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| joshcryer | I wish someone like Hitchens would advocate cryonics. | 01:04 |
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| joshcryer | He's not dead yet, but will be soon, and we keep losing great thinkers. Old age mostly, but cancer and other ailments are candidates, too. | 01:04 |
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| kanzure | hrm i wonder when genspace.org got content | 08:45 |
| kanzure | http://genspace.org/ (the nyc diybio hackerspace.. thing) | 08:45 |
| kanzure | quite a poorly made site :x | 08:46 |
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| kanzure | http://seqanswers.com/ next generation DNA sequencing community forum | 08:52 |
| kanzure | huh? there's already a humanity+ nyc 2011? bah | 08:57 |
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| kanzure | http://congenement.org/2010/12/the-congenement-will-participating-in-humanity-conference/ | 09:11 |
| kanzure | their about page gets odd: http://congenement.org/about/ | 09:11 |
| kanzure | "We are Transhumanists who believe that we must master our own evolution. It is our duty as thinking human beings to use all technological means necessary to enhance the human genome only, thus in turn leaving our bodies untainted through lesser ways like cybernetic and robotic enhancements." | 09:11 |
| kanzure | "enhance the human genome only" | 09:11 |
| kanzure | "leaving our bodies untained through lesser ways like cybernetic and robotic enhancements" | 09:11 |
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| kanzure | a brochure they are posting up at the conference: | 09:30 |
| kanzure | http://diyhpl.us/~bryan/irc/hplusbrochure.pdf | 09:30 |
| kanzure | weird how i've not been told about the "research initiative" | 09:30 |
| kanzure | the "internet of things" thing is because of david orban's company (widetag) | 09:30 |
| kanzure | opencog is because of ben goertzel | 09:30 |
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| uniqanomaly | meat-made-only humans, what a bunch of retards | 09:33 |
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| kanzure | fitzsim: http://diyhpl.us/cgit/nanoengineer but i'm trying to decide if i should fix all of the "committer" attributes (i'm listed as the committer for everything instead of the original authors) | 09:52 |
| kanzure | otherwise it's working now. | 09:52 |
| fitzsim | ok, I'll play around with the repo later today | 09:56 |
| fitzsim | you mean you're listed as the committer for the synthetic commits, right? | 09:57 |
| kanzure | no i'm listed as the committer for everything in master after my fake merge | 10:03 |
| kanzure | check it out: http://diyhpl.us/cgit/nanoengineer/commit/?id=cc5226c42f4ae0fc00db9e4cb55928883a90f1be | 10:04 |
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| kanzure | Arsenic-eating microbe may redefine chemistry of life http://www.nature.com/news/2010/101202/full/news.2010.645.html | 10:21 |
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| Utopiah | should be announced in http://www.nasa.gov/multimedia/nasatv/ soon? | 10:22 |
| kanzure | "Wolfe-Simon will be one of the participants at NASA's news conference on an astrobiological discovery on 2 December 2010.[3] Wolfe-Simon will announce that there are microorganisms in Mono Lake which use arsenic in their DNA instead of phosphor" | 10:23 |
| kanzure | guess so | 10:23 |
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| kanzure | the DOI link to science magazine doesn't really work (the one on nature.com) | 10:23 |
| kanzure | broken: http://dx.doi.org/10.1126/science.1197258 | 10:24 |
| kanzure | the paper's title is "A bacterium that can grow by using arsenic instead of phosphorus" | 10:26 |
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| kanzure | nope.. not listed here http://www.sciencemag.org/content/early/recent | 10:27 |
| kanzure | ah here we go.. her site http://www.ironlisa.com/ | 10:30 |
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| kanzure | a previosu paper about arsenic/phosphate http://www.ironlisa.com/WolfeSimon_etal_IJA2009.pdf | 10:32 |
| kanzure | recent review about arsenic microbial pathways in an astrobiological context http://www.ironlisa.com/Oremland_etal_GeomicroJournal2009.pdf | 10:34 |
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| kanzure | shadow biosphere strategies http://www.ironlisa.com/Davies_etal_Astrobio2009.pdf | 10:40 |
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| kanzure | heh she cites ellington a lot (because of his RNA world work) | 10:43 |
| Utopiah | do you have a tool to make bibliography analysis of her papers? like a distribution of journals, author, etc? | 10:44 |
| kanzure | no, i can't even get ocr to work properly on citations | 10:45 |
| kanzure | i just read the citations *shrug* | 10:45 |
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| kanzure | public video: http://www.youtube.com/watch?v=ObkqIMPmaJw | 10:50 |
| kanzure | supposedly where the pdf will be: http://www.sciencemag.org/lookup/doi/10.1126/science.1197258 | 10:50 |
| kanzure | i wonder why nasa is making a big deal out of this- we've seen a handful of different biochemistries before | 10:54 |
| phryk | mhh reminds me: what happened to TARDigrades In Space? | 11:00 |
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| kanzure | Utopiah: it's on | 11:14 |
| kanzure | http://www.nasa.gov/multimedia/nasatv/index.html?param=public | 11:14 |
| kanzure | hm.. totem can play it but not mplayer? http://www.nasa.gov/55644main_NASATV_Windows.asx | 11:21 |
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| kanzure | i don't think traditional sanger or pyrosequencing would work for this | 11:55 |
| kanzure | felisa says that the amount of phospherous in her cell culture is not enough to account for the cell growth she recorded | 11:56 |
| kanzure | OTOH, arsenic is a quasi-stable replacement for phospherous so maybe traditional phospherous-based would work | 11:57 |
| kanzure | radioactive arsenic labeling might work to characterize its nucleotides | 11:57 |
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| kanzure | posted my DNA sequencing woes: http://groups.google.com/group/diybio/browse_thread/thread/4a8a6c1b2dddc253 | 12:15 |
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| kanzure | "It takes from 170 to 250 years for Lamellibrachia luymesi to grow 2 meters in length, and even longer worms have been discovered." | 12:57 |
| kanzure | cite http://www.sciencedaily.com/releases/2000/02/000203075002.htm | 12:57 |
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| eridu | hey kanzure | 13:47 |
| eridu | why does death live in bethesda: http://fuckdeath.org/main.htm | 13:48 |
| eridu | ? | 13:48 |
| kanzure | hm that's the residence of Minda G. Nieblas | 13:52 |
| kanzure | also lockheed martin | 13:55 |
| kanzure | eridu: i thought fuckdeath.org was an immortality shock thing.. i.e. i got it through the transhumanist community originally | 13:57 |
| kanzure | but maybe it was specific to lockheed martin | 13:58 |
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| eridu | sure seems to be immortality shock | 14:09 |
| eridu | nothing even addresses lockheed martin | 14:09 |
| eridu | (as far as I can tell) | 14:09 |
| kanzure | maybe they figure lockheed martin has a lead on death's current whereabouts | 14:11 |
| eridu | he might be an employee | 14:11 |
| eridu | it*, I guess | 14:12 |
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| kanzure | deh? "Sounds good except for the fact that you're forgetting that arsenate is more reactive than phosphate which means the arsenate based backbone of DNA should be constantly getting ripped to shreds. Either this bacteria has found a way to protect the backbone or it has a hyper effective repair mechanism." | 14:42 |
| kanzure | hi delinquentme | 14:43 |
| delinquentme | kanzure, howdy :D woot for hyper effective repaid mechs | 14:43 |
| QuantumG | or the researcher is just wrong. | 14:44 |
| kanzure | copy of the nasa tv video http://www.wuala.com/danathar/public | 14:48 |
| kanzure | slashdot speculation http://science.slashdot.org/article.pl?sid=10/12/02/151204 | 14:49 |
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| kanzure | slashdot post-speculation http://science.slashdot.org/article.pl?sid=10/12/02/1934223 | 14:49 |
| kanzure | fitzsim: ok, now it's really really fixed | 15:22 |
| kanzure | http://diyhpl.us/cgit/nanoengineer | 15:22 |
| kanzure | this should be the last full-clone you'll be doing :P | 15:22 |
| kanzure | git clone git://diyhpl.us/nanoengineer | 15:25 |
| fitzsim | kanzure: cloning | 15:35 |
| kanzure | uh oh | 15:37 |
| kanzure | nevermind my "uh oh"- git log was showing a duplicate commit, that was because of -m | 15:38 |
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| fitzsim | Receiving objects: 100% (112253/112253), 371.69 MiB | 318 KiB/s, done. | 15:57 |
| fitzsim | real22m45.158s | 15:57 |
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| kanzure | fitzsim: that's significantly longer than last time.. | 16:00 |
| kanzure | last time it was 102000 objects (a factor of 10 less) and 401 MiB (about the same), 1.45 MiB/sec (4 times faster) | 16:03 |
| kanzure | ok so it just seems to be your bandwidth this time | 16:04 |
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| kanzure | fitzsim: iirc you asked for this http://diyhpl.us/~bryan/irc/nanoengineer/polosims.svn.tar.gz | 16:20 |
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| kanzure | Utopiah: what do you make of this? http://healthcybermap.org/ | 16:48 |
| kanzure | looks like they are trying to map healthcare-stuff by various document ids on a multidimensional graph | 16:48 |
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| kanzure | hmm so this is what aaron swartz has been up to http://demandprogress.org/ :/ | 16:54 |
| jrayhawk | might go a bit faster if you git gc and git pack-refs | 17:05 |
| kanzure | ok done | 17:08 |
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| kanzure | i knew andrew was crazy (as all molecular biologists) are, | 19:43 |
| kanzure | but this is insane: http://nsseff.ida.org/pages/cvs/Ellington-CV.pdf | 19:43 |
| joshcryer | how so | 19:46 |
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| kanzure | algorithmic generation of molecular structures http://willware.net/agj/ag.html | 19:56 |
| kanzure | yeah i'm not sure about the atomically-precise gear :P | 19:58 |
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| kanzure | distributed molecular modeling http://www.foresight.org/Conferences/MNT05/Papers/Ware/index.html | 20:16 |
| kanzure | old nanotech wiki http://web.archive.org/web/20070509064126/http://www.willware.net/cgi-bin/nanowiki/wiki.cgi | 20:19 |
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| fitzsim | kanzure: I noticed that the three "Moving files in preparation for merge." commits appear as the latest commits | 22:22 |
| fitzsim | kanzure: so when I select "All branches" in gitg I don't just see the master branch at the top of the list, I see 4 branches | 22:23 |
| fitzsim | kanzure: did you look at setting the date on those commits to e.g. August 10th, 2007? | 22:25 |
| kanzure | the moving-files commits that i made should have a timestamp of 2010-something but not be the HEAD of anything except sim, cad or Distribution | 22:30 |
| kanzure | my commits happened in 2010 so i think it's fine to keep those dates like that.. | 22:30 |
| fitzsim | yeah, ok | 22:30 |
| fitzsim | I switched to topological ordering and things make more sense in that mode | 22:31 |
| fitzsim | did you fix all file-move branches, or just the major merge one? | 22:32 |
| kanzure | just the merge one | 22:32 |
| kanzure | but the other branches do have history leading up to where-ever the branch point was and on down, just not where-ever they got merged back into trunk/master | 22:33 |
| fitzsim | ok, so basically all branches have first-class git branch points, but not merge points | 22:34 |
| fitzsim | let me try tracing back a moved file on a branch | 22:34 |
| kanzure | git branch points are nothing special as far as i can remember | 22:34 |
| kanzure | fitzsim: the example i've been using is sim/doc/TableforBsdata.xls on HEAD | 22:35 |
| kanzure | just remember to pass --follow to git log | 22:35 |
| fitzsim | yeah, I had been using sim/src/cube.mmp | 22:35 |
| fitzsim | and I confirmed it follows it all the way back to the initial version which is nice | 22:35 |
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| fitzsim | kanzure: tried: git log --follow cad/src/operations/undo_UI.py | 22:43 |
| fitzsim | looks like it doesn't follow the move from cad/src/undo_UI.py to cad/src/operations/undo_UI.py | 22:43 |
| fitzsim | I guess what I'm wondering is where to draw the line on history traceability | 22:45 |
| fitzsim | at one end of the spectrum is nanoengineer-fixed, where history is a wrote transcription of SVN (and cvs2svn) steps | 22:46 |
| fitzsim | at the other end of the spectrum would be making sure all file moves can be followed back, and (to that end) even making the file-subset branches into real git branches | 22:47 |
| fitzsim | e.g., where someone moved cad/src/operations/* to just src/ on an SVN branch, then worked on them | 22:48 |
| fitzsim | we'd change that to replay all the changes they made to src but on a git branch replayed to cad/src/operations/ | 22:49 |
| fitzsim | so that's at the "perfect git history" end of the spectrum | 22:50 |
| fitzsim | (I'm not considering merge point re-creation which would likely be off the end of the perfect spectrum) | 22:51 |
| fitzsim | and nanoengineer.git as it is right now is somewhere in the middle of this spectrum | 22:51 |
| fitzsim | where file tracking works on the main development lines but maybe not on individual (historical) branches | 22:52 |
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| --- Log closed Fri Dec 03 00:00:07 2010 | ||
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