--- Log opened Mon May 14 00:00:09 2012
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01:56 < jennicide> kanzure, are you awake?
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06:05 <@kanzure> jennicide: somewhat
06:10 < jennicide> If philosophers concede Bunge's binary conception of knowledge, then it follows that knowledge of multiple subsets of knowledge are commonsensical.
06:10 < jennicide> how does that read
06:10 < jennicide> If one were to accept Bunge's binary conception of knowledge, then it follows that knowledge of multiple subsets of knowledge are commonsensical.
06:10 < jennicide> is
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06:13 <@kanzure> jennicide: it reads like a philosophy paper
06:13 < jennicide> it is
06:13 < chevbird> kanzure: do you sleep?
06:13 < jennicide> If one were to accept Bunge's binary conception of knowledge, then it follows that knowledge of multiple subsets of knowledge is commonsensical as it is not scientific. As such, the argument should be framed to appeal to an individual's commonsense.
06:17 <@kanzure> chevbird: only with women, etc. etc.
06:18 <@kanzure> jennicide: do you mean "is as commonseniscal as not scientific"?
06:19 < jennicide> If one were to accept Bunge's binary conception of knowledge, then it follows that knowledge of multiple subsets of knowledge is commonsensical, because it is not scientific knowledge. As such, the argument should be framed to appeal to an individual's commonsense.
06:20 <@kanzure> "the argument" being.. accepting his notion?
06:21 < jennicide> oh
06:22 < jennicide> As such, the argument for philosophically derived knowledge should be framed to appeal to an individual's commonsense.
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06:28 <@kanzure> "Unlike scientific knowledge, an argument for philosophically derived knowledge-- such as Bunge's binary conception of knowledge-- should be framed to appeal to an individual's commonsense."
06:29 < jennicide> bunge's conception of knowledge doesnt really include a space for philosophically derived knowledge
06:29 < jennicide> not implicitly
06:29 < jennicide> im just kind of shoe horning it in
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06:33  * nsh offers around a plate of complementary hyphens
06:36 <@kanzure> nsh: what's up? i saw your distress signal the other day
06:38 < nsh> dealing with a few health issues
06:38 < nsh> gam zeh ya'avor
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10:16 <@kanzure> win 6
10:16 <@kanzure> dasdasfadasdasdfasda
10:16 <@kanzure> jrayhawk: i've been using p/n i swear
10:17 < jrayhawk> ha ha ha
10:18 <@kanzure> maybe i should tie it to some financial incentive
10:19 <@kanzure> every time i use /win, irssi will transfer money from my account to yours
10:19 <@kanzure> however, this might just incentivize me to not switch windows at all
10:20 < jrayhawk> You can also use /window move to shuffle your most-used windows closer to eachother.
10:20 <@kanzure> yep, i have them clustered
10:20 <@kanzure> i try to avoid moving over 'active' windows that i don't intend to immediately respond to
10:20 <@kanzure> this way, the notifications are still pending
10:21 < jrayhawk> alt-1 through alt-9 are also faster than /win
10:22 <@kanzure> alt-n is tied into my gnome-terminal session
10:22 < jrayhawk> assuming you're not foolishly attempting to use screen
10:23 <@kanzure> i suppose i should setup different gnome-terminal profiles with different keyboard bindings, one for the session with ssh/irssi
10:23 < jrayhawk> window management functions should really use Super_L instead of alt
10:24 <@kanzure> true i sorta ignore that key for some reason
10:24 <@kanzure> this is stupid, if i had enough monitors i wouldn't need hidden windows
10:24 < jrayhawk> i like that attitude
10:26 <@kanzure> i want something like this for rotating out a certain monitor in my 10-set:
10:26 <@kanzure> http://www.youtube.com/watch?v=2L03za762jA#t=2
10:28 <@kanzure> possibly better example: http://www.youtube.com/watch?v=ol_sFbcKekM#t=16
10:31 < jrayhawk> http://www.ergotron.com/ stepper motors+ergotrons+face tracking to keep the monitors perfectly aligned
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10:35 < nmz787> i read something crazy eariler about what i think was implying something like quantum entanglement between DNA/genes, their mRNA, and subsequently proteins... as well as between chromosomes of a multicellular body
10:35 < nmz787> http://www.emergentmind.org/gariaevI3.htm
10:36 < nmz787> i have no idea if its prodigal genius that most normal ppl couldn't possibly understand for another 100 years
10:36 < nmz787> or if its just quackery
10:38 <@kanzure> jrayhawk: http://www.forecast-consoles.com/products/sightline/mounting_options is a wall-rail mounting system, but i'm not convinced
10:39 <@kanzure> jrayhawk: i'm not satisfied until individual monitors are under mechanical control and can be switched out via the keyboard
10:39 < nmz787> "Controlling metabolism by IR laser beams and DNA functioning
10:39 < nmz787> by maser beams?"
10:39 < nmz787> sect 6, pg 34 http://www.emergentmind.org/PDF_files.htm/conscholo0302.PDF
10:40 < jrayhawk> why do you want to swap them out, anyway
10:41 <@kanzure> jrayhawk: i have a limited field of vision. i could rotate my chair and possibly surround myself with monitors, but there is still a physical limit to how many monitors can be stuffed in front of me
10:42 <@kanzure> i suppose at that point, virtual desktops are okay :/
10:43 <@kanzure> http://www.stocktradingtogo.com/wp-content/uploads/2007/09/multi-monitor-setup.jpg identify the blue bottle!
10:43 < nmz787> how big and how many panels you have now?
10:44 <@kanzure> sadly i am down to two, but at one point i had seven-ish
10:44 <@kanzure> oh, sorry, three right now
10:44 < jrayhawk> http://www.omgwallhack.org/home/jrayhawk/img/hovel/20120512_008.jpg NOT ENOUGH
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10:45 <@kanzure> i spy with my little eye.. a bad taste in shoes
10:45 < ThomasEgi> epic picture
10:46 < nmz787> The basic theme of this evolution would be the gradual de-entanglement.
10:46 < nmz787> The ancient world has survived in fairy tales. In this world remote mental
10:46 < nmz787> interactions like telepathy, remote healing, and witchcraft were every-day life.
10:46 < nmz787> Incredible-to-us physical feats like building of pyramids might have been made
10:46 < nmz787> possible by the liberation of energy and coherent momentum in the formation of
10:46 < nmz787> collective bound state entanglement. The rhytmic work songs helping to gener-
10:46 < nmz787> ate body synchrony are a remnant from this period, but are not sung in modern
10:46 < nmz787> IT companies.
10:47 < nmz787> hah, kanzure, we need a rhythmic work song
10:47 <@kanzure> sounds like quackery to me
10:48 < jrayhawk> i liked those composite-toe shoes
10:48 <@kanzure> also, nmz787 was kind enough to fetch that DNA stability paper
10:48 <@kanzure> http://diyhpl.us/~nmz787/instability%20and%20decay%20of%20the%20primary%20structure%20of%20DNA.pdf
10:50 < nmz787> Inhibition by various neurotransmitters could be seen as a measure for the degree of de-entanglement. Inhibition acts as the filter, which de-entangles the brain from other brains and the body from the bodies of other life forms. During hallucinatory experiences, generated by say drugs, inhibition "fails". The degree of inhibition indeed increases, as one climbs along evolutionary tree and in human brain most of the neural acti
10:50 < nmz787> (this paper mentioned the other paper i posted first, which talks about bio-entanglement on different abstract levels)
10:51 < nmz787> (i.e. cell to cell, cell of multicellular organism being able to regenerate another multicellular organism... gene to RNA to protein)
10:52 <@kanzure> "It is therefore as incredible as the report of bacterial growth at 250 degrees Celsius" neat
10:52 < nmz787> (though it was also implying that they were physically entangled via quantum mechanics as well as abstractly/ideologically entangled)
10:52 < Mariu> won't those HDDs screw those CRT monitors ?
10:52 <@kanzure> wait, i'm pretty sure we know of some bacteria that can grow at atleast 50C,right?
10:53 < nmz787> deep sea thermal vents
10:53 < nmz787> dunno what temp they are
10:53 <@kanzure> yeah.. but that's def. not 250C
10:53 <@kanzure> oh geeze.. 407C
10:53 < nmz787> wiki says thermophiles up to 122C
10:54 <@kanzure> maybe those thermal vent thermophiles were only recently discovered in the 90s
10:55 <@kanzure> nope.. "Hyperthermophiles were first discovered by Thomas D. Brock in 1969, in hot springs in Yellowstone National Park, Wyoming."
10:55 <@kanzure> "An extraordinary heat-tolerant hyperthermophile is the recently discovered Strain 121[2] which has been able to double its population during 24 hours in an autoclave at 121°C (hence its name); the current record growth temperature is 122°C, for Methanopyrus kandleri."
10:55 < jrayhawk> Mariu: not a whole lot; hard drive magnets are pretty small. far more annoying is poorly shielded monitors interfering with eachother with radiation.
10:55 <@kanzure> "However, it is thought unlikely that microbes could survive at temperatures above 150°C, as the cohesion of DNA and other vital molecules begins to break down at this point"
10:56 < Mariu> got it, jrayhawk
10:56 < nmz787> kanzure: 2.  Baross J A ,  D e m i n g  J W  (1983)  G r o w t h   o f  " b l a c k  s m o k e r "  b a c t e r i a  a t  t e m p e r a t u r e s   o f  a t  l e a st  250"C.  N a t u r e   ( L o n d o n )   3 0 3 : 4 2 3 - 4 2 6
10:57 < jrayhawk> In general, Sonys and Viewsonics are pretty good at shielding both in and out.
10:57 < nmz787> kanzure: Ba ros s  JA,   D e m i n g  JW,   Be cke r  R R   (1984)  E v i d e n c e  f o r  m i c r o b i a l  g r owt h   in  high-pr e s sur e , h i g h - t e m p e r a t u r e   e n v i r o n m e n t s .   In:   K.tug M J ,   R e d d y   C A  (eds)  C u r r e n t   p e r s p e c t i v e s   in  m i c r o b i a l  e cology.  A m   Soc  Mi c r o b i o l ,  Wa s h i n g t o n ,   DC ,   pp  1 8 6 - 1 9 5
10:57 <@kanzure> ah i see
10:58 <@kanzure> jrayhawk: i never had trouble with my ancient viewsonics. </anecdote>
10:59 <@kanzure> bosslab should totally team up with "boston science club for girls"
10:59 < nmz787> http://www.nature.com/nature/journal/v303/n5916/abs/303423a0.html
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11:01 <@kanzure> nmz787: was it disproven?
11:03 < nmz787> http://diyhpl.us/~nmz787/growth%20of%20black%20smoker%20bacteria%20at%20temperatures%20of%20at%20least%20250%20celsius.pdf
11:03 <@kanzure> oh neat, we've cultured bacteria from a depth of 10,476 meters? go science..
11:10 < jrayhawk> Degaussing poorly shielded monitors right next to eachother is fun, though.
11:11 < Mariu> :p
11:12 < nmz787> http://matpitka.blogspot.com/
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11:39 <@kanzure> http://www.kickstarter.com/projects/joylabs/makey-makey-an-invention-kit-for-everyone
11:40 <@kanzure> hrm. this feels like a media lab thing.
11:42 < klafka1> oh of course
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11:43 < delinquentme> hio all~ =]
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11:50 < Mariu> hey =]
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11:57 < nmz787> i guess this disproves all of those water memory and homeopathy papers http://www.nature.com/nature/journal/v434/n7030/full/nature03383.html
12:14 < klafka1> homeopathy was disproven? holy crap
12:22 < nmz787> I just don't understand how people can uphold this stuff with words, rather than with physical proof
12:23 < nmz787> like all this was done ~10 years ago http://en.wikipedia.org/wiki/Water_memory#Subsequent_research
12:23 < nmz787> and yet i'm finding homeopathy referenced in recent articles (which are pretty weird/farout articles in general)
12:24 < jrayhawk> homeopathy is a network of related observations and proposed mechanisms; a mechanistic study is not going to "disprove" the observational portions
12:29 < chris_99> huh
12:31 < chris_99> what observational portions
12:36 < jrayhawk> http://scholar.google.com/scholar?q=homeopathy+meta-analysis
12:37 < jrayhawk> though i don't know specifically what portions klafka1 was attempting to invoke with his rather uncharitable leap
12:37 < chris_99> i'm confused what you're trying to say jrayhawk, you don't think it can be disproved
12:37 < chris_99> ?
12:38 <@kanzure> "water memory"?
12:38 < chris_99> the idea that water remembers what chemicals it mixes with, utter BS
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12:45 < jrayhawk> While I do find it highly unlikely that a body of evidence as large as homeopathy, even if it is the product of bias, will ever be "disproven", that belief doesn't seem particularly relevant to the conversation at hand...?
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12:47 < chris_99> i don't know what is the conversation at hand
12:47 < chris_99> i've just joined
12:47 < jrayhawk> Nah, you caught everything.
12:48 <@kanzure> 'disasterbationists'
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12:49 <@kanzure> hi mensch
12:49 < mensch> Hi
12:49 <@kanzure> mensch: are you from bosslab?
12:50 < mensch> No
12:50 < mensch> But I am in the Boston area...
12:50 <@kanzure> ah. might be worth checking out bosslab.org then
12:50 < mensch> Yes, I think so, thanks for the link haha
12:51 <@kanzure> oh god they updated their site. it used to be better.
12:51 <@kanzure> now it's some tumblr crap
12:51 < mensch> Yeah, it looks pretty preppy
12:52 <@kanzure> i swear just a week ago it was legit :(
12:53 <@kanzure> mensch: http://web.archive.org/web/20110621191534/http://bosslab.org/
12:53 < mensch> Oh, wow, that looked pretty decent.
12:54 <@kanzure> yeah.. who the hell decided to go with tumblr instead of that?
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13:03 < docl> http://lesswrong.com/lw/8f4/neil_degrasse_tyson_on_cryonics/6l8r
13:05 <@kanzure> please describe your links when they have awful urls
13:05 < docl> me doing a data dump on the cryoprotectant toxicity issue.
13:05 <@kanzure> pookie isn't smart enough to figure out when and when not to do that :(
13:05 <@kanzure> i see
13:05 <@kanzure> docl: how experienced are you with vitrification? i mean, have you done tissue samples?
13:05 < docl> not personally. this is all second-hand.
13:06 < docl> I know chana de wolf personally, she does it pretty often. I've watched her perfuse rats.
13:06 <@kanzure> i met aschwin's brother-in-law at a bus stop in austin, texas once
13:06 <@kanzure> it was pretty awkward
13:07 < docl> heh, her family's fundamentalist from her descriptions.
13:07 < docl> oh wait, you said aschwin
13:07 <@kanzure> yes, her husband's brother-in-law (i forget the exact relation)
13:07 < docl> chana's brother then?
13:08 <@kanzure> that's one possibility
13:08 < docl> austin texas, sounds like it.
13:08 < docl> heh, what was he like?
13:09 <@kanzure> gangly, sorta proud that he had something topical to suggest
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13:10 < docl> how did you find out he was aschwin's brother in law?
13:11 <@kanzure> at the time, fenn was living with me and we would ride buses to places and be talking about random transhumanist projects
13:12 < delinquentme> actually thats a good point ... Im assuming that no one has cryoed a mouse and brought it back
13:12 < docl> kanzure: so you had a high enough profile, and he was all 'hey my brother-in-law is a transhumanist'?
13:12 <@kanzure> delinquentme: there are various tissue/ice problems, some of which have been resolved by proper temperatuer curves
13:13 < delinquentme> is this in the vitrification process or the thawing?
13:13 <@kanzure> docl: something like that, he said, "oh, hey, i think my inlaw/brother does that ... yeah, aschwin de wolf"
13:13 <@kanzure> in san francisco i would expect something like that, but not in austin
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13:16 < docl> delinquentme: both. if you vitrify (using high concentrations of CPA) that postpones the damage in a sense, as the worst of it (I believe) happens during the thawing phase.
13:18 < docl> basically the cryoprotectants are toxic, but that only matters if the tissue is warm and exposed to them for a long enough time.
13:18 < docl> also it matters if the concentration is high. lower concentration means more time is safe.
13:19 < docl> ice-blockers such as antifreeze proteins or certain polymers can prevent freezing with lower concentrations of cryoprotectant
13:19 < docl> the trouble is these do not penetrate the cells well
13:20 < docl> you might be able to work around by making the cell produce an antifreeze protein or perhaps a sugar like trehalose
13:20 < docl> Tardigrades can survive LN2 immersion because they produce trehalose inside their cells.
13:21 < docl> http://en.wikipedia.org/wiki/Tardigrade
13:22 < chris_99> isn't glycerol one of the chemicals they use in cryogenics
13:22 <@kanzure> Juul: did you get around to doing the antifreeze protein project?
13:25 < klafka1> hey are parameters coming into classes in python pass by value or reference?
13:25 <@kanzure> klafka1: reference
13:25 <@kanzure> klafka1: from copy import copy, deepcopy
13:30 < klafka1> gotchya
13:30 < klafka1> hey also if you have a variable without a self inside a class method, that's just a variable scoped to the method right?
13:30 < klafka1> but if you have self. it's a class instance variable right?
13:31 <@kanzure> correct
13:32 < klafka1> ok cool
13:33 < chris_99> are there any "must read" books on transhumanism
13:33 <@kanzure> chris_99: no, they are all terrible
13:33 <@kanzure> in fact, you should *not* read them
13:33 < chris_99> heh
13:34 < klafka1> HAHAH
13:35 <@kanzure> even that one 'diy biohacking' book is questionable
13:36 < chris_99> which one?
13:36 <@kanzure> http://www.amazon.com/Biopunk-Scientists-Hack-Software-Life/dp/1617230022
13:36 <@kanzure> oops i mean
13:36 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/biopunk.pdf
13:36 < chris_99> ive read that
13:37 <@kanzure> 'the singularity is near' is the standard staple book that everyone recommends, but it's not particularly useful
13:37 < chris_99> i've read most of that too
13:37 <@kanzure> 'biology is technology' is the one that people recommend if they enjoy rob carlson
13:38 <@kanzure> but you can probably just get the same content out of his blog
13:38 < docl> chris_99: yes, glycerol is one of the cryoprotectants they use
13:39 < docl> terminology nitpick: cryonics (or cryobiology), not cryogenics
13:39 <@kanzure> terminology nitpick accepted
13:39 < chris_99> aha. i find it difficult to imagine that the glycerol or whatever
13:39 < chris_99> could permeate the entire brain
13:39 < docl> the circulatory system is used.
13:40 < docl> the brain is fairly well vascularized, as organs go
13:40 < docl> but it does take time to permeate. especially if you want to prevent osmotic shock.
13:40 < chris_99> hmm, but each cell needs to absorb it right?
13:40 < docl> yes. but these are small molecules that penetrate very well.
13:41 < docl> DMSO, glycerol, ethyline glycol
13:41 < chris_99> has there been any sucessful cases of cryobiology with mammals
13:41 <@kanzure> there has been some tissue experiments, and an old cat/rabbit brain
13:42 < docl> with tissue samples, sure... not whole mammals, not at cryonics temperatures at least.
13:42 < chris_99> aha
13:42 < docl> mammals have been brought to below zero centigrade and brought back though.
13:43 < docl> part of the problem is getting the cryoprotectant out again without giving it time to have toxic effects on cells. that is a part that might go away with advanced nanotech (along with certain others).
13:44 < chris_99> oh i didn't realise you had to extract it again
13:44 < chris_99> is glycerol toxic?
13:44 < docl> yeah, they all are in the concentrations needed to prevent ice formation.
13:45 < docl> however they interfere with each other's toxicity to some extent, so mixtures are better than any one of them
13:45 < chris_99> interesting
13:46 < docl> http://en.wikipedia.org/wiki/Cryoprotectant
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13:57 < nmz787> I started the conversation on homeopathy through crazy fringe/pseudo/too-complex-to-be-proven papers I stumbled across
13:57 < Mokbortolan_> I use a homeopathic remedy to successfully treat the symptoms of pompholyx
13:58 < Mokbortolan_> do I doubt the "science"? Yes.  Do I care now it works? No.
13:58 < Mokbortolan_> it's probably placebo, but I don't care, it works
13:58 < Mokbortolan_> and is cheap
14:00 < Mokbortolan_> Would I trust the health of a seriously ill child to homeopathy? no
14:01 < docl> trouble with placebo is there's hardly any room for improvement... I mean, what are you gonna do, make it more convincing?
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14:14 < docl> I'm trying to think where the low-hanging fruit is for cryo research... maybe cultured neurons could be induced to produce trehalose or antifreeze proteins, thereby reducing cryoprotectant requirements.
14:16 < Mokbortolan_> docl: yeah, but that doesn't mean you can't use them
14:17 < nmz787> why not Mokbortolan_?
14:21 < Mokbortolan_> what?
14:22 < Mokbortolan_> why not what?
14:22 < Mokbortolan_> why doesn't that mean you can't use them?  Why does (not) that mean that you can (not) use them... why does that mean you can use them.... because they work in some cases?
14:29 < nmz787> why cant you use them?
14:29 <@kanzure> docl: antifreeze proteins would be worth studying, yes
14:29 <@kanzure> docl: some of the equipment could be simplified
14:29 < delinquentme> docl, is there use for frozen body parts?
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14:30 < delinquentme> certainly hearts but I dont think you've got that working yet
14:30 < delinquentme> sooo what about arterial valves?
14:30 < delinquentme> maybe those dont decompose
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14:30 < delinquentme> so something more complex ... umm eyes?
14:30 <@kanzure> delinquentme: um.. what are you talking about?
14:30 < delinquentme> correct me if im wrong but thats just a sweet spot issue
14:30 < docl> kidneys maybe
14:30 < delinquentme> kanzure, what to cryo thats 'low hanging fruit'
14:31 <@kanzure> delinquentme: organs aren't low-hanging fruit
14:31 < delinquentme> docl, i think kidneys are pretty complex no?
14:31 < delinquentme> *nods*
14:31 <@kanzure> "is there a use for frozen body parts?" what kinda question is that
14:31 < delinquentme> kanzure, you talk too much
14:31 <@kanzure> like, are you asking if anyone has done it before?
14:31 < docl> delinquentme: I'm trying to think of what experiments can be done on a shoestring to improve the state of the art
14:31 <@kanzure> docl: antifreeze protein stuff can be done for <$10k
14:31 < delinquentme> docl, well plant cells are cheap as hell
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14:32 < delinquentme> and kanzure it was meant as rhetorical
14:32 <@kanzure> no it wasn't
14:33 < delinquentme> kanzure, now you're being retarded
14:33 < delinquentme> i said it. how would I not have the authority to say whether its rhetorical or not?
14:33 <@kanzure> "is there use for frozen body parts?" how is that rhetorical
14:33 < delinquentme> because it obviously leads to the conclusion of YES
14:33 < delinquentme> there is
14:33 < docl> well, neurons are the most important-to-cryonics.
14:33 <@kanzure> why the hell ask it then?
14:33 < delinquentme> *stupidity abounds today*
14:34 < delinquentme> kanzure, why does anyone ask a rhetorical question?
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14:34  * kanzure feels better
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14:34 < docl> :)
14:34 < delinquentme> nice
14:34 < delinquentme> kanzure, listen man is that how you're going to run the channel
14:34 < delinquentme> not funny not cute
14:34 < delinquentme> not a joke
14:34 < delinquentme> dont be a prick
14:35 <@kanzure> i will be as big of a prick as i want to be
14:35 < delinquentme> dont be
14:35 < delinquentme> because acting smart gets you nowhere
14:35 <@kanzure> look, do you have any relevant cryonics experience or are you just talking out of your ass
14:35 < delinquentme> esp when you're just trying to fucking nitpick
14:35 < delinquentme> kanzure,  i was talking to docl  on what the low hanging fruits are
14:35 < delinquentme> now if you had read the thread you'd have known that
14:35 <@kanzure> organs aren't low-hanging fruit
14:36 < delinquentme> instead you just want to fire off shit
14:36 < delinquentme> again
14:36 < delinquentme> rhetorical question
14:36 < docl> yeah organs aren't low-hanging fruit. they are a possible down-the-line product.
14:36 < delinquentme> docl, so yeah the question is just which of these things are sufficiently simple
14:37 < delinquentme> that you can apply it
14:37 <@kanzure> delinquentme: you are banned from asking rhetorical questions for the time being, i might reconsider later
14:37 < delinquentme> so like noses you can freeze and have good luck .. but IDK if there is a market for noses
14:37 <@kanzure> (you might find it an interesting challenge even)
14:37 < delinquentme> kanzure, fuck you
14:37 <@kanzure> docl: whatdduya think about ken hayworth's brainpreservationprize stuff
14:37 <@kanzure> i haven't heard from him in a while
14:38 <@kanzure> oops i mean his http://brainpreservation.org/ stuff
14:38 <@kanzure> the la biohacking group was doing some neural tissue cultures, but they don't have any cryoprotectant results yet
14:38 < docl> hmm... I am not so sure about the connectome hypothesis. talking to kalla724 on lesswrong makes me think there are solvents you'd be losing that might encode important info
14:39 <@kanzure> what do you consider to be the connectome hypothesis? that things are connected?
14:39 < docl> so you would probably need cryo, not chemical fixation.
14:39 < docl> yeah
14:39 < eudoxia> that the connectome is all that one has to preserve for cryonics to succeed?
14:39 < docl> well, that the connections are the main thing
14:39 <@kanzure> i think it's pretty well proven that neurons are connected and that synpases are real
14:39 <@kanzure> ah
14:40 <@kanzure> docl: are you familiar with 3scan.com?
14:40 < docl> no
14:40 <@kanzure> they are doing destructive scanning of microtome slices
14:40 < docl> interesting
14:40 <@kanzure> well, they are also making microtome slices and catching the connectivity as they cut
14:40 <@kanzure> then they do image analysis to reconstruct the individual neurons
14:41 <@kanzure> docl: i was talking with them recently, and they might be using http://github.com/kanzure/netmorph soon to generate sample slices
14:41 <@kanzure> and then run it through their image processing code
14:42 <@kanzure> to confirm that they can extract the exact networks
14:43 <@kanzure> docl: does kalla724 have a specific list of things that he'd want to keep? "solvents" is p. vague, any cell will have some ph balance from random crap floating around
14:44 < docl> haven't seen anything specific yet :(
14:45 < docl> http://lesswrong.com/lw/8f4/neil_degrasse_tyson_on_cryonics/6l0k
14:45 < docl> In general, uploading a C. elegans, i.e. creating an abstract artificial worm? Entirely doable. Will probably be done in not-too-distant future.
14:45 < docl> Uploading a particular C. elegans, so that the simulation reflects learning and experiences of that particular animal? Orders of magnitude more difficult. Might be possible, if we have really good technology and are looking at the living animal.
14:45 < docl> Uploading a frozen C. elegans, using current technology? Again, you might be able to create an abstract worm, with all the instinctive behaviors, and maybe a few particularly strong learned ones. But any fine detail is irretrievably lost. You lose the specific "personality" of the specific worm you are trying to upload.
14:46 <@kanzure> someone has already done a c. elegans upload project
14:46 <@kanzure> very disappointing that nobody remembers it
14:46 < docl> I get the idea we're in deeply hypothetical realms here still
14:46 < eudoxia> wasn't the nematode upload done in 1997
14:46 <@kanzure> eudoxia: ancient news by now :(
14:46 < eudoxia> maybe it was a species-generic thing but I suppose it counts
14:47 <@kanzure> eudoxia: to be fair, it wasn't a microdialysis upload, maybe that's why people choose not to remember it
14:48 <@kanzure> eudoxia: also, that was before NEURON existed (i think?), so maybe they still have the data and would be willing to release it
14:48 <@kanzure> actually, why the hell don't i have a backup of all their data
14:48 < eudoxia> I backed up the electron micrographs but haven't found a connectivity map or whatever it's called
14:49 <@kanzure> docl: "A collaboration led by Eugene Leitl. Its aim is to achieve the 3D reconstruction and functional emulation of individual specimens of C.elegans from scanned images of the vitrified original."i
14:49 <@kanzure> http://web.archive.org/web/20070814044636/minduploading.org/research/data.nematodeupload.html
14:49 <@kanzure> eudoxia: you have all of those?
14:50 < eudoxia> except the ones that are corrupt: PAG726L, 746, 745, 755, 760, 766 and 767
14:50 < docl> cool, Eugene Leitl is on cryonet
14:52 <@kanzure> docl: he's also in here occassionally ;) he runs 'transhumantech', a mailing list he spams with somewhat-better-than-terrible transhumanist news clippings
14:52 <@kanzure> eudoxia: can you email me explaining the situation? i want to loop in a few people who can help
14:52 <@kanzure> eudoxia: i mean, with respect to the integrity of the files
14:53 <@kanzure> also, do you have a web host that can store those files? or would you like a hosting account from me to place that data temporarily?
14:53 < eudoxia> I have most of my dropbox free, and these are ~820 MB, I can upload them
14:54 <@kanzure> ok lemme know the link when it's done, and we can loop in eugen leitl and the others
14:54 < eudoxia> as for the integrity, I'm not sure: Image viewers tell me they can't recognize the format
14:54 <@kanzure> probably eugen/3scan/randal/some other people we can blame
14:54 <@kanzure> oh, i'll check them then..
14:55 < eudoxia> I guess it could be just corrupt header data
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14:56 <@kanzure> are your files from internet archive? if so i can probably grab those real quick
14:56 < eudoxia> yeah
14:56 <@kanzure> yashgaroth: vitrification!
14:56 < yashgaroth> oh boy
14:57 <@kanzure> "2012-05-14 14:57:46 ERROR 502: Bad Gateway."
14:58 <@kanzure> first one that works is PAG722L.png :(
14:58 < eudoxia> the whole ABC group is gone
14:58 < eudoxia> what do ABC and PAG mean?
14:59 <@kanzure> 13.9 MB/sec
15:01 <@kanzure> ok i got it
15:02 <@kanzure> http://diyhpl.us/~bryan/papers2/neuro/nematodeuploadproject
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15:06 < eudoxia> i thought about writing a neurite tracer with that data but then I remembered I don't know wha parts of the images are what :)
15:09 <@kanzure> the reason the internet archive doesn't have A.jpg is because it's 1nm/pixel
15:12 < chevbird> any biochem nuts in here?
15:13 < Mokbortolan_> hah
15:13 < Mokbortolan_> probably better to ask who isn't...
15:13 < Mokbortolan_> smaller list
15:13 < yashgaroth> what sort of biochem
15:14 < chevbird> transposase
15:14 < chevbird> specifically how it dissociates after done cleaving
15:14 < yashgaroth> oh good, I thought you meant like krebs cycle biochem
15:14 < Mokbortolan_> probably just a text saying "I'll call you.."
15:14 < docl> wow, eugen just burst my bubble on whether things can be nanorepaired in a vacuum
15:14 < docl> http://iubio.bio.indiana.edu:7131/bionet/mm/neur-sci/1996-August/025042.html
15:15 < docl> Vitrified
15:15 < docl> tissue does not take vacuum too well (sublimates), but nanocritters need
15:15 < docl> very hard vacuum to operate.
15:15 < eudoxia> well technically
15:15  * docl was hoping vitrified tissue is fine in a vacuum
15:15 < eudoxia> mechanosynthesis needs UHV, machines made out of mechanosynthesized diamond could work outside of UHV
15:15 < docl> point
15:15 < yashgaroth> well I'd imagine it depends on the specific transposase, but generally the final site wouldn't be recognized by the enzyme and it'd just fall off
15:16 <@kanzure> machines could have internal UHV chambers, and probably for much less energy than a giant UHV chamber
15:16 <@kanzure> docl: for mechanosynthesis.. http://github.com/kanzure/nanoengineer#readme
15:17 < chevbird> yashgaroth: tn5 and others, but in vitro ive been seeing that its pretty hard to "knock off" of the dna
15:17 < docl> so maybe the vitrified tissue could be kept out of UHV whereas the parts of the micron-range nanoagents are kept under UHV?
15:17 < yashgaroth> even if you heat it or add a detergent or something?
15:18 < chevbird> and i cant find much info in the patent
15:18 < yashgaroth> you don't need to know how it works to patent it :/
15:19 < chevbird> well, heating is a no go, right? cause there's an overhang that gets left between the mozaic end and your dna
15:19 < chevbird> so you dont want to play too close to t50
15:19 < chevbird> the detergent, maybe
15:19 < yashgaroth> or high salt or something
15:19 < yashgaroth> then again a lot of that will lower the Tm anyway
15:20 < chevbird> the salt may or may not work (i suspect it does but nothing for sure yet)
15:20 < chevbird> im more interested in the why
15:20 < chevbird> rather than guessing
15:20 < chevbird> and i cant find much material
15:20 < yashgaroth> hmm well let me take a look around
15:21 < chevbird> and very true.  im almost sure the patent was filed because "oh shit this might be useful if someone understands it"
15:21 < yashgaroth> generally one expects transposases to be slow by default
15:21 < chevbird> sure
15:21 < yashgaroth> heh most gene patents are just "haha I sequenced it screw you give me money for the next 20+ years"
15:23 < docl> eudoxia: I wonder how high of a probability I should be giving to diamond mechanosynthesis not needing UHV.
15:23 < eudoxia> docl: it could work on noble gases (herp derp) and for some reason I seem to remember someone saying it could work on water
15:25 < chevbird> im really trying to avoid reading a paper (laziness), but i think its unavoidable
15:25 < yashgaroth> hell it might just sit there until a polymerase knocks it off
15:26 < chevbird> perhaps
15:26 < chevbird> i know it's not Pol I though
15:26 < chevbird> cause ive tried that
15:29 < yashgaroth> wait do you mean cleavage as in when it excises the transposon, or after insertion into a target strand?
15:30 < chevbird> so youve got some dsDNA and your Tnp, it goes in, associates, cleaves and then just sits there
15:31 < yashgaroth> maybe it's looking for a suitable integration site
15:32 < chevbird> the active site is pretty unspecific if thats what youre getting at
15:33 < yashgaroth> ah okay then...you could also try gel separation, and why does it matter too much if the strands melt? they should figure out how to reassociate
15:34 < nmz787_> Chevbird is this something you're doing?
15:34 < chevbird> well i'm looking to preserve unique molecules and i'm not sure i want to introduce more error than i can get away wirh
15:35 < chevbird> by pol or otherwise
15:35 < yashgaroth> you're afraid it'll start polymerizing if you melt the strands?
15:36 < chevbird> im going to have to pol and phosporylate later anyway to fill in the gaps, so id rather just fill in the small nicks then go the entire stretch of the molecule
15:38 < chevbird> im not afraid of it happening right then, but if things become mostly ssdna then i'm not looking too good for downstream applications
15:38 < nmz787_> What are you asking? It will dissociate because of a confrontational change
15:38 < yashgaroth> anything below a few thousand basepairs should re-anneal no problem
15:39 < nmz787_> Or after a enzyme-substrate intermediate bond is cleaved
15:40 < chevbird> nmz787_ thats not what i've been seeing.  mind you this is not wildtype tnp
15:40 < chevbird> yashgaroth yea i'm going to be about 10kb
15:41 < yashgaroth> that should anneal fine, unless you've got a bunch of gDNA sitting around in the reaction
15:41 < nmz787_> I'm just not sure what your question is.
15:42 < chevbird> yash: hopefully not but not sure.  would be interesting to qc and find out
15:42 < yashgaroth> maybe try adding EDTA? though I don't know if the metal ions are relevant to the DNA binding per se or just the cleavage
15:42 <@kanzure> nmz787_: started with how transposase dissociates from dna
15:45 < nmz787_> Right but thats all i saw about it
15:46 < nmz787_> Chevbird didnt say they were doing experiments, just studying.... what the goal is
15:47 < chevbird> here's the idea http://www.google.com/patents/US20100120098?printsec=abstract#v=onepage&q&f=false
15:48 < chevbird> if you look at figure 2 it magically dissociates with a  black arrow
15:48 < chevbird> im all out of black arrows
15:48 < chevbird> so idk
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15:48 < yashgaroth> Transposome™ pfft
15:48 < chevbird> haha
15:50 < chevbird> i do like the edta idea
15:53 < nmz787_> Hows this better than sonication then adapter ligation?
15:53 < chevbird> time
15:53 < nmz787_> Or using a covaris g-tube
15:53 < chevbird> time
15:54 < chevbird> not really a gtube fan
15:55 < yashgaroth> so the downstream application is sequencing?
15:55 < chevbird> but "better" depends on who you are and how many samples you're running, how good you analysis is blah blah blah
15:56 < chevbird> http://www.genomeweb.com/sequencing/transposase-library-prep-method-promises-easy-automation-less-dna-input
15:56 < nmz787_> Does it mention a restriction site in the transposon? It could be a re fused to the trabsposase
15:57 < chevbird> i dont believe so
15:57 < chevbird> by restriction site you meannnnnnn a non-random target?
15:58 < nmz787_> Yeah, if the removed peripheralbindin domains and fused it to the transpoaase to localize it binding domain
15:58 < nmz787_> Shit
15:58 < nmz787_> Thats outta order
15:59 <@kanzure> i think nmz787_ is on a mobile phone
15:59 < chevbird> im thinking rotary phone
15:59 < nmz787_> If they removed the REs peripheral binding domain(s), relyin on transposase for localization to RE site
16:02 < chevbird> looking for an animation, found this instead.  win  http://www.youtube.com/watch?v=Nv74Ks1Nhlo&feature=player_embedded
16:16 < chevbird> anyway, thanks for the chat, i find it interesting
16:21 < yashgaroth> it's an intriguing problem...also maybe a pH change, but high salt is probably your best bet
16:28 < chevbird> shifting gears...
16:29 < chevbird> im planning on joining up with the bosslab guys this weekend to help out
16:29 < chevbird> should be interesting
16:29 < chevbird> dare i say. fun
16:30 <@kanzure> mensch: you should go with him
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16:37 < nmz787_> Chevbird fig 2 looks like the transposon got cleaved, doest look like insertion
16:37 < nmz787_> Looks like fig 1 is the insertion diagram
16:37 < chevbird> it does stay on
16:38 < chevbird> i guess you have to trust me on that
16:38 < chevbird> haha
16:38 < nmz787_> Stay on?
16:38 < nmz787_> Transposon is DNA right?
16:38 < nmz787_> Transposase is the enzyme
16:38 < chevbird> the "transposome" stays on
16:38 < nmz787_> ??
16:38 < chevbird> the complex
16:38 < chevbird> yea
16:39 < nmz787_> So fig 1 is insertion of transposon by transposone?
16:39 < chevbird> correct
16:39 < nmz787_> then magically non-classical transpoaon behaviour happens?
16:39 < chevbird> and 2 is no insertion, just putting on mozaic ends
16:39 < nmz787_> Mozaic ends?
16:39 < nmz787_> Dunno what they are
16:40 < chevbird> well the repeat sequences.  different people say different things
16:40 < nmz787_> I tjought transposons were just cut-paste genes with flanking adapters on the end to facilitate the cut anf paste
16:41 < chevbird> yes
16:41 < chevbird> and this is a modified one
16:42 < chevbird> where the adapter is a modified sequence
16:42 < chevbird> basically, so you can throw tags on it later
16:42 < nmz787_> Not classical transposase behavior cracked
16:42 < nmz787_> Korekt
16:43 < nmz787_> Android voice recognition fail
16:43 < chevbird> so you're just talking to me
16:44 < chevbird> i assume on a bus or train or somewhere where people are staring at you
16:44 < nmz787_> Driving alone in car
16:45 < chevbird> what app is this?  i think i may need it
16:45 <@kanzure> hahaah ##hplusroadmap Learing how to use irc with ever decreasing amounts of responsibility
16:46 <@kanzure> s/Learing/Learning
16:46 < chevbird> indeed
16:51 < nmz787_> Androirc from google play store
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16:57 < chevbird> looks like he's home
17:01 <@kanzure> ping timeout just means he's out of signal range
17:02 < chevbird> drats
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17:13 < docl> oh, looks like they selected a project for the longecity cryoprotectant fundraiser
17:13 < docl> http://www.longecity.org/forum/page/index.html/_/science/projects/cryopreservation-fundraiser-r36
17:15 < docl> they will be focusing on endothelial cells to see what neutralizes CPA toxicity
17:16 < docl> a good idea since endothelial cells are part of the perfusion impairment problem and apparently inexpensive.
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17:24 < delinquentme> perfusion impairment problem?
17:25 < delinquentme> docl,
17:25 < delinquentme> ^
17:25 < yashgaroth> I'm guessing they mean that since all the cryopreservants have to pass through the endothelial to reach all the other cells
17:27 < yashgaroth> heh "Graduate student (six months): $6,000"
17:29 <@kanzure> aww yeah minimum wage
17:29 <@kanzure> well, below minimum wage
17:32 < delinquentme> Quora gets $50 mil from Thiel
17:32 < delinquentme> http://online.wsj.com/article/SB10001424052702303505504577404510443769988.html?mod=wsj_nview_latest
17:32 < yashgaroth> grad students would kill to make minimum wage
17:32 < delinquentme> valued at $400 million =]
17:32 < delinquentme> yashgaroth, thats why that system needs banged up
17:33 < delinquentme> you know why they make such shit cash? because their PIs and tenure
17:33 < yashgaroth> and because there's hordes of bio grad students
17:33 < delinquentme> and the whole idea that you're guaranteed one of these positions if you're a student
17:33 < docl> just found a podcast about the de wolfs research as well: http://www.longecity.org/media/LongeCityPodcast_DeWolf2012_A01.mp3
17:33 < delinquentme> yarp
17:34 < docl> yashgaroth: yeah. perfusion impairment is pretty bad in real world scenarios. especially if there's any kind of delay.
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18:26 <@kanzure> https://upverter.com/tkousar/356d3c3c43d1739c/Stepper-Motor-Driver/
18:26 <@kanzure> https://upverter.com/tkousar/0000000000006070/A-DIY-breathalyzer/
18:26 <@kanzure> man their urls suck
18:27 <@kanzure> https://upverter.com/tkousar/0000000000006067/A-device-that-detects-magnetic-fields-and-poles-and-makes-a-different-sounds-depending-on-the-magnetic-field/
18:27 <@kanzure> https://upverter.com/tkousar/3e6527eacd1c1e69/Digital-Oscilloscope/
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18:33 <@kanzure> hrmm.. http://resources.upverter.com/how-to-add-a-github-repository-to-your-projec
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19:12 <@kanzure> yashgaroth: you might appreciate this.. "short list of what's actually required" http://88proof.com/synthetic_biology/blog/archives/174
19:12 <@kanzure> however, i think much of that could be compressed into a bootcamp
19:13 <@kanzure> like "0.5 semesters of engineering design — usually done as “introduction to engineering” classes at theoretical universities these days" is really just 5 hours of how to draw isometric boxes and produce standard engineering documents
19:13 < yashgaroth> haha math is listed
19:14 < yashgaroth> "significant work can be outsourced" doesn't seem to jive with the DIY approach
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19:15 < yashgaroth> two semesters of general bio and one of micro seems a little...small, esp. without biochem
19:16 < yashgaroth> 99% of ochem and physics is also worthless
19:19 < Burninate> kanzure: Drafting was combined with parametric 3D CAD and a model-building course at my CC
19:19 < yashgaroth> oh well at least they can show it to the vast majority of people on the DIYbio list who have no fucking clue what they're doing
19:25 <@kanzure> Burninate: i've been doing some coding on parametric CAD if you want to talk about that sometime
19:26 <@kanzure> also, it's hilarious to see mac in the comments trying to recruit jonathan cline to the diybio group: http://88proof.com/synthetic_biology/blog/archives/52/comment-page-1#comment-8
19:26 <@kanzure> (jonathan cline was already a core diybio member)
19:26 < Burninate> nah, it was years ago, with Pro/E
19:26 < Burninate> what project have you been coding for
19:26 <@kanzure> lolcad. http://diyhpl.us/cgit/lolcad
19:26 <@kanzure> also nanoengineer: http://github.com/kanzure/nanoengineer#readme
19:27 < yashgaroth> hey mac is too busy doing...whatever it is he does, to know things like whether jcline is in diybio
19:28 <@kanzure> mac was doing uh.. cofactor bio, then snp-party, then genelaser, then
19:28 <@kanzure> well, now he's on to something else
19:29 < yashgaroth> uh huh
19:30 <@kanzure> seems to be doing this http://diybioftw.com/
19:30 < nmz787> yashgaroth: i think ochem was damn useful
19:30 < yashgaroth> I naturally despite anyone who's said "FTW" in the past 10 years
19:30 < yashgaroth> despise*
19:30 <@kanzure> wtf.. http://diybioftw.com/post/19671614110/structured-protocols
19:30 <@kanzure> why didn't he share that with the diybio group?
19:30 < yashgaroth> it sort of was, but then again I'm not planning to do any chemical synthesis
19:31 <@kanzure> so instead of emailing that link out, it takes me three months to somehow end up at his random blog to see his reply?
19:32 < nmz787> thats not very recent either
19:32 < yashgaroth> I will admit ochem lab was a lot of fun
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19:55 < klafka1> ochem lab was a lot of fun
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20:27 <@kanzure> http://code.google.com/p/openworm/wiki/CElegansNeuroML
20:27 <@kanzure> "Even the C. elegans connectome is missing a complete account of its ion channels, something that some groups are trying to address"
20:27 <@kanzure> nice.. models of single neurons: http://senselab.med.yale.edu/modeldb/ModelList.asp?id=3537
20:28 <@kanzure> that's a pretty long list
20:29 < klafka> did you see the back and forth on the connectome in that one video?
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20:37 <@kanzure> klafka: no?
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20:45 < nmz787> kanzure: chandni is having a 2nd interview w/SF company
20:46 <@kanzure> neat
20:46 < nmz787> so if you signed a lease, does moving out there make synthesis work easier?
20:47 <@kanzure> not really, it makes it slightly more annoying to move out of austin
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21:49 <@kanzure> hi nate_
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22:00 < Cat4D> i need a 200kw gunn diode transistor or heterooptical driver
22:01 < Cat4D> an associated rectifier, and info on how to buffer/store the DC for pulse modulation
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22:16 <@kanzure> yashgaroth: ugh http://medicalxpress.com/news/2012-05-scientists-successfully-gene-therapy-aging-associated.html
22:16 <@kanzure> "virally delivered telomerase extends lifespan of 1-year old mice by 24%"
22:17 < lichen|2> does it say how much increase of cancer risk that induced?
22:17 < yashgaroth> lolol "This might be the only practical solution for an anti-ageing therapy"
22:19 <@kanzure> i wonder what mouse line they were using
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22:20  * yashgaroth tries to find the article
22:21 < yashgaroth> ehh doesn't matter what mouse strain they use, they're all just as inbred
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22:28 < yashgaroth> well they didn't waste any time before patenting it
22:31 < yashgaroth> I don't think they'd be able to measure an increased risk of cancer, since mice don't get it as often as humans and telomerase might not even be a limiting factor for it
22:32 < yashgaroth> also I hate reading patents but using GFP as the control seems biased since GFP is toxic
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23:00 < nmz787> kanzure: know this guy? http://www.matzkefamily.net/doug/papers/quantum/Mensa2008BiologicalQuantum.pdf
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23:03 < nmz787> "Brain could be folded 3D antenna"
23:03 < nmz787> "Evolutionary advantage if bio-quantum link"
23:03 < yashgaroth> um
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23:04 < Mokbortolan_> that's why you wear the tinfoil hat
23:05 < Mokbortolan_> not to shield your brain from the government, that's clearly ridiculous
23:05 < yashgaroth> this stuff is almost colander hat level
23:05 < Mokbortolan_> it's to serve as a waveguide for the folded 3d bio-quantum antenna that is your brain
23:06 < Mokbortolan_> and then, by focusing your innate N-Rays, you can have powers untold
23:10 < Mokbortolan_> i'm sure it's in the bible somewhere
23:10 < Mokbortolan_> methuselah or something
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--- Log closed Tue May 15 00:00:10 2012