--- Log opened Thu Feb 19 00:00:58 2015
00:05 < nmz787> kanzure: seen any naturally-occuring fullerene-type structures in biomolecules? not something like camp-fire smoke though.
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05:02 < archels> https://mariakonovalenko.wordpress.com/2015/02/12/transhumanism-strategy/#more-2138
05:04 < archels> "Radical life extension idea is extremely complicated and burdening it with making money overcomplicates everything."
05:04 < archels> aww, look at the cute idealists
05:06 < archels> in all fairness though, the jist of the post seems to be a call for action, which is of course a great mindset
05:06 < archels> "30% are for cyberpunk. We think it wouldn’t hurt to try."
05:07 < archels> .wik Rose's law
05:07 < yoleaux> "Rosa's Law (Pub. L. 111-256) is a United States law which replaces several instances of "mental retardation" in law with "intellectual disability". The bill was introduced as S.2781 in the United States Senate on November 17, 2009 by Barbara Mikulski (D-MD)." — http://en.wikipedia.org/wiki/Rosa's_Law
05:07 < archels> y... no
05:08 < archels> Rose's law is the extension of Moore's law to quantum computing
05:08 < archels> https://www.flickr.com/photos/jurvetson/8054771535/in/photostream/
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08:01 < kanzure> "Vanadis Labs is a BTNB startup company whose focus is in the area of protein chemistry and immunology with an emphasis on surveying products for latex antigenic proteins. "
08:01 < kanzure> "Join us on February 25 for an information and Q&A session with Mike Shields on how BTnB can be a resource for your HPLC needs"
08:01 < kanzure> brutal
08:03 < kanzure> nmz787: there are some vesicles, spores and virus capsids that could be mistaken for fullerenes
08:03 < kanzure> nmz787: but this is more fenn's domain. he's the shape person.
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09:19 < nmz787_i> mmm
09:20 < nmz787_i> I saw some human-modified proteins that they added fullerenes to
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10:56 < maaku> archels: "30% are for cyberpunk" <-- is this a definition of cyberpunk I'm not familiar with?
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11:12 < nmz787_i1> yay, 40 seconds on the BBC! http://www.bbc.co.uk/programmes/p02k96t4
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11:12 < kanzure> .title
11:12 < yoleaux> BBC World News - Click, 21/02/2015 GMT, Webscape: How to take tech apart
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11:56 < nmz787_i1> if i pushed a git branch to the remote (not master branch), can I still rebase on master to make things look clean, or since I pushed to the server will rebasing now mess things up?
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12:10 < kanzure> in general it is rude to push a rebased branch to a remote, especially if someone else has already fetched that branch and is working on the previous version
12:10 < kanzure> if nobody else has those commits, then you can force-push your new rebased version
12:25 < nmz787_i1> uh, well I am the only one working on the branch... and I bet people have fetched the most recent master (which I merged into my branch)
12:37 < kanzure> why did you want to do a rebase?
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14:39 < nmz787_i1> i had a lot of waypoint commits that would break the code, so I thought to squash them so master branch doesn't look ugly
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15:04 < kanzure> well, you have a few options.. you can force-push whatever you want, but this can have negative side effects especially since you have team members using that git repo.
15:05 < nmz787_i1> hrmm, I don't know anything about force-push
15:05 < kanzure> another option is that you could have a separate branch where you create your squashed commit, and then merge that squashed commit into master so that you have both the original commit history and the new commit history. this way, you have the clean version in the history, which seems to be important to you. also you don't have the negative effects of force-pushing a differen thistory.
15:05 < kanzure> i'm not sure i should tell you about `git push -f` because if i do then you might use it. and then i'll have to be blamed for all your force pushing in the future.
15:09 < kanzure> (astute observers will note that `git push -f` is how you force-push anyway)
15:09 < fenn> not aware of any C60 compounds in biology, but i would be surprised if forest decomposers didn't use them in some way, since huge quantities would be produced during a forest fire
15:09 < fenn> according to rose's law we now have quantum computers nearly faster than the universe
15:10 < kanzure> .g kegg pathway database
15:10 < yoleaux> http://www.genome.jp/kegg/pathway.html
15:10 < kanzure> .g site:genome.jp fullerene
15:10 < yoleaux> http://www.genome.jp/dbget-bin/www_bget?pdb:1EMT
15:10 < kanzure> "ANTI-FULLERENE ANTIBODY"
15:10 < nmz787_i1> so i merged master into my branch, then git rebase -i, rearranged the commits I didn't do so they were subsequent, put all my commits after, then squashed most of my commits together... there was an excel file it couldn't merge/apply rebase to... so it errored out and then I tried git rebase --skip, which also then errored on some permission denied (I think I have the file open) and ended with 'fatal: Could not reset index file to
15:10 < nmz787_i1> revision 'HEAD'.'
15:10 < nmz787_i1> :(
15:11 < fenn> quick someone patent ANTI-ANTI-FULLERENE ANTI-ANTIBODY
15:11  * kanzure pokes patentbot
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15:12 < fenn> i didnt realize carbon nanotubes weren't "discovered" until 1991
15:12 < kanzure> what's the status on those anyway, are we still unable to grow superlong carbon nanotubes?
15:13 < fenn> before that i definitely read some scifi book with "linked buckyball diamondoid fibers" in the space elevator
15:13 < kanzure> you were around before 91?
15:13 < fenn> yes
15:14  * fenn casts a vote for the theory of continuing existence of physical reality
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15:15 < fenn> it was probably an arthur clarke book
15:15 < kanzure> isn't it a little unusual that genehacer's the only one super-obsessed with carbon nanotubes in here
15:15 < fenn> tallakahath, but i guess she's not here huh
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15:15 < kanzure> i thought carbon nanotubes would be worth at least a handful of people
15:15 < fenn> well, they're expensive
15:15 < kanzure> i think she got distracted by trains
15:16 < fenn> trains?
15:16 < fenn> i think the bulk of zyvex's income is from covalently modified nanotubes for carbon fiber epoxy binder strengthening
15:17 < fenn> "functionalized" whatever that means
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15:19 < fenn> i've been somewhat obsessed with 18650 batteries lately and ordered 10 laptop battery packs to tear apart
15:19 < fenn> i hope this turns out to have been a good idea
15:21 < fenn> there aren't that many actual materials science people in the world
15:24 < kanzure> "institute for the advancement of vulnerable fringe sciences"
15:25 < fenn> there really should be such a thing
15:25 < fenn> the entirety of physical chemistry received ~$2 million this year from NSF (?)
15:25 < cluckj> there is, it's called the NSF
15:25 < cluckj> booooom
15:26 < fenn> NSF is biased and subject to the whims of congressmen and other washingtonians
15:26 < fenn> i'm saying that $2m is a small amount for an entire field
15:26 < kanzure> blood feuds between middle-aged professors trying to hit career milestones is not the right way to organize science
15:27 < cluckj> yep
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15:39 < nmz787_i1> kanzure: will git rebase --abort get me back to the state where I was before I ever tried git rebase -i?
15:39 < kanzure> yep i think so
15:39 < nmz787_i1> it says some crap about taking you back to HEAD, but I have no idea what that means or where HEAD will be
15:39 < kanzure> git rev-parse HEAD
15:40 < nmz787_i1> emits a hash
15:40 < kanzure> well there you go
15:40 < kanzure> fenn: did you meet with maaku yet, or blockstream, or transcriptic?
15:40 < nmz787_i1> how do I get the commit message for that hash?
15:40 < kanzure> git show <commit-id>
15:41 < maaku> not with me :(
15:41 < kanzure> this story is tragic
15:42 < nmz787_i1> wat... the hash from git rev-parse isn't the same as what gitk shows
15:42 < nmz787_i1> someone really needs to come along and make better revision control and profit insanely, because this suck
15:43 < nmz787_i1> sucks
15:43 < kanzure> ls ./git/refs/heads/
15:43 < kanzure> er
15:43 < kanzure> ls ./.git/refs/heads/
15:43  * nmz787_i1 wants to flee
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15:45 < nmz787_i1> huh, weird, catting the files in that dir show different hashes than the rev-parse emitted
15:46 < kanzure> git rebase --abort will remove the changes you made to your files in your working directory
15:47 < nmz787_i1> so if they were all committed, I'll be ok?
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15:48 < kanzure> you mean your squashed changes?
15:50 < nmz787_i1> uh, no, I don't care about that since it
15:50 < nmz787_i1> 's not working
15:50 < kanzure> yep then you can abort safely
15:52 < nmz787_i1> :( it left merge crap in my files
15:55 < kanzure> you can use git reset something to fix
15:55 < kanzure> git reset --soft HEAD
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16:27 < nmz787_i1> hah, best youtube ad video, opening line: 'how do you get a ferrari in your garage like this, DROP OUT OF COLLEGE'
16:30 < nmz787_i1> "He spent two-and-a-half years living with the Amish; spent time working at a leper colony in India; and helped Joel Salatin pioneer grass-fed, sustainable agriculture on Polyface Farms."
16:34 < kanzure> yashgaroth: someone should put anabolic steroids into ultrasound-activated delivery microspheres
16:35 < nmz787_i1> so babies get a hit when their mom checks their heartbeat?
16:35 < nmz787_i1> in-utero
16:35 < kanzure> i was thinking of targeted delivery actually
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16:49 < nmz787_i1> am I right to think that since I pushed my branch to remote, that rebasing is pointless?
16:50 < kanzure> you can force push a rebased branch to a remote, but again it's a little rude to the other users
16:51 < nmz787_i1> that doesn't seem to answer my question though
16:51 < nmz787_i1> since I don't know what a force push does
16:51 < nmz787_i1> and haven't used it
16:52 < nmz787_i1> my understanding was that rebase was to hide your intermediary commits from the world, since they are often numerous and thus could be noisy
16:52 < nmz787_i1> but i'm asking that, since I pushed my branch to the remote... they see that
16:52 < nmz787_i1> see that 'noise' anyway
16:52 < kanzure> force pushing is exactly like a regular push except instead of git complaining that the other branch is ahead, you will be able to override the remote branch with your current local commits
16:53 < kanzure> force-pushing replaces the history attached to that branch
16:53 < kanzure> s/attached to/referenced by
16:53 < nmz787_i1> oh, well that doesn't apply as my branch was ahead of remote/master
16:54 < nmz787_i1> i had just pulled master into my branch, so I know my branch was up-to-date and only ahead
16:54 < nmz787_i1> no one here would care anyway... as long as the code works
16:55 < nmz787_i1> in the future i think it'll be easier to just add the keywork WIP for work-in-progress to such intermediary commits
16:56 < kanzure> instead of force-pushing to master, you can push the same commit as remote master to another remote branch (which isn't master), and then you can experiment with force-pushing to that remote branch that isn't master
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17:09 < kanzure> http://techcrunch.com/2015/02/19/cloud-based-bio-lab-startup-transcriptic-lands-8-5-million-in-series-a-funding-to-help-it-scale/
17:09 < kanzure> maaku: ^
17:10 < kanzure> "It also bought just over $800,000 worth of new robotic equipment for the new lab in January"
17:10 < kanzure> https://www.transcriptic.com/blog/2015/02/19/series-a.html
17:11 < kanzure> .title https://www.transcriptic.com/blog/2015/02/16/resource-reservations.html
17:11 < yoleaux> Buying Reagents Through Transcriptic - Transcriptic
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17:55 < nmz787_i> the most exciting thing about that is https://www.transcriptic.com/blog/2015/02/16/resource-reservations.html
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18:06 < kanzure> gene_hacker: hi
18:24 < maaku> awesome
18:29 < gene_hacker> ?
18:36 < nmz787_i> what's the word on nanotubes?
18:36 < cluckj> "tiny"
18:36 < bbrittain> small
18:39 < gene_hacker> everyone's more excited about graphene right now
18:39 < gene_hacker> even though nanotubes would probably have better crack propagation properties
18:41 < kanzure> longest nanotubes we can make?
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18:51 < gene_hacker> half a meter
18:51 < gene_hacker> http://pubs.acs.org/doi/abs/10.1021/nn401995z
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18:52 < gene_hacker> so you could make a very tiny space elevator
18:53 < cluckj> for very tiny astronauts
18:54 < gene_hacker> or ants
18:54 < kanzure> 0.5m is pretty good
18:57 < gene_hacker> yeah
18:57 < gene_hacker> they can't really mass produce long nanotubes though
19:02 < kanzure> vascular smooth muscle cytoskeleton http://www.nature.com/ncb/journal/v5/n7/images/ncb0703-598-i1.jpg
19:03 < kanzure> nice images on http://en.wikipedia.org/wiki/Cytoskeleton
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19:28 < nmz787_i> http://moviecode.tumblr.com/
19:28 < nmz787_i> is there a market for long nanotubes today?
19:29  * nmz787_i thinks of zoolander
19:33 < kanzure> "Bits of Javascript/jQuery/HTML mixed with some random spam in the Doctor Who episode The Bells of Saint John. Seems to be using the Supersubs/Superfish jQuery plugin. Apparently this code uploads human souls to the cloud?"
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19:34 < nmz787_i> or would there be a market if they were available?
19:34 < kanzure> super-long carbon nanotubes would be immediately used to make supertall skytouchers
19:35 < kanzure> "In one of the sidestories of Gundam SEED, Mobile Suit Gundam SEED C.E. 73 Stargazer, a special team is testing a new mobile suit (the Gundam Stargazer). This mobile suit features artifical intelligence. Commanders are interacting with the suit via a terminal but there seems also some bits of HTML involved"
19:36 < kanzure> "When the Ninja Turtles hack Aprils computer this wall of code is displayed on her laptop. It is in fact a testing script to show how Linux error codes work."
19:36 < nmz787_i> oO i didn't get that far into the blog yet
19:37 < kanzure> "Dilbert and his coworkers attempt to update an old server which they think may break when the year 2000 rolls around. While looking at the code above, the intern Asok claims that it is COBOL code, which he learned about in history class, although the code actually appears to be C++"
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19:39 < kanzure> "Everyone knows the Anime “Serial Experiments Lain” has a famous scene with Conway’s Game of Life, the next code snippet shown is less famous for some reason and uses parts of http://ftp.sunet.se/pub/lang/lisp/code/codewalk/walk/new_walk.cl, a portable code walker for Common Lisp programs, written in Common Lisp. Since being meta is part of the series, I’d say it’s at least semi-relevant."
19:39 < kanzure> "The anime Captain Earth features code on various displays, some of the Python code in this screenshot seems to have been taken from a USB library."
19:40 < kanzure> "In RoboCop (2014), we can see that the main character is not only running Java in his brain but suddenly before aiming at the villain in the final scene, the source code [link] of a library management system comes up."
19:41 < kanzure> "The code just makes a simple 64 bit division which of course is required in order to take down the entire nuclear power plant"
19:41 < kanzure> "In Agents of S.H.I.E.L.D. Season 1, Episode 18, while Skye is wiping all record of the team from the Internet, code from CocoaGlk, an Interactive Fiction engine."
19:42 < kanzure> "Albert Gonzales is seen hacking into a credit card database using a Hello World DOS program from a “hacker” forum: http://www.gaiaonline.com/forum/c-t-tech-talk/hackers/t.53424339_16/"
19:43 < kanzure> holycrap gaiaonline.com is still around
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20:01 < kanzure> "I have an investor who is giving me a great warehouse inside the city of Bucharest to turn into a research center for this field
20:01 < kanzure> it's a natural research field for the perfusing of large animals\"
20:01 < kanzure> .wik bucharest
20:01 < yoleaux> "Bucharest was first mentioned in documents in 1459. It became the capital of Romania in 1862 and is the centre of Romanian media, culture and art. Its architecture is a mix of historical (neo-classical), interbellum (Bauhaus and art deco), communist-era and modern." — http://en.wikipedia.org/wiki/Bucharest
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20:48 < kanzure> http://philosophycommons.typepad.com/xphi/2013/02/preliminary-evidence-that-the-world-is-simple-an-exercise-in-stupid-epistemology.html
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21:43 < yashgaroth> kanzure I'm fairly sure steroids have a systemic effect, though I know you do like ultrasound microbubbles
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21:48 < fenn> just chatting with a guy at steep hill labs and he says they get 500kbase contiguous reads on the pacbio rs-II
21:49 < fenn> not sure if that means the individual reads were that long or it's assembled from smaller pieces
21:49 < fenn> maybe it's not even clear to the end user
21:49 < fenn> er, instrument runner
21:49 < yashgaroth> also accuracy
21:50 < fenn> what about accuracy
21:50 < yashgaroth> assuming it is "single molecule reads"
21:50 < fenn> the accuracy is higher or lower with single molecule reads?
21:51 < fenn> better or worse i mean
21:51 < yashgaroth> one presumes much lower
21:51 < yashgaroth> like that oxnano stuff, <90% accuracy but it's fast
21:51 < fenn> do you not sequence the original genomic dna? why would it be worse?
21:52 < yashgaroth> compared to traditional sequencing
21:52 < yashgaroth> by which I mean illumina
21:53 < yashgaroth> idk I just heard pacbio tech didn't work years ago, and haven't looked into them since
21:53 < fenn> i knew they had problems with signal to noise ratio, but that's an electronics/optics issue, not necessarily because of the single molecule aspect
21:54 < fenn> there's a tradeoff between number of parallel reads and SNR
21:54 < yashgaroth> poly-whatever repeats always tend to be an issue with pore or single-molecule stuff, though it's not insurmountable
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22:11 < jrayhawk> all the cool papers on epigenetics are using pacbio stuff these days
22:14 < fenn> i'm afraid to ask
22:22 < fenn> gnusha seems slow today
22:23 < fenn> oh maybe it's me, nevermind
22:25 < fenn> i feel like "ultrasound activated steroids" should be put on the wiki, but i don't know where to put it
22:37 < fenn> also i don't know what to say to transcriptic
22:38 < fenn> "hey dudez i've been thinking about this for about 10 years and made a halfassed attempt at a protocol specification language and built some robots and know what biology is, oh look money"
22:39 < fenn> max hodak kinda scares me
22:39 < fenn> most entrepreneurs are borderline psychotic so it's to be expected
22:40 < fenn> borderline is the wrong word, but there's definitely a trend toward hypomania
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22:47 < fenn> "Alternative serializations such as XML, Protocol Buffers or custom formats shall not be used." lol
22:49 < fenn> i hope they plan on extending their units a bit.. having to specify everything in nanometers would get tiring
22:50 < fenn> for autoprotocol.org
22:51 < nmz787> can you do fractions?
22:51 < fenn> "Measures may contain decimals"
22:53 < fenn> i'm not sure i agree with completely banning logic (if/then structures) from an experimental protocol
22:59 < fenn> just in the context of machine control, this destroys the possibility of doing closed loop anything (positioning, pH, temperature, concentration, cell count)
23:00 < fenn> you would have to rely on an instruction existing beforehand to do the thing you want, and if it doesn't exist you're screwed
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23:16 < fenn> ractopamine sounds like a great dystopian all-purpose drug of ill repute
23:16 < fenn> .wik ractopamine
23:16 < yoleaux> "Ractopamine is a feed additive to promote leanness in animals raised for their meat. Pharmacologically, it is a beta-adrenergic agonist. It is the active ingredient in products known as Paylean for swine and Optaflexx for cattle, developed by Elanco Animal Health, a division of Eli Lilly and Company, for use in food animals for growth promotion." — http://en.wikipedia.org/wiki/Ractopamine
23:18 < fenn> "The metabolic fate of ractopamine hydrochloride is similar in the target species (pigs and cattle), laboratory animals, and humans. Besides the pharmacology effect, ractopamine may cause intoxication effect; ... tachycardia and other heart rate increases, tremor, headache, muscle spasm, or high arterial blood pressure."
23:19 < fenn> "ractopamine added to feed can be distributed via the blood to the muscle tissues, where it serves as a full agonist at TAAR1. (trace amine associated receptor) A cascade of events will then be initiated to increase protein synthesis, which results in increased muscle fiber size. Ractopamine is known to increase the rate of weight gain, improve feed efficiency, and increase carcass leanness"
23:21 < fenn> "The endogenous trace amines are para/meta-tyramine, tryptamine, phenylethylamine (PEA), and para/meta-octopamine. These share structural similarities with the three common monoamines: serotonin, dopamine, and norepinephrine."
23:22 < fenn> octopamine is found in bitter orange, a weight loss supplement that has safety issues
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23:41 < fenn> Quashie: hello, and welcome?
23:41 < fenn> oh it's just reconnecting
23:44 < fenn> worms brains etc etc http://plif.courageunfettered.com/archive/wc083.gif
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--- Log closed Fri Feb 20 00:00:59 2015