| --- Log opened Sun Jan 20 00:00:35 2013 | ||
| gene_hacker | a lot actually | 00:10 |
|---|---|---|
| gene_hacker | thorium reactors have become quite popular recently | 00:11 |
| 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 | 00:13 |
| @kanzure | what is the "Googlebot-IA" user agent used for? | 00:25 |
| @kanzure | what http://books.google.com/booksrightsholders/ | 00:28 |
| @kanzure | http://www.springerprotocols.com/botsv/test.txt | 00:31 |
| -!- lichen_ is now known as lichen | 01:00 | |
| 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. | 01:05 |
| JayDugger | At least you can still discuss religion with them. | 01:25 |
| nsh | precautionary principle? | 01:26 |
| @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. | 01:27 |
| nsh | bleh | 01:28 |
| @kanzure | nsh: here, have some koolaide http://diyhpl.us/wiki/declaration/ | 01:28 |
| JayDugger | Yum! almondy. | 01:28 |
| nsh | tastes like salvation! | 01:29 |
| JayDugger | Don't confuse the delight of finding like-minding people for a sacrament. | 01:29 |
| JayDugger | You want #areyousavedbrother on irc.godbotherer.us for that. :) | 01:30 |
| JayDugger | Or maybe #emacs, depending on your taste. | 01:31 |
| nsh | i have never met anyone like-minded | 01:32 |
| nsh | which may be constituted as an optimistic assessment of the human condition | 01:32 |
| JayDugger | What, we don't count? | 01:33 |
| JayDugger | I think I'll go have a good cry. | 01:33 |
| * nsh smiles | 01:35 | |
| gene_hacker | why powered exoskeletons? | 01:53 |
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| nsh | (non-powered things tend to exhibit less interesting behaviours) | 02:56 |
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| chido | http://science.slashdot.org/story/13/01/20/0313206/scientist-seeks-adventurous-human-woman-for-neanderthal-baby | 04:39 |
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| @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 | 08:17 |
| @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 | 08:20 |
| @kanzure | http://timothy-judge.com/documents/Ambition-JAPINPRESS.pdf | 08:22 |
| @kanzure | "Ambition had significant total effects with all of the endogenous variables, except mortality." damn | 08:23 |
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| @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 | 08:42 |
| @kanzure | he settled | 08:44 |
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| @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 | 10:14 |
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| eudoxia | anders would be my hero if he hadn't stuck with philosophy | 10:44 |
| @kanzure | what went wrong so that we can stop that from happening with others? | 10:48 |
| eudoxia | oh kanz if only i knew | 10:55 |
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| 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 | 13:22 |
| chris_99 | heh, i've been reading a lot about the Oculus Rift today, seems pretty awesome :) | 13:24 |
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| @kanzure | what's the fastest way to dump 300 GB to s3? | 14:36 |
| ThomasEgi | sendig a courrier pidgin with a stack of micro-sd cards to the server center? | 14:37 |
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| @kanzure | i think i hurt anders by saying that | 15:53 |
| @kanzure | http://lists.extropy.org/pipermail/extropy-chat/2013-January/075752.html | 15:54 |
| @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 | 15:57 |
| @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. | 15:59 |
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| @kanzure | eudoxia: join me in the anders bashing :\ | 16:03 |
| 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 | 16:04 |
| @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" | 16:05 |
| @kanzure | what an awful opinion to develop | 16:06 |
| @kanzure | where's all that "dynamic optimism" he was spouting | 16:06 |
| 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 | 16:07 |
| @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 | 16:08 |
| 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 | 16:09 |
| 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 | 16:10 |
| @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 | 16:11 |
| @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" | 16:12 |
| @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. | 16:13 |
| 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) | 16:14 |
| 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 | 16:15 |
| eudoxia | on* | 16:16 |
| 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 | 16:17 |
| strages_home | so is there a basic library of nanomechanical structures? | 16:21 |
| @kanzure | yes, it's in nanoengineer.git | 16:22 |
| @kanzure | https://github.com/kanzure/nanoengineer/tree/master/cad/partlib | 16:23 |
| strages_home | alright, cool. thanks | 16:23 |
| 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 | 16:24 |
| eudoxia | remember when freitas said we'd have 1500 parts within a few years? | 16:30 |
| @kanzure | no | 16:30 |
| eudoxia | some kurzweilai interview | 16:33 |
| @kanzure | well there you go. those aren't reliable. | 16:34 |
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| eudoxia | well bye guys | 16:57 |
| eudoxia | time to watch homeland | 16:57 |
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| * rigel reads backscroll | 17:41 | |
| rigel | i am in fact pro-precautionary principle, and think transhumanism is garbage | 17:41 |
| yashgaroth | gasp | 17:41 |
| 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 | 17:42 |
| rigel | so to speak | 17:43 |
| yashgaroth | watch out, one day we'll forcefully put you inside a computer simulation or something | 17:43 |
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| delinquentme | do we have anyone whos cracked open hardcore liquid handlers before? | 18:52 |
| delinquentme | specifically ones which can handle cell-manipulation? | 18:53 |
| yashgaroth | they're just multichannel pipette heads attached to a robot arm | 18:55 |
| yashgaroth | the cell manipulation ones, that is; nothing separates them from regular liquid handlers except they're in a sterile environment | 18:58 |
| yashgaroth | though that depends what exactly you mean by 'cell manipulation', and also 'hardcore' | 18:59 |
| delinquentme | so I've seen this: http://88proof.com/synthetic_biology/blog/archives/318 | 19:02 |
| delinquentme | I wonder if making one vrs reprogramming one | 19:03 |
| delinquentme | would be easiest | 19:03 |
| @kanzure | yashgaroth: by hardcore he probably refers to the music genre | 19:04 |
| yashgaroth | why reprogram it when you can just, uh, program it | 19:05 |
| @kanzure | mostly because documentation/specifications/tools are purposefully hidden away in the name of proprietorship | 19:06 |
| 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 | 19:07 |
| @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' | 19:09 |
| @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 | 19:10 |
| 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 | 19:11 |
| @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 | 19:12 |
| delinquentme | yashgaroth, what do DNA methlyization | 19:13 |
| delinquentme | methylation* | 19:13 |
| yashgaroth | don't worry about that for now dearie | 19:13 |
| 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 | 19:14 |
| 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 | 19:15 |
| 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 | 19:16 |
| 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 | 19:17 |
| delinquentme | yeah thats what I was reading | 19:19 |
| delinquentme | does the DNA still wrap up neatly around histones even if methylated? | 19:20 |
| yashgaroth | even more so, it is believed | 19:20 |
| 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 | 19:21 |
| delinquentme | so theres all kinds of things which can influence transcription | 19:25 |
| yashgaroth | and dozens of PhDs have been based on each | 19:25 |
| 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 ... | 19:26 |
| 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 | 19:27 |
| delinquentme | so RNA polymerase is what is actually reading the DNA | 19:28 |
| yashgaroth | yes | 19:28 |
| delinquentme | how large of a molecule is this? say in comparison to a ribosome | 19:29 |
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| joshcryer | http://www.kurzweilai.net/kim-suozzi-cryopreserved-january-17-at-alcor | 19:29 |
| 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 | 19:30 |
| 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? | 19:31 |
| 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? | 19:32 |
| 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. | 19:33 |
| yashgaroth | atheists aren't all ratheists | 19:34 |
| 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 | 19:35 |
| yashgaroth | what does that have to do with rna polymerase | 19:36 |
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| 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 | 19:36 |
| yashgaroth | this may surprise you, but dna polymerase interacts with dna | 19:37 |
| joshcryer | delinquentme, pm | 19:37 |
| delinquentme | joshcryer, +1 | 19:39 |
| brownies | yashgaroth: shocking | 19:39 |
| 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? | 19:40 |
| yashgaroth | sure, some japanese guy got a nobel prize for writing one | 19:41 |
| 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 | 19:43 |
| yashgaroth | targeting a specific site, or a number of specific sites, is so far beyond current tech that you should stop thinking about it | 19:44 |
| nmz787 | yashgaroth: really there's no demethylase? | 19:46 |
| nmz787 | like a general non-selective one? | 19:46 |
| 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 | 19:47 |
| nmz787 | yashgaroth: http://en.wikipedia.org/wiki/Demethylase | 19:48 |
| nmz787 | http://www.blatny.com/Epigenetika2007/2007-10-23/papers/Bhattacharya%201999.pdf | 19:48 |
| nmz787 | or do you think that's excision based? | 19:49 |
| yashgaroth | am reading | 19:49 |
| 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! | 19:51 |
| 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 | 19:53 |
| 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 | 19:54 |
| 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 | 19:55 |
| 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 | 19:56 |
| yashgaroth | well this whole subject seems remarkably controversial in the literature | 19:58 |
| * 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 -_- | 20:01 |
| delinquentme | brownies, you're going to not sign a petition over a spelling error? | 20:03 |
| delinquentme | ... really? | 20:03 |
| yashgaroth | I wouldn't | 20:03 |
| 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 | 20:05 |
| 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 | 20:06 |
| 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 | 20:07 |
| 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 | 20:08 |
| delinquentme | Congressmen ? Paul ? | 20:09 |
| yashgaroth | oooh you're getting warm | 20:09 |
| delinquentme | Sept. ? and word | 20:09 |
| 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 | 20:10 |
| 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 | 20:11 |
| 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 | 20:12 |
| delinquentme | nothing? | 20:13 |
| delinquentme | no one? | 20:13 |
| 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 | 20:14 |
| delinquentme | ... | 20:15 |
| * kanzure gets popcorn | 20:15 | |
| delinquentme | congressmen vrs congressman | 20:15 |
| delinquentme | fml | 20:15 |
| 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 | 20:16 |
| 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 | 20:17 |
| 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? | 20:18 |
| joshcryer | http://www.competitivespace.org/issues/the-senate-launch-system/ | 20:20 |
| 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 | 20:22 |
| 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 | 20:23 |
| 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 | 20:24 |
| 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 | 20:25 |
| 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 | 20:26 |
| @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 | 20:27 |
| 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." | 20:28 |
| 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. | 20:29 |
| @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 |
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| @kanzure | and follow along with the conversation | 20:30 |
| nmz787 | i'm inconsistent in chat | 20:30 |
| @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 | 20:31 |
| @kanzure | but now that i look it seems to have been a conversation with delinquentme | 20:32 |
| @kanzure | so.. nevermind. | 20:32 |
| @kanzure | anyone want to rewrite paperbot to not suck so hard? | 20:40 |
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| juri_ | irony: i signed the petition. | 20:47 |
| juri_ | and, the conversation was educational. i was glad to read the backlog. | 20:48 |
| brownies | joshcryer++ | 21:09 |
| brownies | hilarious. | 21:09 |
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| @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." | 21:22 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=29a122ad Bryan Bishop: add a new diybio-seattle victim | 21:58 |
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| nmz787 | kanzure: can you turn off charging in software on android without unplugging power? | 22:09 |
| nmz787 | to cycle the battery and keep it fresh | 22:10 |
| yashgaroth | I thought that didn't work with li-ion batteries | 22:11 |
| nmz787 | hmm | 22:11 |
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| rigel | were we talking about dna methylation and epigenetics in here a bit ago? | 22:33 |
| * rigel is available to answer non-insane questions | 22:33 | |
| 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 | 22:35 |
| 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 | 22:36 |
| 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 | 22:37 |
| 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 | 22:38 |
| 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 | 22:39 |
| 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 | 22:40 |
| rigel | no actual experimental work. | 22:41 |
| yashgaroth | not uncommon for a masters', really | 22:41 |
| 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 | 22:42 |
| yashgaroth | ah yes "microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming" | 22:43 |
| 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 | 22:45 |
| 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 | 22:46 |
| 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 | 22:47 |
| 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 | 22:48 |
| 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... | 22:49 |
| 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? | 22:50 |
| rigel | http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution | 22:51 |
| yashgaroth | ahh okay | 22:51 |
| rigel | sometimes the marks are heritable, sometimes they arent | 22:52 |
| rigel | and there are certainly C->T mutations that would make a difference | 22:52 |
| yashgaroth | there was that big study about glucose regulation being heritable from people whose parents experienced starvation or something | 22:53 |
| 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 | 22:54 |
| @kanzure | i would appreciate a citation for that one | 23:13 |
| 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 | 23:15 |
| @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 | 23:18 |
| @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 | 23:20 |
| 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 | 23:21 |
| 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 | 23:22 |
| 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 | 23:23 |
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| @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! | 23:24 |
| rigel | regulatory capture by pharma, device makers, biotech | 23:25 |
| yashgaroth | oh that, yeah | 23:25 |
| 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 | 23:27 |
| 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 | 23:29 |
| rigel | brownies: that's the direction it's going | 23:30 |
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| 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 | 23:31 |
| 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 | 23:32 |
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