| --- Log opened Sat Apr 27 00:00:09 2013 | ||
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| ParahSail1n | <venturecommunist> had a good talk with marcin today | 01:01 |
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| ParahSail1n | <venturecommunist> big event | 01:01 |
| ParahSail1n | <venturecommunist> basically getting the whole taxonomy / data formats / gamification / onboarding / documentation thing for open source hardware looked at from all angles | 01:01 |
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| eudoxia_ | isn't venturecommunism the guy who thought skdb was a metor.js gamified cloud-aware massive-multiplayer-online package manager or some crap like that | 07:41 |
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| ParahSail1n | probably | 08:33 |
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| @kanzure | ParahSail1n: yes he's probably referring to that eyebeam/oshwa event.. but i don' think those guys know about file formats anyway, based on talking with them over email last month. "hur what's STL? what's STEP?" | 10:47 |
| @kanzure | *don't | 10:47 |
| ParahSail1n | heh | 10:49 |
| ParahSail1n | kanzure, so what sort of wet lab stuff would you potentially like to see me do? | 10:55 |
| ParahSail1n | or hardware engineering for that matter | 10:55 |
| @kanzure | i think COA is worth exploring but there's probably zero market in houston, and it's more businessy oriented than an on-topic relevant project | 10:56 |
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| ParahSail1n | coa? | 10:56 |
| @kanzure | biotech contract organization. i am probably getting the acronym wrong. | 10:57 |
| @kanzure | san diego has 'em booming. | 10:57 |
| @kanzure | oh CRO. | 10:57 |
| @kanzure | as far as hardware things.. basically anything beyond a damn thermocycler has been entirely unexplored by open source hardware enthusiasts. | 10:59 |
| @kanzure | however, if you want to sell lab equipment, some of that has to be constrained by what the 'market' actually wants, which can be anything from "nothing" to "hardly anything". | 11:00 |
| @kanzure | because the market is something like 300,000 labs total or something. | 11:00 |
| @kanzure | https://code.google.com/p/google-glass-kernel-source/ | 11:10 |
| @kanzure | https://google-glass-kernel-source.googlecode.com/files/kernel-glass-XE04.0-RC06.tar.xz | 11:11 |
| @fenn | ParahSail1n: why would a nanodrop spec cost so much to make? what's special about it? | 11:20 |
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| @fenn | http://www.nanodrop.com/Productnd2000specs.aspx don't see anything special here; xenon flash lamp, linear CCD | 11:26 |
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| @fenn | the 3300 fluorospectrometer uses blue, white, and UV LEDs | 11:28 |
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| @fenn | finally someone steps up to confront the hard issues, "whether cyborg, Controlled Humanoid Terminal, or whatever you call it, they should wear underwear! In order for other humans to accept cyborgs as 'human', they must follow human ethics and morals (like wearing underwear)." | 12:00 |
| @kanzure | i think nate is in a better position to complain about the nanodrop, considering his work on an open source spectrophotometer. | 12:04 |
| @kanzure | iirc his BOM for his spectrophotometer was a little pricey too, although nowhere near nanodrop/10k levels | 12:05 |
| @fenn | i'm more interested in why ParahSail1n thinks what he does, as i understand nate's mindset | 12:05 |
| @fenn | i could see that quartz fiber as being pricy, but not thousands of dollars | 12:06 |
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| jrayhawk | Urrr? http://www.ncbi.nlm.nih.gov/pubmed/23611879?dopt=Abstract | 12:19 |
| @kanzure | .title | 12:23 |
| yoleaux | Born to yawn? Understanding yawning as a ... [Interact J Med Res. 2012] - PubMed - NCBI | 12:23 |
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| @fenn | my understanding is that yawning evolved as a group signal *not* to fall asleep | 12:48 |
| @fenn | i think they've got the causality backwards; yawning should increase cortisol levels to keep you from falling asleep when you're tired. it's not a "warning" of cortisol being elevated (what would be the point of that?) | 12:50 |
| * brownies yawns at fenn | 12:50 | |
| brownies | it does spike oxygen intake, so i'm willing to buy the anti-falling-asleep bit. this is the first i've heard of social signaling though. | 12:51 |
| @fenn | of course it's a social signal, why else would it be communicable (like laughter) | 12:51 |
| EnLilaSko | paperbot: http://www.sciencedirect.com/science/article/pii/S1096637408000063 | 12:54 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Effect%20of%20topical%20application%20of%20raspberry%20ketone%20on%20dermal%20production%20of%20insulin-like%20growth%20factor-I%20in%20mice%20and%20on%20hair%20growth%20and%20skin%20elasticity%20in%20humans.txt | 12:54 |
| ParahSail1n | maybe i should buy one of those guangzhou specs and do put the schematics up somewhere | 13:08 |
| ParahSail1n | it could probably be replicated for 2k of materials | 13:09 |
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| nmz787 | ParahSail1n: i've got schematics already | 14:36 |
| nmz787 | i'm working on the PCB now | 14:36 |
| nmz787 | nanodrops are simply a box with a perkin-elmer xenon flashbulb and an ocean optics USB2000 inside | 14:37 |
| nmz787 | or at least that was the model i took apart | 14:37 |
| nmz787 | my BOM for a comparable (actually faster data throughput) than the nanodrop is | 14:39 |
| nmz787 | https://groups.google.com/forum/#!msg/diybio/XL6kR56o1KM/XnwVjHXt8y0J | 14:39 |
| nmz787 | the microcontroller has changed, but otherwise it's pretty much the same | 14:39 |
| nmz787 | <$350 UV-Vis spectrometer that should be good for DNA | 14:39 |
| nmz787 | or if the chinese grating sucks and a U.S.A. made is needed, then it would increase to around $7550 | 14:40 |
| nmz787 | $750 | 14:40 |
| nmz787 | * | 14:40 |
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| ParahSail1n | nmz787, cool | 15:12 |
| ParahSail1n | nmz787, so you have something nearly ready for work? | 15:13 |
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| ParahSail1n | why did drchrono come up in here the other day? | 17:07 |
| @kanzure | rigel was complaining about not making money, so i told him he could sell his soul | 17:09 |
| @kanzure | a few days ago someone was pestering me to join him on a quest to make an EMR startup and i just laughed and laughed, then showed him drchrono.. so that's probably why it was on my mind. | 17:09 |
| @kanzure | EMR is not exactly on the top of my list of fun problems | 17:09 |
| @kanzure | plus, it seems like my time could be better spent than chasing after venture capital for EMR reasons.. | 17:09 |
| ParahSail1n | talked to the drchrono guy today, they wanna fly me out there to meet the team | 17:16 |
| ParahSail1n | im only really interested in getting offers to negotiate raise where i am | 17:17 |
| ParahSail1n | might be fun to go visit the valley again though | 17:17 |
| brownies | you an engineer too ParahSail1n ? | 17:19 |
| @kanzure | ParahSail1n is putting time as a haskell slinging bioinformatics goon | 17:19 |
| @kanzure | *putting in time | 17:19 |
| brownies | interesting niche. | 17:21 |
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| ParahSail1n | these things have really been helping with my tendonitis http://www.amazon.com/Captains-of-Crush-Hand-Gripper/dp/B005NSF8OW | 17:25 |
| ParahSail1n | for much of last year i had rsi sorts of problems with my hands | 17:26 |
| klafka | interesting | 17:37 |
| klafka | so oyu've been using that to strengthen your hand | 17:37 |
| ParahSail1n | acute stresses seem to stimulate better healing that chronic low level stresses | 17:46 |
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| @kanzure | "The United States Supreme Court yesterday (April 15th) heard arguments over the controversial question of whether human genes can be patented. Although no final decision will be reached until later in the year, the tone of proceedings suggested that the justices will find that isolated DNA sequences are natural products and therefore not valid for patents, reported Nature." | 18:54 |
| @kanzure | "The assertion was barely challenged by the justices, according Nature. On that score, they may have been influenced by a friend-of-the-court brief from Eric Lander of MIT, who countered a lower court’s assertion that snippets of DNA isolated from the chromosome do not occur in nature and are structurally different enough to qualify for patenting. In his brief, Lander argued that isolated chunks of DNA are in-fact found circulating in the ... | 18:54 |
| @kanzure | ... blood, including fragments that contain BRCA-1 and BRCA-2." | 18:54 |
| @kanzure | haha dna fragments in blood. nice. | 18:55 |
| @kanzure | " “I would be very surprised if the Supreme Court says isolated gene sequences would be patent eligible subject matter after today’s argument,” Supreme Court blogger Tom Goldstein told Nature. Indeed, many of the questions asked by the justices centered on what effect invalidating gene patents would have on the biotech industry, suggesting the justices were more concerned with exploring the impact of ruling against gene patenting, ... | 18:55 |
| @kanzure | ... rather than the validity of the plaintiff’s argument." | 18:55 |
| @kanzure | "Myriad and other advocates of gene patenting claim that ruling against the practice would undermine billions of dollars of investment from biotech companies in genetic tests, drugs, and DNA-based vaccines. " | 18:56 |
| @kanzure | well this is fun. | 18:56 |
| @kanzure | is this one of those times when shorting some stocks would be a wise decision | 18:56 |
| ParahSail1n | whose stocks? | 18:59 |
| @kanzure | dunno, pick some random companies that hold gene patents | 18:59 |
| ParahSail1n | ah, speculation is that scotus will dismiss them? | 19:00 |
| @kanzure | dunno how scotus will handle it if they find genes unpatentable.. grandfather it? invalidate all the gene patents? | 19:01 |
| @kanzure | and it might be a specific decision about this patent, but not others. which wouldn't be very helpful to a short position. | 19:01 |
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| @kanzure | like this: http://www.icis.com/Articles/2000/03/15/107843/uk-pharma-stocks-fall-on-clintonblair-gene-patent-speech.html | 19:07 |
| @kanzure | i mean, the president can't do shit. scotus has actual power here. | 19:07 |
| @kanzure | "The slumps followed in the wake of falls on biotech stock on the Nasdaq exchange, which saw shares in US firm Celera Genomics - the prime private-sector firm trying to decipher the human DNA code - close yesterday 18% down at $155 (Euro161)" | 19:07 |
| ParahSail1n | wow myriad gets 4000/patient for two genes | 19:15 |
| @kanzure | haha ""The March 14 statement about sharing raw, fundamental genomic data had nothing to do with patents where the utility standard - identification of a potential commercial application - is met. The Clinton-Blair statement actually included a specific endorsement of patent protection. We appreciate the president's effort to make this point clear and to reassure investors who fund this vital research." | 19:15 |
| @kanzure | ""We also appreciate the president's implicit endorsement of the current process at the U.S. Patent and Trademark Office (PTO) in setting guidelines for issuing patents on gene-based inventions," Ludlam said. "We strongly support the PTO's efforts, which we find to be totally professional and fundamentally on the right track."" | 19:15 |
| ParahSail1n | id say its not a bad stock to short | 19:17 |
| @kanzure | huh, "The Supreme Court pointed to that legal principle in 1854 when it invalidated part of Samuel Morse’s telegraph patent because it sought to cover the use of electric current to transmit characters or letters." | 19:19 |
| @kanzure | "When the ACLU's lawyer, Christopher A. Hansen, said scientists may still be motivated by curiosity and the chance of a Nobel Prize, Kagan responded: "I hoped you were going to say something else, which is that, notwithstanding that you can't get a patent on this gene, that -- that there are still, you know, various things that you could get a patent on that would make this kind of investment worthwhile in the usual case. But if that's the ... | 19:21 |
| ParahSail1n | i try to avoid kremlinology whenever possible | 19:22 |
| @kanzure | ... case, I want to know what those things are rather than you're just saying, you know, we're supposed to leave it to scientists who want Nobel prizes. And I agree that there are those scientists, but there are also, you know, companies that do investments in these kinds of things that you hope won't just shut them down."" | 19:22 |
| @kanzure | "Hansen ultimately was bailed out by Justices Anthony M. Kennedy and Sonia Sotomayor, who suggested that the incentive might be the opportunities that isolating a particular gene sequence create to develop patentable processes or uses of the gene." | 19:22 |
| @kanzure | where is the kremlinology here? | 19:22 |
| ParahSail1n | guessing what the scotus is gonna do | 19:22 |
| @kanzure | oh i see. | 19:22 |
| @kanzure | "The Obama administration has suggested a potential middle ground, urging the Supreme Court to hold that companies can't patent genes but they may be able to patent complementary DNA chains that they create in the process of isolating a DNA sequence. Myriad asserted that the cDNA molecules it produced were different from the cDNA found in nature because it extracted extraneous, non-protein-forming substances." | 19:22 |
| @kanzure | pfft "Chief Justice John G. Roberts Jr. and Justice Samuel A. Alito Jr. floated a different idea: Rather than declaring genes ineligible for patents, it could leave it to patent examiners to decide whether any particular sequence was too obvious to qualify for protection. Such an approach wouldn't end lawsuits over the validity of specific gene patents, but it would be less disruptive to the industry" | 19:23 |
| @kanzure | here's a transcript of some testimony: | 19:25 |
| @kanzure | http://www.supremecourt.gov/oral_arguments/argument_transcripts/12-398-amc7.pdf | 19:25 |
| ParahSail1n | too bad we dont have intrade anymore to tell us the important answers | 19:25 |
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| @kanzure | wow, this reads pretty poorly | 19:33 |
| @kanzure | i understand it's a high pressure environment, but the arguments against gene patents here are not very thorough | 19:33 |
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| @kanzure | haha it is funny to watch the supreme court trying to understand basic molecular biology | 19:35 |
| brownies | so what happened? can we patent genes or not? | 19:37 |
| @kanzure | they were just being briefed. | 19:39 |
| @kanzure | no ruling yet | 19:39 |
| brownies | oh i see. | 19:40 |
| ParahSail1n | june | 19:45 |
| ParahSail1n | nmz787, what linear ccd are you using? | 19:47 |
| @kanzure | breyer seems to have his head on straight. "Since neither of us are scientists, and you are telling me that you think it's wrong as a matter of science, then you should tell me what I should read from a scientist to understand this correctly." | 19:48 |
| @kanzure | but none of these people giving testimony seem to have a clear understanding of the entire process of how dna works, how genes work, etc. | 19:51 |
| ParahSail1n | given the result of the monsanto patent, the supreme court composition now seems to be weighted towards the "if we dont protect this, then how would X make a viable business model out of r&d" | 19:57 |
| @kanzure | "reactions that have been around for 100s of years just like snipping has been" uh... exonuclease activity hasn't been around for 100s of years, has it? | 20:00 |
| @kanzure | i mean, our use of exonuclease activity | 20:00 |
| @kanzure | damn, i hope some professors have bothered to file some explanatory briefs with the supreme court, because this shit suuucks | 20:03 |
| @kanzure | http://www.supremecourt.gov/Search.aspx?FileName=/docketfiles/12-398.htm | 20:05 |
| @kanzure | hah, "biotechnology industry organization" is represented by a firm out of austin | 20:06 |
| @kanzure | "Jan 31 2013Brief amicus curiae of James D. Watson, Ph.D. in support of neither party filed" | 20:06 |
| @kanzure | "Jan 31 2013Brief amicus curiae of Knowledge Ecology International filed" pfft isn't that the organization that presented at open science summit | 20:07 |
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| @kanzure | haha.. some startup is getting biocurious to write a mobile app for them.. or something. looks like a scam. | 22:21 |
| brownies | link? | 22:26 |
| @kanzure | hmm | 22:28 |
| @kanzure | i wish it was easier to figure out the url from an email sent from a mailing list. it should be in the headers. but it isn't. | 22:29 |
| @kanzure | https://groups.google.com/forum/?fromgroups#!topic/biocurious-bioinfo-hacking/LV3B6Xg6pFg | 22:32 |
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| @kanzure | ah yeah the other part is private | 22:32 |
| brownies | ah. | 22:32 |
| @kanzure | "'ll still have to finalize this with a biotech startup that does test kits and bioinformatics analysis, but this was a project I wanted us to do. I don't want to make official announcements yet though until I can confirm that interest with them and that we have a diy team that would be able to do this." | 22:32 |
| @kanzure | anyway... taking advantage of community help, not cool. unless it's paid. | 22:33 |
| @kanzure | ah "No that's not the point. We could use their data and get a cheaper rate for members." | 22:39 |
| brownies | i see. | 22:40 |
| @kanzure | still sounds like a lame deal | 22:41 |
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| ParahSail1n | holy crap, a link to the actual journal paper, and it actually works http://www.abc.net.au/science/articles/2013/04/25/3744552.htm | 23:06 |
| @kanzure | time to give them a science journo award | 23:06 |
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| --- Log closed Sun Apr 28 00:00:10 2013 | ||
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