| --- Log opened Thu Jun 13 00:00:55 2013 | ||
| archels | paperbot: http://www.pnas.org/content/early/2013/06/05/1221127110.full.pdf+html?with-ds=yes | 00:19 |
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| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Distributed%20cortical%20adaptation%20during%20learning%20of%20a%20braincomputer%20interface%20task.pdf | 00:19 |
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| archels | eleitl, where art thou | 00:49 |
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| nmz787_ | paperbot: http://www.sciencemag.org/content/335/6074/1326 | 03:15 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Laser%20Scribing%20of%20High-Performance%20and%20Flexible%20Graphene-Based%20Electrochemical%20Capacitors.pdf | 03:15 |
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| nmz787_ | paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=1028675&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D1028675 | 05:36 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/16063060f3cd759b8eefa62b4f1070cd.txt | 05:36 |
| chris_99 | apparently it doesn't like that type of formatting nmz787_, you need to give it the url= part http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D1028675 after you've urldecoded it | 05:38 |
| chris_99 | i dont suppose anyone here owns a centrifuge and also brews beer per chance | 05:47 |
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| fenn | abetusk: not exactly a democracy, but interesting nonetheless: http://newcdn.flamehaus.com/Valve_Handbook_LowRes.pdf | 06:28 |
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| kanzure | abetusk: i don't recommend "business as a democracy" | 07:42 |
| kanzure | fenn: that's "open allocation". apparently github is another adherent. | 07:43 |
| kanzure | scotus decision on dna http://www.supremecourt.gov/opinions/12pdf/12-398_8njq.pdf | 08:07 |
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| kanzure | whaat "Investors in Myriad appear pleased with the ruling; the stock is up 6%, and has been up as much as 9%." | 08:16 |
| nmz787_ | chris_99: i just got a centrifuge and could start brewing | 08:34 |
| chris_99 | cool :) see i was thinking of getting something like http://www.ebay.co.uk/itm/130923741568?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649 to try and separate the yeast from the beer, but i was just wondering with a lab centrifuge, how quickly the yeast falls to the bottom | 08:37 |
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| kanzure | "I don't know-- Michael Fishbach pointed out the following to me from the opinion--- the new composition of matter in which a bacterium habors 4 plasmids rationally designed is considered patentable. However, a mixture of natural bacteria not found together in nature is not. :)" | 08:58 |
| ParahSailin | paperbot: http://www.nature.com/nature/journal/v498/n7453/full/nature12295.html | 09:05 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Locomotion%20dynamics%20of%20hunting%20in%20wild%20cheetahs.pdf | 09:05 |
| kanzure | "I'm not entirely convinced this ruling is a win...making cDNA patentable is, from my view in academic research, not a good thing. I also don't understand why the Court is under the impression that cDNA is something magical that is synthesized originally by some complex thing (OK, it's complex but not groundbreaking and has been used for a long time now). cDNA is synthesized by reverse transcription of mRNA, which already contains the exons ... | 09:16 |
| kanzure | ... yet for some reason the court finds that "exon only" DNA is patentable. There are millions of cDNA fragments with a good proportion of known relevance. There's nothing inherently "unnatural" about creating cDNA using reverse transcription; it's how retroviruses like HIV work!" | 09:16 |
| kanzure | http://www.forbes.com/sites/danielfisher/2013/06/13/supreme-court-rejects-human-gene-patents-sort-of/ | 09:18 |
| kanzure | https://news.ycombinator.com/item?id=5874274 | 09:18 |
| kanzure | https://news.ycombinator.com/item?id=5874182 | 09:18 |
| gradstudentbot | Who has the latest version of the paper? | 09:18 |
| kanzure | ha "Does this mean that someone born with synthetic DNA is guilty of infringement if they have children? Do they need to buy a licence to keep living? Perhaps as a compromise, the court can decide that they count as three fifths of a person." | 09:18 |
| kanzure | http://www.genomicslawreport.com/index.php/2013/05/01/some-thoughts-on-myriad-after-the-supreme-court-argument/ | 09:19 |
| kanzure | "Somewhat buried in the announcement about CAS registering the 70-millionth substance (http://pubs.acs.org/userimages/ContentEditor/1366214379428/acs_excellence_spring2013.pdf page 26) are two interesting stats:" | 09:24 |
| kanzure | "1) “This year alone, 63 percent of all chemical patents covered by CAS originated in Asia.”" | 09:24 |
| kanzure | "2) “In fact, more than 70% of new substances from the literature registered in 2012 originated from patents.”" | 09:24 |
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| kanzure | jrayhawk: thoughts about setting up jenkins with piny? | 09:49 |
| kanzure | i guess it would just be a git hook somewhere | 09:49 |
| kanzure | but theoretically your jenkins config comes from somewhere | 09:50 |
| gradstudentbot | God, why won't they just kick me out. | 09:52 |
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| wizrobe | http://www.usatoday.com/story/news/nation/2013/06/13/supreme-court-gene-breast-ovarian-cancer-patent/2382053/ | 10:40 |
| superkuh | Yay! | 10:42 |
| kanzure | http://www.bloomberg.com/news/2013-06-13/the-supreme-court-s-bad-science-on-gene-patents.html | 10:43 |
| kanzure | "it is not the scientists who removed the introns from the officially unpatentable original DNA sequence to make the new, patentable cDNA sequence. It is nature itself, through the magic by which pre-RNA, which includes the introns, becomes messenger RNA, which does not. The Supreme Court described this process by saying, “the pre-RNA is then naturally ‘spliced’ by the physical removal of the introns” -- that is, the introns are ... | 10:43 |
| kanzure | ... removed as part of the ordinary process by which messenger RNA is created. The role scientists then subsequently play is to take the messenger RNA and use it to synthesize the intron-free cDNA." | 10:43 |
| kanzure | "To put it much more simply, there is nothing that a 6-year-old would consider “invented” about the patentable cDNA. It is nothing more than the messenger RNA flipped into a DNA sequence that omits unnecessary elements that nature already excluded. The sequence that codes the proteins is just as naturally occurring as the original DNA itself, which the court held couldn’t be patented because it was naturally occurring. The distinction ... | 10:43 |
| kanzure | ... is, to put it bluntly, a lawyer’s distinction, not a scientist’s." | 10:43 |
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| kanzure | "This decision affirms a previous decision that synthetic modifications to DNA sequences are patented - regardless of whether they have introns. You see, the ruling suggests that the act of creating a new synthetic, modified DNA molecule (in this case without introns) is patent-able" | 12:03 |
| kanzure | that's pretty crazy | 12:03 |
| kanzure | that means you can synthesize dna right now | 12:03 |
| kanzure | and apply for patents | 12:03 |
| kanzure | quick! to the dna obfuscation lab! | 12:03 |
| kanzure | i guess they also want you to make accurate claims about the synthetic dna | 12:04 |
| kanzure | so you can't just mutate random receptors | 12:04 |
| heath | google just increased the amount of free space from 10gb to 15gb | 12:08 |
| heath | grr | 12:08 |
| kanzure | ha ha | 12:08 |
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| jrayhawk | kanzure: I have no particular desire to support jenkins in particular, but I do dynamically generate at least a post-update hook and there's a post-receive hook already for the IRC announcements that I can move into post-update.d/ and post-receive.d/ with appropriate glue if you want. | 12:57 |
| jrayhawk | which would presumably make room for whatever stuff you'd want. | 12:58 |
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| kanzure | jrayhawk: any particular reason you are against jenkins? | 13:07 |
| jrayhawk | if your API for a local application is HTTP, you have made some very poor decisions | 13:08 |
| kanzure | is there a better continuous integration integrator you prefer? | 13:09 |
| jrayhawk | only other one i know of is hudson, which hilariously works the same way | 13:10 |
| brownies | there are a bunch of continuous integrators | 13:19 |
| brownies | i have been looking at Travis and codeship.io lately | 13:19 |
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| kanzure | "More broadly, I am struck by how far behind science and technology are the relevant law and precedent. The SCOTUS opinion hinges on the chemical nature of a particular DNA molecule, and upon breaking and reforming covalent bonds to construct that molecule, and explicitly rejects the notion that it is the information encoded by DNA that is important. It is an opinion firmly rooted in the belief that atoms, rather than bits, are where the ... | 14:05 |
| kanzure | ... action is." | 14:05 |
| kanzure | "If part of the rationale for Thomas' opinion is that commerce would be disrupted by SCOTUS embracing a modern scientific/technical understanding of DNA, then they are about 10 years behind in grasping where the commercial value (and general technical utility) actually resides. If I have got this right, then the decision opens the door to information encoded in magnetic or optical media not being patentable, but information encoded in DNA ... | 14:05 |
| kanzure | ... being patentable because of the forming of covalent bonds." | 14:05 |
| kanzure | "So here is something that has me scratching my head: given that information in the form of books (and by extension all "performances") can be encoded in DNA, and given that the court says it is the molecule and not the information that is relevant to a patent, it seems that this opinion means performances can now be patented, even though this is in direct conflict with earlier court decisions to the contrary." | 14:05 |
| gradstudentbot | My parents keep asking when I'm going to finish. | 14:08 |
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| archels | gradstudentbot: who is your maker? | 14:22 |
| gradstudentbot | Actually, I didn't do that part, it was already here when I joined the lab. | 14:22 |
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| Ummon | hello | 14:53 |
| kanzure | Ummon: hi | 14:57 |
| Ummon | aloha | 14:58 |
| Ummon | so what do you guys discuss here? | 14:58 |
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| kanzure | projects. | 15:00 |
| kanzure | we bug each other to fix bugs in our projects. | 15:00 |
| kanzure | then we write hate mail to each other to complain about even more bugs. | 15:00 |
| Ummon | do you have a page where you list/share your projects? | 15:01 |
| Ummon | Kind of interested in doing my own stuff, but I am a newb | 15:01 |
| Ummon | so I have no idea where to start | 15:01 |
| kanzure | http://diyhpl.us/wiki/declaration | 15:02 |
| kanzure | http://diyhpl.us/cgit | 15:02 |
| kanzure | http://diyhpl.us/wiki/diybio/faq | 15:02 |
| Ummon | gratsi | 15:03 |
| Ummon | I met some dudes from ##biohack at the LA futurist festival | 15:06 |
| Ummon | but I have been interested for several years | 15:06 |
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| delinquentme | I wonder what the blood glucose level is for optimum brain focus | 17:35 |
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| kanzure | http://blog.carbocation.com/post/52902698213/supreme-courts-myriad-decision-is-deeply-confused-over | 18:07 |
| kanzure | "Section I.C. starts off with a bang: | 18:07 |
| kanzure | "cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments. As already explained, creation of a cDNA sequence from mRNA results in an exons-only molecule that is not naturally occurring." | 18:07 |
| kanzure | "From a scientific standpoint, these opening sentences are hard to reconcile with reality. cDNA naturally occurs quite frequently: it is created by cells infected with retroviruses. The way that we make cDNA is by using reverse transcriptase–which we discovered thanks to retroviruses that exist in the wild–to reverse transcribe RNA to its reverse complement (hence the “c” in cDNA). Is natural cDNA accidentally omitted, intentionally ... | 18:07 |
| kanzure | ... omitted, or is the Court re-defining cDNA to only be artificially reverse transcribed DNA? (Probably not the latter.)" | 18:07 |
| kanzure | "s putting an isolated enzyme (reverse transcriptase) in a test tube with mRNA the “magic juice” that triggers the Court’s deference to the technician’s “creation”? If it weren’t for the splicing work that nature did to remove introns from the mRNA, the technician’s work would simply reproduce already-existent DNA, introns and all." | 18:09 |
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| kanzure | "I am not convinced by the Court’s reasoning for permitting cDNA patents on otherwise non-modified genetic sequences. If the Court does not extend this analogy beyond cDNA synthesis, one can imagine ways to show natural occurrence of many important cDNAs, or to alter or create new mRNA sequencing techniques to avoid cDNA intermediates in many RNA applications. However, if the Court extends its analogy beyond the reverse transcription step, ... | 18:10 |
| kanzure | ... then it has stepped into territory that seems quite hazardous for the progress of science and the useful arts." | 18:10 |
| kanzure | "Should DNA strands created by completely artificial synthesis of DNA–with no RNA step–be patentable? Should they be considered infringing on patented cDNA of the same sequence?" | 18:12 |
| kanzure | "Should we focus on the Court’s special emphasis on the reverse transcription of spliced mRNA as the definitive act of human invention? What does this mean for rtPCR? RNA-seq? How can we prevent potential patents on cDNAs in this realm from hindering scientific research?" | 18:12 |
| gradstudentbot | That remains an open question. | 18:14 |
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| brownies | you see? that robot is too good. | 18:28 |
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| yashgaroth | I like all the idiots of the 'oh no corporations are gonna patent my genes and charge me money to be alive' type think that the ruling was any sort of blow to biopharma | 18:32 |
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| delinquentme | GUH | 20:26 |
| delinquentme | wants neural implants | 20:26 |
| kanzure | here, have some anime | 20:28 |
| kanzure | .title http://www.youtube.com/watch?v=QEpAO7bF8i8 | 20:28 |
| yoleaux | MOBILE SUIT GUNDAM SEED DESTINY Remaster - Episode 11:The Chosen Path (ENG sub) - YouTube | 20:28 |
| delinquentme | http://en.wikipedia.org/wiki/Bogosort#Related_algorithms | 20:31 |
| delinquentme | this | 20:31 |
| delinquentme | fucking haha dont read | 20:31 |
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| kanzure | "We lost Assay Depot as a corporate sponsor; the loss was unrelated to Biocurious activities." | 20:39 |
| kanzure | "There has been no net membership growth. We currently have 30 members." | 20:39 |
| kanzure | biocurious has only.. 30. members. | 20:40 |
| yashgaroth | assaydepot as a sponsor of what, biocurious? | 20:40 |
| kanzure | yes | 20:40 |
| kanzure | no idea how much they were paying | 20:40 |
| yashgaroth | gotta put all their diybio money in close to home, nawmsayn | 20:40 |
| kanzure | my guess is "not much" since their competition had a $10k prize only | 20:41 |
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| kanzure | "Many members suggested that the community re-evaluate the governance structure of Biocurious. In comparison to similar spaces, it seems odd that Biocurious's members do not have voting rights." | 20:44 |
| kanzure | "Members also feel that there si a lack of transparency in how the board operates." | 20:44 |
| kanzure | *is | 20:45 |
| kanzure | yashgaroth: we should organize a roast of jojack for one of his bdays | 20:49 |
| yashgaroth | aww yee so bad | 20:49 |
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| archels | kanzure: I might be heading to the West coast in a few months, any interesting events I should try to synchronize with? | 23:39 |
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| --- Log closed Fri Jun 14 00:00:56 2013 | ||
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