
18:23 < kanzure> don't be modest
18:23 < genehacker> but making tool tips is very difficult
18:23 < genehacker> you cannot synthesize them in solution
18:24 < kanzure> you can make type 3 secretion systems in solution (i know, it's not atomically precise) http://upload.wikimedia.org/wikipedia/commons/c/c5/T3SS_needle_complex.svg
18:25 < bbrittain> looks... kinda like a flagellum
18:25 < genehacker> but you can't make the tooltips which you need to do useful stuff
18:25 < kanzure> bbrittain: http://en.wikipedia.org/wiki/Type_three_secretion_system
18:25 < genehacker> it's a bacterial drill
18:25 < maaku> can't is a strong word
18:25 < maaku> it's a hard, hard problem
18:25 < genehacker> in solution at least
18:25 < bbrittain> shit. I was so right.
18:26 < nmz787_i> genehacker: need some tips made?
18:26 < nmz787_i> I just got some work making some today
18:27 < maaku> nmz787_i: different tooltips : http://www.molecularassembler.com/Papers/MinToolset.pdf
18:27 < nmz787_i> genehacker: did you see the few comments I sent you while you were not in the room?
18:27 < genehacker> sure, I'll take 10,000 dimerP tools
18:27 < nmz787_i> from a few nights ago
18:27 < genehacker> no
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18:27 < maaku> genehacker: do you work on this stuff full time?
18:28 < genehacker> well not molecular manufacturing no
18:28 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has joined ##hplusroadmap
18:28 < nmz787_i> maaku: that's 102 pgs long, can you sum up the required hardware briefly?
18:28 < genehacker> but I'm trying to design molecules to do something mechanical
18:28 < kanzure> nmz787_i: here's my summary.. http://diyhpl.us/~bryan/papers2/nanotech/freitas_process/notes.txt
18:29 < genehacker> as a research project
18:29 < nmz787_i> genehacker: basically from the top (and maybe a little from the prev day bottom) http://gnusha.org/logs/2014-11-08.log
18:29 < nmz787_i> kanzure: thx
18:29 < maaku> nmz787_i: it's a set of 9 tooltips which you could use to mechanically construct diamandoid structures
18:30 < genehacker> you want a solid state vacuum pump?
18:30 < maaku> genehacker: academia? cool.
18:30 < maaku> this is what I do only when my brain is burnt out from working on bitcoin, so progress is slow :(
18:31 < nmz787_i> kanzure / maaku why is #4 needed... isn't that the opposite of #2 ?
18:31 < nmz787_i> (of the indented #s)
18:31 < nmz787_i> (at the top)
18:31 < kanzure> reusable tips
18:32 < nmz787_i> Attach tooltip molecule to deposition surface ....  Separate finished tool from deposition surface
18:32 < kanzure> when you tell a chemist to make a bond he will make a bond
18:32 < nmz787_i> (do work in between)
18:32 < nmz787_i> (on the tip)
18:32 < genehacker> nmz787_i, if we get this stuff to work, we might be able to make that solidstate vacuum pump thingy
18:32 < nmz787_i> genehacker: seems like it would be game-changing
18:33 < genehacker> right now it's a pretty big if
18:33 < nmz787_i> well I can help with steps 2,3, and 4 I believe... of the Fritos process
18:33 < nmz787_i> mmmm
18:33 < kanzure> hmm it looks like freitas was doing vasp simulations
18:33 < kanzure> (tallakahath is now my vasp person)
18:33 < maaku> i'll take a solidstate vacuum pump please!
18:33 < nmz787_i> genehacker: yeah but seems like a perfect goal, of the multitude out there
18:34 < nmz787_i> I kind of just had a mind splurge and needed to vent :)
18:35 < nmz787_i> I still don't understand the 'separate tool'
18:35 < genehacker> wait so is the vasp stuff recent for freitas?
18:35 < nmz787_i> isn't it attached to the handle
18:35 < tallakahath> No lets not talk about vasp
18:35 < kanzure> nah i think freitas has been doing vasp simulations for a while now
18:35 < nmz787_i> which you attach to a gantry
18:35 < maaku> nmz787_i: when the tool interacts with the surface, it bonds
18:35 < kanzure> tallakahath: too late
18:35 < maaku> so tool separation is not identical
18:35 < nmz787_i> is this not just a functionalized AFM type tip?
18:37 < genehacker> it probably is
18:37 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-zoasnqbzxsmqjsbq] has quit [Quit: Connection closed for inactivity]
18:37 < genehacker> but you need one hell of an AFM
18:37 < genehacker> to get the necessary resolution
18:37 < maaku> yes iirc the trajectories they use would be compatible with an AFM
18:37 < maaku> if you had an unobtainium AFM
18:37 < nmz787_i> nah
18:37 < nmz787_i> voice coil should be OK
18:38 -!- Vutral [~ss@mirbsd/special/Vutral] has quit [Excess Flood]
18:38 < nmz787_i> from like a laser driv
18:38 < nmz787_i> CD/bluray etc
18:38 < nmz787_i> with a super awesome DAC
18:38 < bbrittain> vasp. vasp. vasp
18:39 < bbrittain> oh. kanzure. thoughts on onecodex?
18:39 < nmz787_i> and AFM tips are what I am going to start making soon with a FIB, or something like that... some probe tip thing
18:39 < genehacker> but you need like angstrom resolution
18:39 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has left ##hplusroadmap ["WeeChat 1.0"]
18:39 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has joined ##hplusroadmap
18:39 < bbrittain> oh. kanzure. thoughts on onecodex?
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18:39 < nmz787_i> hmm
18:39 < genehacker> which is really ridiculous
18:39 < nmz787_i> you'd need SEM/TEM to verify thickness I guess then
18:39 < kanzure> bbrittain: ask ParahSailin_
18:39 < bbrittain> oh. kanzure. thoughts on onecodex?
18:39 < nmz787_i> they easily achieve sub-nm res these days
18:39 < maaku> nmz787_i: the other problem is that these are very specific highy strained structures
18:39 < bbrittain> argh
18:40 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has left ##hplusroadmap ["WeeChat 1.0"]
18:40 < genehacker> easily?
18:40 < kanzure> maaku: liquid phase assembly might be more achievable
18:40 < nmz787_i> I think so
18:40 < maaku> and there doesn't currently exist a pathway to synthesis
18:40 < nmz787_i> they quote sub-angstrom on TEM on websites
18:40 < nmz787_i> for product sales
18:40 < maaku> kanzure: right, that's my assuption. liquid phase assembly of tooltips using custom enzymes
18:41 < nmz787_i> maaku: makes more sense now... the actual tip of the tip is the hard/novel part?
18:41 < nmz787_i> maaku: have ppl made them?
18:41 < maaku> nmz787_i: yes
18:41 < maaku> no
18:41 < nmz787_i> what 'chemical paint set' do you paint with?
18:41 < nmz787_i> after it's made?
18:41 < maaku> yes it's the hard part, no i don't think any have been made
18:41 < maaku> (also, it's patented by merkle and freitas, fyi)
18:41 < kanzure> there have been simulations
18:42 < maaku> nmz787_i: they are tool tips for depositing carbon and hydrogen
18:42 < maaku> e.g. to make diamandoid surfaces, nano gears, rods, and assemblies, etc.
18:42 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has joined ##hplusroadmap
18:42 < bbrittain> is my internet backkk?
18:42 < nmz787_i> maaku: not too sure, just looks like a conical shape to me basically
18:42 < bbrittain> sweet. I think it is
18:42 < maaku> nmz787_i: it's part of this project : http://www.molecularassembler.com/Nanofactory/
18:43 < bbrittain> kanzure: any thoughts on onecodex?
18:43 < nmz787_i> you can get some super-awesome features with CVD and DRIE
18:43 < bbrittain> https://onecodex.com/
18:43 < kanzure> bbrittain: ask ParahSailin_
18:44 < bbrittain> ParahSailin_, thoughts?
18:44  * bbrittain wonders why ParahSailin_
18:44 < kanzure> his job
18:44 < kanzure> bbrittain: at this point ParahSailin_ is like the version of you except 20 years into the future
18:44 < bbrittain> fuck that. gimme 3 years
18:44 < kanzure> except the future is the past and it sucks
18:45 < bbrittain> well, I actually think I'm at the perfect time to be doing this
18:45 < kanzure> actually he may have started in biology
18:46 < nmz787_i> hah, they want to be the google for genomic data, but google is also doing that
18:46 < bbrittain> by the time I have stuff figured out in a few years, synthesis/sequencing will be cheap enough to actually do shit
18:46 < bbrittain> without the big $$$
18:47 < kanzure> maaku: http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf this is some background on nmz787_i
18:47 < bbrittain> kanzure: my first real job was at NIH :P
18:47 < bbrittain> so I kinda started in bio
18:47 < genehacker> isn't BLAST like the google for genetic data?
18:48 < bbrittain> I've been learning that BLAST isn't as useful as I once thought
18:48 < bbrittain> hmms are far more useful
18:48 < bbrittain> "Why DRM doesn't work"
18:49 < bbrittain> tell that to my coworkers and darpa :(
18:49 < maaku> bbrittain: ssshhhhhhh you'll dry up the funding
18:49 < genehacker> here have a genome: http://www.ncbi.nlm.nih.gov/nuccore/158539108
18:50 < kanzure> .title
18:50 < yoleaux> Marburg marburgvirus isolate Marburg virus H.sapiens-tc/KEN/1980/Mt. E - Nucleotide - NCBI
18:50 < bbrittain> http://www.genewiz.com/public/news-Ebola-Virus-Synthesis.aspx
18:50 < bbrittain> for china
18:50 < kanzure> .title
18:50 < yoleaux> Lt. Governor Guadagno Celebrates GENEWIZ Expansion
18:50 < bbrittain> "the China CDC sent an emergency request to GENEWIZ for the synthesis of key EV genes"
18:50 < bbrittain> and GENEWIZ was like "sounds great to me!"
18:51 < genehacker> awesome
18:51 < genehacker> it's not the whole virus though, so we're safe
18:51 < bbrittain> totes
18:52 < bbrittain> anyways, a biophysics friend was interviewing at onecodex and he wanted the dirt
18:53 < nmz787_i> and that's why I stopped pursuing China for funding
18:53 < genehacker> I thought these companies had some big genome blacklist of stuff we are absolutely not going to synthesize no matter what
18:53 < bbrittain> nmz787_i: 为什么我学习中文？！
18:54 < bbrittain> china seems like it might be useful
18:54 < bbrittain> nmz787_i: I forget, what do you do right now?
18:55 < maaku> genehacker: when i was at transcriptic we didn't, although that was a concern
18:55 < kanzure> you worked at transcriptic
18:55 < bbrittain> maaku: oh. you worked at transcriptic
18:55 < bbrittain> tell me
18:55 < bbrittain> the dirt
18:55 < bbrittain> now
18:55 < maaku> i don't know if there is anyone with a blacklist
18:55 < genehacker> you what?
18:55 < yashgaroth> there's a list but legitimate organizations can get around it
18:55 < kanzure> i really wanted to work with max
18:55 < maaku> yeah i wrote scheduling algorithms for their robotic lab
18:56 < kanzure> lkdsalkfdksaflksa;kfdad
18:56 < maaku> before dropping out to do bitcoin full time
18:56 < kanzure> lolz
18:56 < maaku> i'm at blockstream.com now
18:56 < kanzure> right
18:56 < bbrittain> oh shit
18:56 < bbrittain> you work with gmaxwell then!
18:56  * bbrittain is friends
18:57 < maaku> yup greg is even awesomer in person :)
18:57 < kanzure> maaku: i have a love/hate relationship with transcriptic.com/platform ... on the one hand, a functional api standard would be nice. on the other hand, centralization of lab equipment....
18:57 < bbrittain> maaku: I worked with him at mozilla
18:57 < genehacker> you mean to tell me that these huge biotech companies aren't implementing controls on what can be synthesized?
18:57 < maaku> bbrittain: small world :)
18:57 < kanzure> maaku: https://github.com/Opentrons/OpenTrons implements transcriptic's json standard thingy.
18:57 < kanzure> http://www.opentrons.com/
18:57 < nmz787_i> currently I'm working on rourting a debug-motherboard automatically
18:58 < bbrittain> maaku: very much so :P
18:58 < maaku> genehacker: it came up while i was there and we agreed that we needed to have a black list, but if such a thing exists it would be news to me
18:58 < genehacker> http://issues.org/26-3/tucker-2/
18:58 < maaku> so it was on our list of one million things to get done asap
18:58 < bbrittain> maaku: how robotisized is transcriptic?
18:58 < kanzure> there is a blacklist
18:58 < kanzure> dna2.0 made claims of such a blcklist
18:58 < kanzure> *blacklist
18:59 < kanzure> http://diyhpl.us/wiki/transcripts/fbi-diybio-2012/howard-simon-dna20.txt
18:59 < genehacker> there's software too
18:59 < nmz787_i> it was a health dept thing
18:59 < maaku> bbrittain: 100%
18:59 < yashgaroth> they'll report all suspicious activity, or just deny your order
18:59 < nmz787_i> or some dept
18:59 < genehacker> http://biotech.craic.com/blackwatch/introduction.html
18:59 < kanzure> "There are some inherent problems, but because this is a voluntary regime, there's nothing that would preclude or prohibit or impede amateur biology community from accessing the blacklist of recipients and the various lists, the agents list, the Australian list, of seuqences and combinations of matter that are suspect. There is no impedance and it's publicly accessible and we're a voluntary regime. In that sense, we all sit in the same ...
18:59 < kanzure> ... relationship to this process."
18:59 < bbrittain> maaku: shit. really?
18:59 < bbrittain> thats... amazing
19:00 < nmz787_i> dtra ?
19:00 < nmz787_i> but yeah, it was a recommendation
19:00 < kanzure> well they have a different model or idea than ginkgo
19:00 < kanzure> ginkgo isn't going for "cloud biology"
19:00 < kanzure> or "heroku"
19:00 < bbrittain> certainly :P
19:01 < kanzure> they are more going for "gene foundry... thing"
19:01 < bbrittain> but our build iteration time is _very_ important
19:01 < kanzure> and "give me all your oil money"
19:01 < kanzure> oh wait, that was craig venter, not ginkgo
19:01 < kanzure> my bad.
19:01 < bbrittain> lol
19:02 < bbrittain> nah, we just make smelly stuff
19:02  * bbrittain winks
19:02 < genehacker> when's craig ever going to finish synthia? it's been like 8 years now
19:02 < kanzure> what happened to making it all produce isoamyl acetate
19:02 < kanzure> bbrittain: http://2013.igem.org/Team:Queens_Canada/Project/Repel
19:02 < kanzure> "Alcohol acetyl-transferase 1 (ATF1) (BBa_J45014) is an enzyme endogenous to Saccharomyces cerevisiae and was first used by MIT iGEM 2006. It catalyzes the conversion of isoamyl alcohol to isoamyl acetate, which has a banana smell."
19:03 < kanzure> andytoshi: ^igem in action
19:03 < bbrittain> yay. igem!
19:03  * bbrittain is sarcastic
19:03 < kanzure> yeah :/
19:03 < kanzure> genehacker: probably when synthesis gets cheaper
19:04 < bbrittain> kanzure: I'm of the opinion that synthia is not worth it
19:04 < kanzure> you can only spend $40 million so many times on a genome
19:04 < bbrittain> or well it is
19:04 < kanzure> at some point you will run out of cash
19:04 < bbrittain> but not the best route
19:04 < kanzure> cheap synthesis would be far more useful at this point
19:04 < kanzure> like $1/genome would be nice
19:04 < nmz787_i> synthia will be possible
19:04 < nmz787_i> for cheap
19:05 < nmz787_i> i seriously could use a lackey
19:05 < kanzure> what do you think this channel is for
19:05 < kanzure> did you pester lichen?
19:05 < bbrittain> I'm on Tom Knight's Mesoplasma florum >> Mycoplasma genitalium train
19:05 < nmz787_i> yeah
19:06 < nmz787_i> they're up for it, but I am not sure how exactly to proceed with fundings
19:06 < kanzure> oh right, it's mycoplasma i forgot about that
19:06 < kanzure> sheena has been trying to kill a mycoplasma genitalium infection for a few months now (in a flock of.. alpaca? geese?)
19:06 < bbrittain> sheena2: wat.
19:06 < nmz787_i> synthia will be possible as a general meme, not the specific species it refers to now
19:07 < nmz787_i> chickens
19:07 < kanzure> oh, chickens.
19:07 < bbrittain> there are some interesting people in this channel
19:08  * bbrittain needs to hang here more again
19:08 < kanzure> yes we are sad you abandoned us
19:08 < bbrittain> I'm back! :D
19:08 < kanzure> i figured tom knight fed you trash talk or something
19:09 < bbrittain> I kinda abandoned all of IRC for a couple of months :/
19:09 < bbrittain> nah, I haven't mentioned you fold, I figured it would rub my new pals the wrong way
19:10 < bbrittain> s/fold/folks/
19:10 < bbrittain> we... don't see eye to eye on a lot of IP stuff
19:10 < bbrittain> I don't see me working there long term
19:10 < bbrittain> I just want to learn
19:10 < bbrittain> and this is a cheap hack
19:10 < kanzure> they are more conservative on IP things?
19:11 < bbrittain> in comparison to other bio labs? probably not.
19:11 < kanzure> is reshma still there btw?
19:11 < bbrittain> yuppers, you know her?
19:11 < kanzure> no
19:12 < bbrittain> I try to infect my coworkers, I am succeeding in some ways
19:13 < bbrittain> and not at all in some of them
19:13 < kanzure> open source is  very nuanced strategy
19:13 < kanzure> it is hard to communicate from scratch
19:13 < bbrittain> yea :/
19:13 < kanzure> because it sounds an awful lot like "don't make ny money"
19:13 < kanzure> *any
19:13 < kanzure> even though it's totally about making money
19:14 < bbrittain> plus it's not like they have prior exposure
19:14 < kanzure> none?
19:14 < bbrittain> or the fact that our competitors don't do it
19:14 < bbrittain> not as in they make open source stuff
19:14 < kanzure> hmm.
19:15  * bbrittain is talking about bio right now, not the software
19:15 < bbrittain> wetware. I love that term.
19:15 < nmz787_i> you know what they say about open-source and biology... 'once you go open-source, your business ends up like a horse'
19:16 < nmz787_i> in a glue factory, on a dinner plate, in a bag of dog chow, or riding off into the sunset
19:16  * bbrittain rolls eyes
19:16 < kanzure> maaku: "i was working with dyna and its handling of algebraic data types at the time was broken somehow"
19:18 < genehacker> it seems to work well for Willow Garage.
19:19 < genehacker> They were able to kick microsoft out of the robotics business
19:20 < bbrittain> yeaaa
19:20 < bbrittain> I don't disagree
19:20 < bbrittain> my coworkers do
19:20 < bbrittain> and don't even ask them about DIYbio, most of them will laugh in your face.
19:20 -!- maaku [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has quit [Remote host closed the connection]
19:21 < bbrittain> the concept that you can do this sorta stuff without uni... bothers them.
19:22 < kanzure> .title https://www.youtube.com/watch?v=UekVSt1cA5Y
19:22 < yoleaux> Brain Backups talk at SingularityNYC on 10/9/2014 - YouTube
19:22 < kanzure> from russell hanson
19:22 < bbrittain> they may be biased by the fact that like half of them have taught at MIT.
19:22 < genehacker> willow garage is also a hardware company and it's beneficial for them to have other people develop for them for free
19:23 < nmz787_i> bbrittain: that's probably because they don't understand diybio
19:24 < nmz787_i> phds in genetics and biochem are part of diybio
19:24 < nmz787_i> etc etc
19:24 < kanzure> "BRAIN BACKUPS IS DEVELOPING NON-DESTRUCTIVE NON-INVASIVE IMAGING OF BRAINS AT HIGH RESOLUTION"
19:24 < kanzure> oh right i forgot about them
19:24 < bbrittain> nmz787_i: can you show me something interesting or novel that has come out of DIYbio?
19:24 < nmz787_i> maybe it's just the type of person, self-determined, etc...
19:24 < kanzure> "With 86bn neurons and 100tn connections the total cost of the data and metadata storage is around $80K."
19:24 < kanzure> "1 terabyte hard drive = ~$90 –> storage for all human neurons and synapses ~$90 * 909.49 = ~$81,854"
19:25 < bbrittain> kanzure: that's... cool.
19:25 < kanzure> "After significant development, our target market is the demographic who can afford the $81,000 and decreasing storage cost, plus the cost of the scanning procedure.  We plan to offer flexible payment/insurance plans once the requisite regulatory, scientific, and technological challenges have been accomplished.  Actual neuroanatomy figures vary greatly, depending on the individual and local neurobiology."
19:25 < nmz787_i> bbrittain: there are a few current kickstarters of folks that started stuff with diybio
19:25 < nmz787_i> bbrittain: me if that counts
19:25 < bbrittain> the robots stuff doesn't really count in their mind
19:25 < nmz787_i> bbrittain: all the stuff patrikd has done
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19:26 < nmz787_i> bbrittain: who is also like double or triple major in EE CS and BioChem/BioComput or something
19:26 < nmz787_i> or simon field, who writes about microscopes and other related stuff
19:26 < bbrittain> nmz787_i: what has he done? I only see him tweet about his new biohacker lab
19:26 < nmz787_i> kanzure: does jmil count?
19:27 < nmz787_i> who 'he'?
19:27 < bbrittain> patrickd
19:27 < nmz787_i> I worked with patrikd at JBEI
19:27 < nmz787_i> 3/4 years ago
19:27 < nmz787_i> and he was an expert then
19:28 < kanzure> what about jmil?
19:28 < kanzure> what are we counting
19:28 < nmz787_i> bbrittain:  someone who could tell you the answer to that codex thing, that's for sure
19:28 < bbrittain> what has he done since "going DIY", I genuinely want examples to show my coworkers
19:29 < nmz787_i> I think it's all been great
19:29 < nmz787_i> use google to find it out
19:29 < kanzure> well he did an igem thing recently
19:29 < kanzure> and jmil became an associate professor at rice doing 3d printing open source tissue biology.. stuff..
19:30 < kanzure> i got the order of those words wrong
19:30 < bbrittain> Patrik D was a scientific advisor for Glowing Plant :/
19:31 -!- maaku [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has joined ##hplusroadmap
19:31 < nmz787_i> tell ya what though, electron microscopy and ion beam stuff is a lot more internet-lonely
19:31 -!- maaku is now known as Guest34189
19:31 < genehacker> internet lonely?
19:31 < nmz787_i> yeah
19:31 < kanzure> you guys are in the same state why do you not hang out
19:32 < nmz787_i> and in real life they're all professionals at places I don't work
19:32 < nmz787_i> idk, do you like camping or hiking genehacker?
19:33 < nmz787_i> i could probably come down there sometime to take a walk
19:33 < genehacker> I'm in oregon, is that even an a question?
19:33  * bbrittain waves hands frantically looking for bostonians
19:33 < nmz787_i> I see some non-movers at the office
19:33 < kanzure> bbrittain: well there's this guy aaronsw
19:33 < bbrittain> kanzure: not cool
19:33 -!- ebowden [~ebowden@147.69.147.27] has quit [Read error: Connection reset by peer]
19:34 < kanzure> oh right
19:34 -!- ebowden [~ebowden@147.69.147.27] has joined ##hplusroadmap
19:34 < kanzure> cluckj is in boston
19:34 < kanzure> you should hang out with cluck
19:34 < kanzure> *cluckj
19:35 < kanzure> "Sure I know Todd. Their method is destructive and doesn't record any electrophysiology data. Ours is not!  I don't know Matt Goodman but we know many people in common.  CLARITY is *extremely* destructive as I'm sure you know. We're more on the nanotech side, nanoparticles tagged with aptamers and antibodies, gold nanorods for plasmons, voltage sensitive dyes for electrical activity. All of which we find infinitely more interesting that ...
19:35 < kanzure> ... knife-edge scanning microscopy :) "
19:35 < genehacker> damn if I only had time to hang out
19:37 < genehacker> so how are they doing that noninvasively?
19:37 < kanzure> http://brainbackups.com/
19:37 < bbrittain> kanzure: you sure cluckj is in boston? he appears to go to RPI now
19:38 < kanzure> my reality is collapsing around me
19:39 < kanzure> also he might be dead too, i haven't heard from him in like two months
19:39 < bbrittain> tweeted yesterday
19:39 < genehacker> so they don't explain how they're going to do it noninvasively?
19:40 < kanzure> i haven't seen an explanation yet (but i haven't looked hard)
19:40 < kragenjaviersita> DigInfo is not as awesome as it appeared at first
19:40 < kanzure> "Brain Backups is actively developing new methods and has developed a number of proprietary techniques for imaging neurons using synthetic biology, MRI, smart contrast agents and sensors, and aptamer-based technology."
19:40 < kanzure> looks like aptamers
19:40 < kanzure> and contrast agents
19:41 < kanzure> probably PET scans
19:41 < kanzure> http://cdn.medgadget.com/wp-content/uploads/2012/02/Siemens-Biograph-mCT-scan-full-body.jpg
19:43 < kanzure> q: if synapses are being regularly created then couldn't you measure total synapse growth in meters per day?
19:44 < genehacker> "nanorods for plasmons, voltage sensitive dyes for electrical activity"
19:44 < genehacker> it's optical
19:44 < kanzure> i think there's a voltage sensitive mri reporter
19:46 < genehacker> so why don't we use it in mice?
19:48 < genehacker> http://newsoffice.mit.edu/2014/mri-reveals-genetic-activity
19:48 -!- bbrittain [~ben@2601:6:7f00:a7d:2acf:e9ff:fe1a:cb25] has quit [Ping timeout: 265 seconds]
19:52 < tallakahath> I've been told to pop back in here?
19:54 < kanzure> genehacker: now's your chance
19:54 -!- genehacker [~chatzilla@8-12.ptpg.oregonstate.edu] has quit [Ping timeout: 244 seconds]
20:01 < kanzure> he chickened out i guess
20:04 < jrayhawk> tallakahath: I'm only going to be paying a little bit of attention in here, but can you detail satiety problems that kanzure has mentioned to me?
20:04 -!- qu-bit [~shroedngr@unaffiliated/barriers] has quit [Read error: Connection reset by peer]
20:07 < jrayhawk> I will probably catch up on them in a few hours.
20:13 -!- yash [~ffffff@2606:6000:cb85:6a00:988e:3b8e:88b7:3ccb] has joined ##hplusroadmap
20:14 < tallakahath> jrayhawk: Uh, I do not feel fullness or any want to stop eating until my stomach is physically distended. But I manage this through conscious calorie counting and use of a food scale so its not really a problem, per-se
20:17 < jrayhawk> A lot of autonomic caloric estimation for ghrelin signaling is done in the cephalic stage; does this happen with solid food that you chew thoroughly?
20:17 -!- yashgaroth [~ffffff@2606:6000:cb85:6a00:988e:3b8e:88b7:3ccb] has quit [Ping timeout: 265 seconds]
20:18 < jrayhawk> Usually anabolic folks deliberately attempt to bypass the cephalic stage with e.g. shakes.
20:19 < tallakahath> jrayhawk: Yes. I've run the full gamut from solid food I don't chew thoroughly, to solid food I chew thoroughly, to soft food, to soup
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20:20 < tallakahath> Makes me a sure champ at AYCE sushi tho
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21:08 < jrayhawk> Have you done any 23andme-type individual sqeuencing to see if you have GOAT or GHSR mutations?
21:10 < tallakahath> No. I am waiting for the tech and the science to mature and cheapen.
21:11 < tallakahath> Again, I believe calling it a 'problem' in earnest is an exaggeration...
21:11 < jrayhawk> Certainly an advantage for anabolics.
21:11 < nmz787_i> have you tried drugs?
21:11 < nmz787_i> if so, which?
21:12 < nmz787_i> and what were the effects/outcome?
21:12 < tallakahath> I run an EC stack for appetite suppression, as many stims grant. But tolerance is a bitch.
21:12 < jrayhawk> Most of that is through raising blood sugar; does that work?
21:13 < nmz787_i> what about other things that are known to mess with food feelings? other than stims
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21:13 < jrayhawk> or, rather, do stims have an appreciable effect?
21:13 < tallakahath> I've done keto; helps mildly. I've tried IF, and had many of the negative results women tend to note with the regimen. 16, 18, and 20 hour versions, all.
21:14 < nmz787> interferon?
21:14 < tallakahath> The stims worked until they stopped working. 600 mg caffeine + 75 mg ephedrine a day, I'm in week... five or so and no longer noticing effects.
21:14 < nmz787> what about thc?
21:14 < tallakahath> THC and I do not get along.
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21:15 < jrayhawk> seems like hammering the endocannabinoids is exactly the wrong way to deal with an overactive appetite.
21:15 < nmz787> meh, i'm pretty sure you get tolerance there too
21:15 < nmz787> which seems like the goal
21:17 < tallakahath> I have run the span from 'sufficient' water to excess water intake, scaled around salt levels, and keep my protein levels at approx. 1 g/lbm with a steady stream of fresh and varied vegetables and meat sources, so I doubt its malnutrition..
21:17 < nmz787> obv some feedback loops are screwed
21:17 < jrayhawk> When did this start?
21:17 < nmz787> so you need to get around the hysterisis
21:17 < tallakahath> Hard to define. In high school I packed lunch, had limited slush funds for junk food purchases and had food cooked by parental units so my intake was usually externally limited.
21:18 < tallakahath> Also my high school was an 8-story walkup and I was still in my growing years so determining 'overating' vs 'teenagers are hungry' is hard
21:18 < nmz787> have you ever done feast/famine regimes?
21:18 < tallakahath> Some time in university, I guess? The board plan was both mandatory and crap so that curtailed mye ating somewhat but stress and availability were... bad
21:18 < nmz787> those seem like it would be a bit easier mentally, as in all or nothing
21:18 < tallakahath> Yes, see the IF routines
21:18 < jrayhawk> okay, that's helpful
21:19 < tallakahath> Unless you mean like 5/2 or something
21:19 < nmz787> like every 3rd day
21:19 < nmz787> 2 on, 1 off
21:19 < nmz787> on food
21:19 < tallakahath> I've done that. I can stick ot it but, long-term, it doesn't help the underlying problem.
21:20 < tallakahath> I have things under control, I just wish I could rely on my internal homeostasis engine to keep things in-check rather than have to be conscious of what I'm eating all the time
21:21 < tallakahath> From empirical observations (weight measurements over time + food log where everything that goes into my mouth goes on a food scale first and is made from scratch/near scratch)
21:21 < tallakahath> I am also sure that my BMR is on the low end for my weight/height range
21:22 < tallakahath> Not 'indicative of defect' levels of low, just, 'there is a range based on various factors and I should use most of the reducing multipliers' low
21:22 < jrayhawk> Do you put on adipose tissue easily, or does it fairly inherently go to muscle?
21:22 < tallakahath> Adipose
21:22 < nmz787> have you tried a calorie restriction regime?
21:23 < tallakahath> I am on one right now
21:23 < jrayhawk> she just said that
21:23 < nmz787> it was hard for me at first, but it's pretty natural now
21:23 < nmz787> goes well with the 2 on 1 off type
21:23 < jrayhawk> Yeah, men seem to do better on IF.
21:23 < nmz787> i don't see calorie restriction mention
21:24 < tallakahath> I am on what should be a -500 kcal deficit
21:25 < jrayhawk> Have you done much in the way of deliberate non-immunogenic dieting, a la paleo/primal/WAPF/SCD/GAPS/Pefect Health Diet/etc.?
21:25 < tallakahath> I've done keto, which intersects pretty well with paleo
21:25 < tallakahath> But the 'organic as possible' 'raw as possible' tenants of paleo fall outside my budgetary ability
21:26 < tallakahath> I quite like keto but it did not like me
21:26 < jrayhawk> Leptin is the master energy homeostasis hormone, but usually when people lower inflammation to sort out leptin resistance, it's essentially impossible to feed them enough calories to get them fatter because the body just allocates it all towards anabolic purposes or metabolic purposes.
21:26 < jrayhawk> So at this point I am suspecting something is fundamentally wrong with either ghrelin or leptin.
21:27 < jrayhawk> ghrelin managing short homeostasis and leptin doing long-term homeostasis
21:27 < tallakahath> It could also be something related to my tendency to stress-eat and being in grad school
21:27 < jrayhawk> s/short/short-term
21:27 < jrayhawk> Yeah, eventually corticosteroid resistance sets in and you lose your primary immune suppressant.
21:28 < nmz787> licorice root seems to have a eating suppression effect
21:28 < nmz787> and it's pretty cheap
21:28 < tallakahath> And I can't stand the taste of it without vomiting, unfortunately
21:28 < nmz787> if i recommend anything 'organic' it's bananas and milk
21:28 < tallakahath> Blame freshman-year me and her lovely bottle of absinthe
21:29 < nmz787> and leafy veggies too if they're cheap enough
21:29 < nmz787> isn't absinthe anise?
21:29 < nmz787> err
21:29 < nmz787> wormwood
21:29 < nmz787> is that the same genus/?
21:29 < tallakahath> Its the licorice smell/taste, which anise, absinthe, fennel, and licorice all share
21:29 < tallakahath> I don't know how it works chemically, but if I smell that family of smells I become nauseated
21:29 < jrayhawk> If you're in a university setting, you might be able to convince some biochem or medical folks to test leptin and ghrelin levels for you and see if one of them is completely haywire.
21:30 < tallakahath> I could see if the health center supports that testing?
21:30 < tallakahath> I am going to an endocrinologist soon for unrelated reasons and could also bring that up there
21:30 < jrayhawk> everything is related
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21:31 < nmz787> how about a currandero?
21:31 < tallakahath> Well, as far as I can find, copper deficiency can cause all sorts of metabolic funtimes, but copper excess doesn't seem to
21:31 < jrayhawk> i guess that would be a fun opportunity to do that. it's possible you can also buy some internet labs for cheaper.
21:31 < jrayhawk> excess copper crashes zinc; pretty easy for that to go wrong
21:32 < tallakahath> I've been hyper-supping zinc in the hopes of reducing my Cu
21:32 < tallakahath> (it hasn't helped)
21:32 < jrayhawk> pyrolurria is an interesting disease that can sink massive amounts of zinc
21:33 < jrayhawk> not sure if it's relevant or not; that's what testing is for
21:36 < tallakahath> Mm. I could just start taking clenbuterol daily. Probably not good for long-term health, though.
21:45 < kragenjaviersita> all that stuff makes me worry about metal poisoning
22:28 < tallakahath> Night, all
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23:30 < ebowden> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/12752463
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--- Log closed Wed Nov 12 00:00:48 2014