--- Log opened Sun Jan 20 00:00:35 2013
00:10 < gene_hacker> a lot actually
00:11 < gene_hacker> thorium reactors have become quite popular recently
00:13 < gene_hacker> but they may not be much better than conventional reactors: http://www.decc.gov.uk/en/content/cms/meeting_energy/nuclear/reactor_report/reactor_report.aspx
00:25 <@kanzure> what is the "Googlebot-IA" user agent used for?
00:28 <@kanzure> what http://books.google.com/booksrightsholders/
00:31 <@kanzure> http://www.springerprotocols.com/botsv/test.txt
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01:05 < strangewarp> rigel: Most people in my family are tech-savvy, non-futurist, and pro-precautionary-principle
01:05 < strangewarp> so I am trying to teach myself to avoid talking about technology or politics around them, because yuck.
01:25 < JayDugger> At least you can still discuss religion with them.
01:26 < nsh> precautionary principle?
01:27 <@kanzure> nsh: http://www.maxmore.com/proactionary.htm
01:27 < JayDugger> https://en.wikipedia.org/wiki/Precautionary_principle
01:27 < JayDugger> The precautionary principle or precautionary approach states if an action or policy has a suspected risk of causing harm to the public or to the environment, in the absence of scientific consensus that the action or policy is harmful, the burden of proof that it is not harmful falls on those taking the action.
01:27 < JayDugger> Guilty until proven innocent.
01:27 <@kanzure> "We should permit no new technology to be developed and no new productive activity to take place unless we can scientifically prove that no harm to health or environment will result."
01:27 < JayDugger> Or, to phrase it combatively, logic for cowards.
01:28 < nsh> bleh
01:28 <@kanzure> nsh: here, have some koolaide http://diyhpl.us/wiki/declaration/
01:28 < JayDugger> Yum! almondy.
01:29 < nsh> tastes like salvation!
01:29 < JayDugger> Don't confuse the delight of finding like-minding people for a sacrament.
01:30 < JayDugger> You want #areyousavedbrother on irc.godbotherer.us for that. :)
01:31 < JayDugger> Or maybe #emacs, depending on your taste.
01:32 < nsh> i have never met anyone like-minded
01:32 < nsh> which may be constituted as an optimistic assessment of the human condition
01:33 < JayDugger> What, we don't count?
01:33 < JayDugger> I think I'll go have a good cry.
01:35  * nsh smiles
01:53 < gene_hacker> why powered exoskeletons?
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02:56 < nsh> (non-powered things tend to exhibit less interesting behaviours)
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04:39 < chido> http://science.slashdot.org/story/13/01/20/0313206/scientist-seeks-adventurous-human-woman-for-neanderthal-baby
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08:17 <@kanzure> paperbot: http://psycnet.apa.org/psycinfo/1963-03848-001
08:17 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/e23b82bf83ba512158bd6e667e5c0480.txt
08:20 <@kanzure> paperbot: http://www.nature.com/nature/journal/v477/n7364/abs/nature10384.html
08:20 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/The%20evolution%20of%20overconfidence.pdf
08:22 <@kanzure> http://timothy-judge.com/documents/Ambition-JAPINPRESS.pdf
08:23 <@kanzure> "Ambition had significant total effects with all of the endogenous variables, except mortality." damn
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08:42 <@kanzure> On Sun, Jan 20, 2013 at 9:26 AM, Anders Sandberg <anders@aleph.se> wrote:
08:42 <@kanzure> > cosmological re-engineering of Dyson and Tipler. The key thing was the
08:42 <@kanzure> > realization that the universe is enormous, yet there exist actions that
08:42 <@kanzure> > allow you to leverage things to ever greater scales. So I just set out to
08:42 <@kanzure> > make myself into some kind of scientist-hero able to do that, pursuing
08:42 <@kanzure> > self-enhancement, learning and networking. I just wish more people did that
08:42 <@kanzure> > kind of attempted life -shaping.
08:42 <@kanzure> yes anders but then you completely crashed
08:42 <@kanzure> doesn't count
08:44 <@kanzure> he settled
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10:14 <@kanzure> aha.. this is why jason morrison appeared in the zotero/translation-server commit history:
10:14 <@kanzure> https://groups.google.com/forum/?fromgroups=#!topic/zotero-dev/FAR2Ct9Touk
10:14 <@kanzure> http://www.papernautapp.com/
10:14 <@kanzure> http://jayunit.net/2013/01/06/papernaut-exploring-online-discussion-of-academic-papers/
10:14 <@kanzure> https://github.com/jasonm/papernaut-engine
10:14 <@kanzure> https://github.com/jasonm/papernaut-frontend
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10:44 < eudoxia> anders would be my hero if he hadn't stuck with philosophy
10:48 <@kanzure> what went wrong so that we can stop that from happening with others?
10:55 < eudoxia> oh kanz if only i knew
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13:22 < archels> [tt] Will We Grapple with Reality or Fully Detach and Live in Fantasyland?
13:22 < archels> damn, I was hoping this was going to be about virtual reality
13:24 < chris_99> heh, i've been reading a lot about the Oculus Rift today, seems pretty awesome :)
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14:36 <@kanzure> what's the fastest way to dump 300 GB to s3?
14:37 < ThomasEgi> sendig a courrier pidgin with a stack of micro-sd cards to the server center?
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15:53 <@kanzure> i think i hurt anders by saying that
15:54 <@kanzure> http://lists.extropy.org/pipermail/extropy-chat/2013-January/075752.html
15:57 <@kanzure> > In my case I am reasonably happy with my plan. While I am doing far less
15:57 <@kanzure> > hands on hard research or coding than my 20-year old self would have
15:57 <@kanzure> > expected, I am doing research that I judge useful and even influential in
15:57 <@kanzure> > the right circles.
15:57 <@kanzure> but... 20 year old anders sandberg wasn't actually interested in research in that sense anyway.
15:57 <@kanzure> and i don't see why he would choose to stop coding anyway
15:57 <@kanzure> > the right circles. Acting as a public intellectual seems to have better
15:57 <@kanzure> > effect in terms of effort for pushing the transhumanist agenda where it is
15:57 <@kanzure> "public intellectual" pffffft
15:59 <@kanzure> > thinkable policy, yet mainstream enough to be listened to). Many of the
15:59 <@kanzure> > self-enhancement techniques I learned early on have become second nature
15:59 <@kanzure> > (stress management, efficient learning, various forms of emotional control),
15:59 <@kanzure> is that seriously what anders saw in transhumanism? that's exceedingly disappointing.
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16:03 <@kanzure> eudoxia: join me in the anders bashing :\
16:04 < eudoxia> yes i was just reading the logs that's why came here
16:04 < eudoxia> man talk about missing the forest for the trees
16:05 <@kanzure> i'm extremely disappointed
16:05 <@kanzure> i am having trouble verbalizing just how ridiculous his email comes off as
16:05 < eudoxia> i mean he did write the Roadmap
16:05 <@kanzure> "when you grow up you will understand that you can't do shit"
16:06 <@kanzure> what an awful opinion to develop
16:06 <@kanzure> where's all that "dynamic optimism" he was spouting
16:07 < eudoxia> to be honest all that extropy principles stuff is kind of meh
16:07 <@kanzure> of course, a defensive reply is to be expected considering how i prevoked him. anybody would be on the defensive after that comment i made.
16:07 <@kanzure> yeah but anders was like the original "actual" transhumanist
16:08 <@kanzure> http://www.aleph.se/Trans/
16:08 <@kanzure> and then it turns out he doesn't actually believe in working on any of this stuff
16:08 < yashgaroth> argh why do mailing lists have to be so fucking annoying to read, no offense eugen
16:09 < eudoxia> he really needs to bring that site into this decade
16:09 <@kanzure> i think the site is fine
16:09 < eudoxia> it's not that i don't like the interface (lol)
16:09 <@kanzure> what, not enough gradients?
16:09 <@kanzure> no jquery
16:09 < eudoxia> it's just, jesus. update the thing once in a while
16:09 <@kanzure> well, to a large extent, transhumanist thought hasn't updated since 1988
16:09 < eudoxia> i actually like it in a retro museum pure-HTML sort of way
16:09 <@kanzure> besides what goes on in here
16:10 < eudoxia> turns out transhumanism requires hard work as opposed to
16:10 <@kanzure> writing emails
16:10 < eudoxia> hurr the robot god daddy figure is coming to breastfeed me knowledge and bring me immortality
16:11 <@kanzure> what i find really surprising is that he thinks "stress management" is transhumanist
16:11 < eudoxia> that's really low
16:11 <@kanzure> stress management isn't going to bootstrap your superintelligent superlolcats
16:12 <@kanzure> http://diyhpl.us/~bryan/papers2/The%20physics%20of%20information%20processing%20superobjects%20-%20Anders%20Sandberg%20-%201999.pdf
16:12 < eudoxia> that's like 0.5 µdysonspheres of transhumanism
16:12 < eudoxia> or 1/10th of a timferris of transhumanism
16:12 <@kanzure> maybe he was a really nervous kid and people told him that being nervous is bad
16:12 <@kanzure> and then he was like "transhumanism means that in the future i won't be nervous, gush gush gush"
16:13 <@kanzure> who cares if you're nervous. bleh.
16:13 < eudoxia> jesus that paper has been on my list for years
16:13 < brownies> just skimming that paper, isn't he assuming too traditional a model of information processing?
16:13 <@kanzure> you haven't read it?
16:13 < eudoxia> no ;_;
16:13 < eudoxia> bear shame for 2 years, etc.
16:14 < brownies> i'm seeing things like "retrieving information from memory" which is a rather non-brain model of computing
16:14 <@kanzure> brownies: it's more about the thermodynamics of how a giant moon-sized computer would work
16:14 <@kanzure> for instance, he used to discuss how you would go about terraforming mars into a supercomputer and where you would have to put the heat conduits
16:14 < brownies> ...assuming that it's built using the same basic concepts as my macbook
16:14 < brownies> which seems to be a rather strong assumption.
16:14 <@kanzure> well in the human brain you have blood to take heat away (among other things)
16:15 < brownies> yeah but my brain doesn't heat up when i think really hard -_-
16:15 <@kanzure> it wasn't so much about intelligence
16:15 < eudoxia> just pure computation
16:15 <@kanzure> actually "superintelligent" doesn't appear in the document.. dunno why i said that.
16:15 < eudoxia> you could implement a posthuman on those computers, or just run NanoEngineer or them
16:15 <@kanzure> oh search doesn't work
16:16 < eudoxia> on*
16:17 < brownies> "...everything intelligent beings do, not just thinking but also economy, art, and motion, can be viewed as information processing."
16:17 <@kanzure> mumble mumble signal processing
16:21 < strages_home> so is there a basic library of nanomechanical structures?
16:22 <@kanzure> yes, it's in nanoengineer.git
16:23 <@kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/partlib
16:23 < strages_home> alright, cool.  thanks
16:24 < eudoxia> i should commit my logic gate
16:24 < eudoxia> i just need to have GROMACS energy-minimize it because i saved over the file after playing the sim movie
16:24 < eudoxia> lololololololol
16:24 <@kanzure> i'm not sure why there should be a partlib actually /in/ the nanoengineer source repository
16:24 <@kanzure> it should probably be a separate repository at least
16:30 < eudoxia> remember when freitas said we'd have 1500 parts within a few years?
16:30 <@kanzure> no
16:33 < eudoxia> some kurzweilai interview
16:34 <@kanzure> well there you go. those aren't reliable.
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16:57 < eudoxia> well bye guys
16:57 < eudoxia> time to watch homeland
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17:41  * rigel reads backscroll
17:41 < rigel> i am in fact pro-precautionary principle, and think transhumanism is garbage
17:41 < yashgaroth> gasp
17:42 < rigel> but i am willing to overlook those differences based on my belief in open access principles
17:42 < rigel> once everyone on earth has access to the sum of all human knowledge, you all will be first up against the wall
17:43 < rigel> so to speak
17:43 < yashgaroth> watch out, one day we'll forcefully put you inside a computer simulation or something
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18:52 < delinquentme> do we have anyone whos cracked open hardcore liquid handlers before?
18:53 < delinquentme> specifically ones which can handle cell-manipulation?
18:55 < yashgaroth> they're just multichannel pipette heads attached to a robot arm
18:58 < yashgaroth> the cell manipulation ones, that is; nothing separates them from regular liquid handlers except they're in a sterile environment
18:59 < yashgaroth> though that depends what exactly you mean by 'cell manipulation', and also 'hardcore'
19:02 < delinquentme> so I've seen this: http://88proof.com/synthetic_biology/blog/archives/318
19:03 < delinquentme> I wonder if making one vrs reprogramming one
19:03 < delinquentme> would  be easiest
19:04 <@kanzure> yashgaroth: by hardcore he probably refers to the music genre
19:05 < yashgaroth> why reprogram it when you can just, uh, program it
19:06 <@kanzure> mostly because documentation/specifications/tools are purposefully hidden away in the name of proprietorship
19:07 < yashgaroth> building one that works nearly as well as a tecan would cost quite a lot of money and time, so it depends how much your time is worth
19:07 < yashgaroth> oh yeah I just got to the part where he has it WASD controlled, that's always fun
19:09 <@kanzure> jcline is still in san diego, right?
19:09 < yashgaroth> yup, he attended the genentech tour and I was like 'who is this jonathan guy' and then I got home and was like 'aww snap it was jcline'
19:10 <@kanzure> sucks man
19:10 < yashgaroth> well he'll be around whenever the fuck we open the diybio lab
19:10 <@kanzure> wouldn't it be cool if we had a device in our pockets that could look up info like that
19:11 < yashgaroth> I mean, hopefully, because I want some sort of arduino-controlled bioreactor up in this
19:11 < yashgaroth> it would involve asking jojack since he's coordinating, last I heard was "oh the city council meeting got delayed" soooo
19:11 < yashgaroth> I know he's responsive and all but I don't want to seem like I'm questioning his ability to get things moving
19:12 <@kanzure> jojack would like nothing more than someone interested in helping him out
19:12 <@kanzure> without secondary motives like "getting an intro to peter thiel" or "getting grant money from someone"
19:12 < yashgaroth> I didn't say I'm helping, just that he needs to get this shit in gear
19:13 < delinquentme> yashgaroth, what do DNA methlyization
19:13 < delinquentme> methylation*
19:13 < yashgaroth> don't worry about that for now dearie
19:14 < delinquentme> its like a bookmarker for a spot on a DNA strand?
19:14 < yashgaroth> nnnno
19:14 < delinquentme> I'm asking about differences bettween hESCs and iPSc
19:14 < delinquentme> and dna methylation does things
19:14 < delinquentme> DNA methylation stably alters the gene expression pattern in cells such that cells can "remember where they have been" or decrease gene expression;
19:14 < delinquentme> ^ wiki
19:15 < yashgaroth> yep that about covers it
19:15 < yashgaroth> methylation occurs on the cytosine of C-G nucleotide pairs, and blocks binding of transcription factors
19:16 < yashgaroth> so if you've got a gene whose promoter region has a lot of said methylation, it will not express
19:16 < yashgaroth> and methylation status is typically passed on after cell division to the daughter chromosome
19:16 < yashgaroth> so that it continues on as a semi-permanent regulator of the gene
19:17 < delinquentme> thats wild. so DNA expression isn't JUST the reading and processing of the genes ... and the promoters have these methylations as kind of antagonists
19:17 < yashgaroth> now, embryonic stem cells typically are not methylated much in several important regions, while most adult cells are, so a key part of inducing pluripotency is blocking that passing of methylation on to the daughter chromosome
19:17 < yashgaroth> welcome to the wacky world of epigenetics
19:19 < delinquentme> yeah thats what I was reading
19:20 < delinquentme> does the DNA still wrap up neatly around histones even if methylated?
19:20 < yashgaroth> even more so, it is believed
19:21 < yashgaroth> a great deal of epigenetics deals with how strongly dna binds to histones - too tightly, and the dna is not accessible to transcription factors
19:21 < yashgaroth> methylation is implicated as a trigger for chromatin condensation, i.e. that strong binding, but it's not a clear cause
19:25 < delinquentme> so theres all kinds of things which can influence transcription
19:25 < yashgaroth> and dozens of PhDs have been based on each
19:26 < delinquentme> we covered earlier what enhancers manage unwrapping of DNA from the histones ... so the methylation can also antagonize that
19:26 < delinquentme> but even in a unraveled state ...
19:27 < delinquentme> it inhibits
19:27 < delinquentme> does it actually interact w ribosomes?
19:27 < yashgaroth> what no
19:27 < yashgaroth> dna does not interact with ribosomes, only rna
19:28 < delinquentme> so RNA polymerase is what is actually reading the DNA
19:28 < yashgaroth> yes
19:29 < delinquentme> how large of a molecule is this? say in comparison to a ribosome
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19:29 < joshcryer> http://www.kurzweilai.net/kim-suozzi-cryopreserved-january-17-at-alcor
19:30 < joshcryer> Glad she got it. Fucking atheists tried to make fun of her and shit on her for wanting to be preserved. Others thought her prognosis was curable with woo shit.
19:30 < yashgaroth> what does the relative size have to do with anything
19:31 < yashgaroth> they're very roughly the same size, counting subunits
19:31 < yashgaroth> joshcryer your link is down
19:31 < delinquentme> joshcryer, what athiests where?
19:32 < delinquentme> yashgaroth, so do we have protocols for modifying methylated sites?
19:32 < yashgaroth> that depends very strongly on what you mean, but generally no
19:32 < brownies> what do atheists have against cryogenics?
19:33 < delinquentme> like what if we wanted to encode logic into the RNA polymerase?  ( side: do people refer to it as just polymerase? )
19:33 < delinquentme> brownies, ignorance and machismo
19:33 < delinquentme> brownies, vin-diesel movies
19:33 < yashgaroth> ok you're going off on weird tangents on both of these topics
19:33 < joshcryer> It's more redditors than anything, she started her campaign to be preserved on reddit.
19:34 < yashgaroth> atheists aren't all ratheists
19:35 < delinquentme> joshcryer, link prez
19:35 < delinquentme> yashgaroth, y no talk on subject?
19:35 < yashgaroth> ok first off you don't just call it 'polymerase' because there's also dna polymerase
19:35 < delinquentme> the base question is " how do we get controlled de-methylation?"
19:35 < yashgaroth> second, what the fuck are you talking about encode logic into the rna polymerase
19:36 < yashgaroth> what does that have to do with rna polymerase
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19:36 < yashgaroth> you can't demethylate dna, you need to have the chromosome duplicate and then block the copying of methylation on the daughter chromosome
19:36 < delinquentme> rna polymerase is what is actively interacting with the DNA ... so if you can control its behavior .. then you've got a molecule which is physically interacting
19:37 < yashgaroth> this may surprise you, but dna polymerase interacts with dna
19:37 < joshcryer> delinquentme, pm
19:39 < delinquentme> joshcryer, +1
19:39 < brownies> yashgaroth: shocking
19:40 < delinquentme> im kinda suprised that r/atheism is actually upvoting cryo
19:40 < delinquentme> hope for humanity +1
19:40 < yashgaroth> mhm, so an essential part of making iPSCs is generating daughter cells that lack methylation on important pluripotency-related genes
19:40 < delinquentme> yashgaroth, and we have protocols for that?
19:41 < yashgaroth> sure, some japanese guy got a nobel prize for writing one
19:43 < yashgaroth> demethylation in that case isn't 'controlled' in any sense, since you're transfecting a million cells and hoping a few get the right pattern
19:43 < yashgaroth> and that is the state of the art right now
19:44 < yashgaroth> targeting a specific site, or a number of specific sites, is so far beyond current tech that you should stop thinking about it
19:46 < nmz787> yashgaroth: really there's no demethylase?
19:46 < nmz787> like a general non-selective one?
19:47 < yashgaroth> not that I'm aware of
19:47 < brownies> what do you guys have against methyl groups anyway?
19:47 < yashgaroth> you can get excision and repair of a segment, but there's no enzyme that pulls of the methyl group
19:47 < nmz787> sometimes metyhls are very nice
19:48 < nmz787> yashgaroth: http://en.wikipedia.org/wiki/Demethylase
19:48 < nmz787> http://www.blatny.com/Epigenetika2007/2007-10-23/papers/Bhattacharya%201999.pdf
19:49 < nmz787> or do you think that's excision based?
19:49 < yashgaroth> am reading
19:51 < nmz787> "In the past decade, many enzymes have been proposed to carry out active DNA demethylation and growing evidence suggests that, depending on the context, this process may be achieved by multiple mechanisms."
19:51 < nmz787> http://www.nature.com/nrm/journal/v11/n9/full/nrm2950.html
19:51 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Active%20DNA%20demethylation%3A%20many%20roads%20lead%20to%20Rome.pdf
19:51 < nmz787> Sept 2010
19:51 < nmz787> nice! paperbot!
19:53 < yashgaroth> http://www.sciencedirect.com.proxy.lib.pdx.edu/science/article/pii/S0092867408007617
19:53 < yashgaroth> oh whoops
19:53 < yashgaroth> paperbot: http://www.sciencedirect.com/science/article/pii/S0092867408007617
19:53 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/b7013a7863ddd5db2317eeeda11b3082.txt
19:54 < yashgaroth> damn it paperbot
19:54 < nmz787> "Although carboncarbon bonds are
19:54 < nmz787> inherently more difficult to break than carbonnitrogen
19:54 < nmz787> bonds, enzymes that have the capacity to do so have been
19:54 < nmz787> reported in the thymidine salvage pathway
19:54 < nmz787> 62
19:54 < nmz787>  and the
19:54 < nmz787> cholesterol synthesis pathway"
19:54 < yashgaroth> if I were a cell I'd just go with excision repair
19:55 < nmz787> paperbot http://www.sciencedirect.com/science/article/pii/S0092867408007617
19:55 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/59b417a3f4f35cd07166d8d93d96dc92.txt
19:56 < delinquentme> le plz sign :D https://petitions.whitehouse.gov/petition/remove-congressmen-paul-broun-united-states-house-committee-science-space-and-technology/PQ90zSGt
19:56 < delinquentme> "All that stuff I was taught about Evolution, Embryology, and Big Bang Theory, all that is lies straight from the pit of hell."
19:56 < yashgaroth> paperbot: http://ac.els-cdn.com/S0092867408007617/1-s2.0-S0092867408007617-main.pdf?_tid=5fe811cc-637e-11e2-88f9-00000aacb360&acdnat=1358740700_d7c43189e8ba290d8dc17261e037b4ad
19:56 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/1a841da774f7154ab34360e0025a4c2e.pdf
19:58 < yashgaroth> well this whole subject seems remarkably controversial in the literature
20:01  * brownies facepalms
20:01 < brownies> it would be a lot easier to take petitions seriously if there wasn't a spelling error in the second word -_-
20:03 < delinquentme> brownies, you're going to not sign a petition over a spelling error?
20:03 < delinquentme> ... really?
20:03 < yashgaroth> I wouldn't
20:05 < delinquentme> yashgaroth, what?
20:05 < delinquentme> you wouldn't sign a petition over a spelling error?
20:05 < yashgaroth> if they can't put forth the effort to read over the the thing once before submitting it
20:06 < delinquentme> yashgaroth, give me a list of your published research papers
20:06 < yashgaroth> what
20:06 < delinquentme> its right there
20:06 < delinquentme> scroll up
20:06 < delinquentme> read it again
20:06 < delinquentme> show me a list of research papers and I'll find a grammatical or spelling error
20:07 < yashgaroth> good luck
20:07 < delinquentme> link?
20:07 < delinquentme> didnt think so
20:07 < delinquentme> also where the hell is this spelling error?
20:07 < yashgaroth> my you seem remarkably defensive
20:07 < yashgaroth> oh haha that explains it
20:08 < delinquentme> yashgaroth, i am!
20:08 < delinquentme> evaluate the petition on its merit
20:08 < yashgaroth> attention to detail is an important factor in merit
20:08 < delinquentme> clearly you saw the quote
20:08 < yashgaroth> also brownies literally told you which word was misspelled
20:09 < delinquentme> Congressmen ? Paul ?
20:09 < yashgaroth> oooh you're getting warm
20:09 < delinquentme> Sept. ? and word
20:10 < delinquentme> sorry yashgaroth  you're a petty fuck
20:10 < yashgaroth> excuse me mister 'give me a list of everything you've ever done'
20:10 < delinquentme> you're actually not signing a petition to get someone like this out of a decision making position in the US government
20:10 < delinquentme> https://github.com/delinquentme go for it yashgaroth
20:10 < yashgaroth> mostly I'm not signing because this whole petition website is laughably ineffective
20:11 < nmz787> what are you guys arguing over???
20:11 < delinquentme> yashgaroth, idk what to say to you
20:11 < nmz787> delinquentme: i think your temper threshold where you get rude is a bit low
20:11 < delinquentme> nmz787, https://petitions.whitehouse.gov/petition/remove-congressmen-paul-broun-united-states-house-committee-science-space-and-technology/PQ90zSGt
20:12 < yashgaroth> the error was "congressmen", it should be "congressman", for fuck's sake man
20:12 < delinquentme> nmz787, i have issues with eliteism over petty insignificant shit
20:12 < delinquentme> which happens to be rife in the scientific community
20:12 < delinquentme> tell me im wrong
20:13 < delinquentme> nothing?
20:13 < delinquentme> no one?
20:14 < delinquentme> yashgaroth, still waiting for that list of research papers
20:14 < delinquentme> you've got my code repo
20:14 < yashgaroth> why do I have your code repo, I don't want your contribs
20:15 < delinquentme> ...
20:15  * kanzure gets popcorn
20:15 < delinquentme> congressmen vrs congressman
20:15 < delinquentme> fml
20:16 < delinquentme> seriously
20:16 < delinquentme> fuck us running. you're a qualified ( ? ) scientist and you've got something up your ass over that?
20:16  * delinquentme blinks
20:16 <@kanzure> delinquentme: please try to form coherent sentences
20:17 < nmz787> delinquentme: a simple error like that doesn't mean science is fucked
20:17 < delinquentme> nmz787, no the error is that yashgaroth refuses to recognize the merit of someones petition because of aforementioned spelling mistake
20:17 < nmz787> lolol
20:17 < joshcryer> he's on that committee so he can shill for the senate launch system
20:17 < joshcryer> he won't be taken off
20:18 < yashgaroth> tbh I have yet to see a petition on that site that doesn't have at least one spelling error
20:18 < delinquentme> joshcryer, shill for the senate launch system?
20:20 < joshcryer> http://www.competitivespace.org/issues/the-senate-launch-system/
20:22 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=a89129b4 Bryan Bishop: fix sciencedirect.com parsing
20:22 < gnusha> paperbot: reload papers
20:22 < joshcryer> It's a jobs program to take the antiquated Space Shuttle tech and make a big expensive launcher .
20:22 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-21 04:22:03)
20:22 <@kanzure> paperbot: http://www.sciencedirect.com/science/article/pii/S0092867408007617
20:22 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20Colorful%20History%20of%20Active%20DNA%20Demethylation.txt
20:22 <@kanzure> well that's not right
20:23 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=eba857dd Bryan Bishop: another fix for sciencedirect.com
20:23 < gnusha> paperbot: reload papers
20:23 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-21 04:23:49)
20:23 <@kanzure> paperbot: http://www.sciencedirect.com/science/article/pii/S0092867408007617
20:24 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20Colorful%20History%20of%20Active%20DNA%20Demethylation.pdf
20:24 <@kanzure> there.
20:24 < joshcryer> nice
20:24 <@kanzure> it would be better to just fix the zotero translators
20:24 <@kanzure> also the way the parsers work in paperbot's phenny module is sub-optimal, not reusable, and hardly testable
20:25 < joshcryer> why are some articles viewable but others require registration?
20:25 <@kanzure> because i'm only using one institution to try to grab a paper
20:25 < delinquentme> yashgaroth, are you an english major?
20:25 < delinquentme> slash minor?
20:25 < yashgaroth> no I work for a living
20:25 < nmz787> def not major
20:25 < joshcryer> ahh, nevermind, I am a dullard, the article I was clicking was a different journal, my bad
20:26 < delinquentme> I just dont get it. But its not in my power
20:26 <@kanzure> joshcryer: also because a single institution is unlikely to have access to everything
20:26 < yashgaroth> I just have an inordinate fixation on correct spelling in such contexts
20:26 < joshcryer> kanzure, got ya
20:27 <@kanzure> yashgaroth: i think you should be more annoyed by the fact that he thought you would respond positively to a whitehouse.gov petition, or ratheism.
20:27 < delinquentme> yashgaroth, but unless you're ready to cough up a full body of work you're a hypocrite
20:27 < delinquentme> its just that simple
20:27 < nmz787> no
20:27 < sivoais> It's even worse when you're reading a technical paper and it has spelling mistakes. It entirely breaks my flow of reading.
20:27 < yashgaroth> kanzure: oh, I am indeed
20:27 < nmz787> especially since it's a .gov website
20:28 < yashgaroth> delinquentme I think you're overreacting to the situation
20:28 < yashgaroth> and while I admit that statement has never calmed anyone down...
20:28 < joshcryer> delinquentme, "It's."
20:29 < delinquentme> looks like it checks out in the legal dictionary ??
20:29 < delinquentme> joshcryer, im sorry
20:29 < nmz787> delinquentme: joshcryer is right
20:29 < joshcryer> delinquentme, "I'm."
20:29 < delinquentme> I'll be looking for your next spelling mistake.
20:29 < delinquentme> also dont be a distracting prick
20:29 <@kanzure> at least be consistent about your apostrophe use, damn
20:29 < delinquentme> fuck me seriously.
20:30 <@kanzure> yeah
20:30 <@kanzure> i think i mentioned it before though
20:30 < delinquentme> you're saying that without a capital letter starting your sentence
20:30 < delinquentme> and just like that this degrades into a fucking circle jerk
20:30 < joshcryer> Just fucking with you delinquentme. I think you're wasting time being annoyed over nothing.
20:30 <@kanzure> well, it's really hard to figure you out
20:30 -!- delinquentme [~asdfasdf@70-90-236-161-Pennsylvania.hfc.comcastbusiness.net] has quit [Quit: Leaving]
20:30 <@kanzure> and follow along with the conversation
20:30 < nmz787> i'm inconsistent in chat
20:31 <@kanzure> yes but you have other traits that make up for that
20:31 < joshcryer> Me too, sometimes I'll go full on punctuate but other times I don't care.
20:31 <@kanzure> anyway i thought there was a conversation going on until delinquentme crashed it
20:32 <@kanzure> but now that i look it seems to have been a conversation with delinquentme
20:32 <@kanzure> so.. nevermind.
20:40 <@kanzure> anyone want to rewrite paperbot to not suck so hard?
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20:47 < juri_> irony: i signed the petition.
20:48 < juri_> and, the conversation was educational. i was glad to read the backlog.
21:09 < brownies> joshcryer++
21:09 < brownies> hilarious.
21:17 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Quit: Lost terminal]
21:22 <@kanzure> "7. Exculpatory Evidence. In paragraph H of the government's letter, the government described but refused to provide almost all of certain exculpatory evidence, including evidence that, during the period covered by the indictment, persons other than Mr. Swartz at Harvard, MIT and China accessed..."
21:22 <@kanzure> "he Acer laptop that was seized by the government, and persons other than Mr. Swartz at MIT and elsewhere were engaging in "journal spidering" of JSTOR data using a "virtual computer" that can be hosted by anyone at MIT."
21:22 <@kanzure> "The government has no basis for withholding the electronic evidence described as exculpatory in its letter."
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21:58 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=29a122ad Bryan Bishop: add a new diybio-seattle victim
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22:09 < nmz787> kanzure: can you turn off charging in software on android without unplugging power?
22:10 < nmz787> to cycle the battery and keep it fresh
22:11 < yashgaroth> I thought that didn't work with li-ion batteries
22:11 < nmz787> hmm
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22:33 < rigel> were we talking about dna methylation and epigenetics in here a bit ago?
22:33  * rigel is available to answer non-insane questions
22:35 < yashgaroth> I think it was all insane questions
22:35 < rigel> darn
22:35 < yashgaroth> heard anything about mammalian cytosine demethylases? they were news to me
22:35 < rigel> not for the last two years or so
22:36 < rigel> i did a crappy master's thesis on epigenetics, which is why i ask
22:36 < rigel> i seem to recall that there are some cytosine demethylases
22:37 < yashgaroth> I'd always assumed demethylation only occurred when maintenance methyltransferases were blocked from daughter chromosomes, at least in mammals
22:37 < yashgaroth> but apparently maybe not
22:38 < yashgaroth> I think delinquentme was on some deep journey into cell reprogramming, but he asks such vague questions that I'm never really sure
22:38 < rigel> look into miR-29
22:39 < rigel> no known DNA demethylases as of my 2010 lit search
22:39 < rigel> i think they may have discovered one since then?
22:39 < rigel> Because there are no known DNA demethylases, it has been
22:39 < rigel> suggested that hypomethylation occurs either through the inhibition of DNMT1 activity,
22:39 < rigel> or through a reduction of available methyl donor, AdoMet.
22:39 < yashgaroth> there was some study with indirect evidence of them...I mean, it's certainly possible
22:40 < yashgaroth> what was the topic of your thesis more specifically, if I may ask?
22:40 < rigel> see also http://dx.doi.org/10.1073/pnas.0707628104 for more on miRNA involvement in methylation
22:40 < rigel> oh, it was just a library thesis, i was drawing parallels in epigenetic mechanisms between developmental processes (e.g. stem cells) and cancer
22:41 < rigel> no actual experimental work.
22:41 < yashgaroth> not uncommon for a masters', really
22:42 < rigel> this is a good one too Because there are no known DNA demethylases, it has been
22:42 < rigel> suggested that hypomethylation occurs either through the inhibition of DNMT1 activity,
22:42 < rigel> or through a reduction of available methyl donor, AdoMet.
22:42 < rigel> dammit
22:42 < rigel> http://dx.doi.org/10.1182/blood-2008-07-170589
22:43 < yashgaroth> ah yes "microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming"
22:45 < rigel> i think a lot of the focus has been on histone modification
22:45 < rigel> research wise
22:45 < yashgaroth> you mean epigenetics in general, or reprogramming?
22:45 < rigel> because there is the assumption that you cant really do anything about the methylated CpG islands
22:46 < rigel> though there are drugs....
22:46 < rigel> an experiment i would like to do is look at people treated for cancer with decitabine (?) who also had been on valproate
22:47 < rigel> i dont remember the specifics now actually
22:47 < yashgaroth> I always worry when people are like "oh here's a histone deacetylase inhibitor for your condition, let's hope it doesn't fuck up the rest of your epigenome"
22:47 < rigel> but it involved looking at people treated with demethylators and valproate
22:48 < rigel> well, the heritability ofthe methylation marks is a complete fucking unknown
22:48 < rigel> as of the last time i looked
22:48 < rigel> methylation and its heritability also has implications for the null mutation hypothesis
22:49 < rigel> since MeC's get converted to T's iirc, by some of the damage cleanup mechanisms
22:49 < yashgaroth> yeah they tend to mutate to Ts quite a lot
22:49 < rigel> and since the null mutation hypothesis is pretty central to a lot of bioinformatics stuff...
22:50 < yashgaroth> haven't heard of said hypothesis
22:50 < yashgaroth> is it just that you're assuming totally random drift, when actually a lot of it will be C->T?
22:51 < rigel> http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution
22:51 < yashgaroth> ahh okay
22:52 < rigel> sometimes the marks are heritable, sometimes they arent
22:52 < rigel> and there are certainly C->T mutations that would make a difference
22:53 < yashgaroth> there was that big study about glucose regulation being heritable from people whose parents experienced starvation or something
22:54 < rigel> yeah. it's not like we couldnt have inferred that from 40 year old data showing that you can induce stable taste preferences in cats during in utero development
22:54 < yashgaroth> heh
23:13 <@kanzure> i would appreciate a citation for that one
23:15 < rigel> wow, i would have to do a good bit of searching there
23:15 < rigel> dug that one out of my memory of undergrad neuroscience courses 10 years ago
23:18 <@kanzure> "Twitter, unlike Genzyme[2], is not fined millions of dollars by the FDA when its site is down."
23:18 <@kanzure> http://www.fiercepharma.com/story/genzyme-submits-175m-fine-fda-consent-decree/2010-05-25
23:20 <@kanzure> "where they approvingly cite the case of Cowan vs. US, where a terminal cancer patient was denied access to experimental medication, denied the right to opt-out of the FDA"
23:20 <@kanzure> http://news.ycombinator.com/item?id=5089359
23:21 < brownies> hm, what's an adaptive clinical trail?
23:21 <@kanzure> "protected”); see also Cowan v. United States, 5 F. Supp.  2d 1235, 1242 (N.D. Okla. 1998) (rejecting a claim that  the plaintiff had the fundamental “right to take whatever  treatment he wishes due to his terminal condition  regardless of whether the FDA approves the treatment”).
23:21 < brownies> http://jama.jamanetwork.com/article.aspx?articleid=1182867#qundefined
23:21 < rigel> brownies: a clinical trial where they can juke the stats in situ
23:22 < brownies> this comment is claiming they are superior to the phase 1/2/3 stuff currently done
23:22 < brownies> rigel: so what do you mean exactly?
23:22 < nmz787> kanzure paperbot should have a copy function
23:22 < nmz787> so i could say paperbot: http://www.media.mit.edu/molecular/HamadNature.pdf
23:23 < rigel> brownies: i'm being glib
23:23 <@kanzure> hehe "Well, before the FDA as such even existed, Banting and Best came up with the idea for insulin supplementation in 1921. A patient was treated by 1922. They won the Nobel Prize by 1923. Today's FDA would have made their methods completely impossible and they would have been criminally prosecuted."
23:23 < nmz787> maybe... should it?
23:23 < brownies> rigel: oh
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23:24 <@kanzure> paperbot: http://www.media.mit.edu/molecular/HamadNature.pdf
23:24 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/c980122e4f2bcd23efbc3223c1522c22.pdf
23:24 <@kanzure> nmz787: seems to work to me
23:24 < yashgaroth> to be fair they do ignore the people who died due to nonexistent regulation back then, but yes, FDA go too far
23:24 < rigel> the FDA doesnt go nearly far enough
23:24 < yashgaroth> what you say!
23:25 < rigel> regulatory capture by pharma, device makers, biotech
23:25 < yashgaroth> oh that, yeah
23:27 < rigel> just like the SEC and DOJ dont go nearly far enough in their regulation of banking and finance, because "too big to fail"
23:27 < rigel> even though at this point a huge proportion of pharma research is contracted out, just like manufacturing, so that pharma companies themselves are essentially just giant marketing companies with a sideline in lobbying
23:29 < brownies> wat
23:29 < brownies> yes, all those scientists they hire are just for show
23:29 < yashgaroth> hey now, they also buy up IP from small companies and then liquidate them
23:30 < rigel> brownies: that's the direction it's going
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23:31 < rigel> Quintiles is probably going to be the first contract research organization to buy out a major pharma brand within the next few years, kind of like how viacom bought out NBC (?) back in the day, years after it was spun off as independent
23:32 < rigel> though, i'm talking out of my ass
23:32 < rigel> of course theyre not going to buy out a pharma brand, the "we contract that out!" excuse is far too valuable for pharma
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--- Log closed Mon Jan 21 00:00:36 2013