--- Log opened Tue Nov 04 00:00:40 2014
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00:25 < archels> http://journal.frontiersin.org/Journal/10.3389/fnins.2014.00349/full
00:25 < archels> very pointed
00:26 < fenn> .title
00:26 < yoleaux> Frontiers | The tale of the neuroscientists and the computer: why mechanistic theory matters | Brain Imaging Methods
00:26 < archels> A little over a decade ago, a biologist asked the question “Can a biologist fix a radio?” (Lazebnik, 2002). That question framed an amusing yet profound discussion of which methods are most appropriate to understand the inner workings of a system, such as a radio. For the engineer, the answer is straightforward: you trace out the transistors, resistors, capacitors etc., and then draw an electrical circuit diagram. At that point you have ...
00:26 < archels> ... understood how the radio works and have sufficient information to reproduce its function. For the biologist, as Lazebnik suggests, the answer is more complicated. You first get a hundred radios, snip out one transistor in each, and observe what happens.
00:31 < ebowden_> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/22532431
00:31 < fenn> he's sleeping
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00:51 < nmz787> archels: we have that paper, it is good
00:52 < nmz787> erhmm, i guess i read it elsewhere http://www.uic.edu/labs/bml/BML/Stuff/Stuff_files/biologist%20fix%20radio.pdf
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02:42 < ebowden_> http://www.ncbi.nlm.nih.gov/pubmed/22532431
02:43 < ebowden_> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/22532431
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03:25 < ebowden_> paperbot: http://www.pnas.org/content/111/23/8458.abstract
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04:38 < archels> kanzure: could you suggset any good library for working with meshes; generating shapes, geometric operations, writing to file and so on?
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05:15 < kanzure> archels: meshlab?
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05:29 < kjskjskjs> that's not a library
05:29 < kjskjskjs> archels: I couldn't find a good one and so I wrote a bad one: https://github.com/kragen/stl3dpy
05:29 < kjskjskjs> CGAL has a bunch of geometric operations (not specifically on meshes)
05:30 < kanzure> salome has lots of mesh stuff
05:30 < kanzure> (from the opencascade people)
05:30 < kanzure> actually, opencascade... but check if salome solves your problems first.
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05:41 < kanzure> http://gregegan.customer.netspace.net.au/FOUNDATIONS/
05:41 < kanzure> podcast about lack of access to academic research http://letstalkbitcoin.com/blog/post/lets-talk-bitcoin-158-ebola-and-the-body-blockchain
05:43 < kjskjskjs> http://www.salome-platform.org/user-section/about/geometry mentions "Pipe creation"
05:43 < kjskjskjs> do you suppose that's the operation CATIA calls "shell"?
05:43 < kjskjskjs> oh, and it also has "fillet" and "chamfer". nice!
05:44 < kjskjskjs> it also mentions "shell" under "topological objects"
05:44 < kjskjskjs> I think this is the library I have been wishing for!
05:48 < kjskjskjs> thank you very much, kanzure!
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05:50 < archels> kjskjskjs: that's about the point I'm at, just some Python loops writing out a WaveFront OBJ file
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05:51 < kanzure> .title http://vimeo.com/102167635
05:51 < yoleaux> DevOpsDays Brisbane 2014 - Sidney Decker - System Failure, Human Error: Who's to Blame? on Vimeo
05:52 < kanzure> "... this year's keynote address focusing on the history of our understanding of system failures and the assumed role of human error."
05:52 < kjskjskjs> archels: yeah.  this SALOME thing looks like it could help a lot.
05:53 < kanzure> meh he's just promoting his own crappy books
05:53 < kanzure> nevermind
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05:54 < archels> geometry to mesh? neat
05:54 < kjskjskjs> yeah!
05:55 < kanzure> "This book explores complexity theory and systems thinking to better understand how complex systems drift  into failure. It studies sensitive dependence on initial conditions, unruly technology, tipping points, diversity—and finds that failure emerges opportunistically, non-randomly, from the very webs of relationships that breed success and that are supposed to protect organizations from disaster. It develops a vocabulary that allows us to ...
05:55 < kanzure> ... harness complexity and find new ways of managing drift."
05:55 < kanzure> "you are fucked"
05:56 < kjskjskjs> I'm still trying to get a handle on topology optimization in mechanical design, now that I know it exists
05:56 < kanzure> if you didn't know about opencascade then i should inform you about https://github.com/tpaviot/oce
05:57 < kanzure> and about http://www.pythonocc.org/
05:57 < kanzure> and https://github.com/dcowden/cadquery
05:59 < kanzure> and the examples and fancypants screenshots on http://opencascade.org/
05:59 < kanzure> (context: salome and opencascade share a lot of code and history)
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06:28 < alusion> http://www.abc.net.au/news/2014-11-04/scientists-reverse-ageing-process-in-mice/5865714
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06:47 < ebowden_> Isn't that fairly old news?
06:53 < kanzure> prolly
06:55 < FourFire> kanzure: what about byzantine fault tolerance ?
06:55 < kanzure> what about it
06:56 < FourFire> which, according to my rather limited understanding of it is a design philosophy which assumes that everything in a system is fucked by default, and anyway attempts to make it work to some extent
06:56 < kanzure> http://2014.igem.org/Team:SF_Bay_Area_DIYbio
06:56 < kanzure> how is that diybio. fucking community labs.
06:57 < chris_99> haha
06:57 < kanzure> "is a community team of more than two dozen individuals from all walks of life, sponsored by DIYbio labs Counter Culture Labs from Oakland and BioCurious from Sunnyvale."
06:57 < kanzure> man i can't believe people tolerate this sort of poor reasoning
06:58 < chris_99> i'm not sure the benefits of vegan cheese, but if they can pull it off...
06:58 < kanzure> er, no i mean if you use a company or organization like biocurious, that's not diybio
06:58 < chris_99> ah sorry, didn't see that
07:00 < chris_99> but how could you do this diy, without expensive synthesizers, or is it possible to easily get hold of the required plasmids somehow?
07:05 < kanzure> why is it important that you do it without expensive synthesizers?
07:06 < chris_99> it's not, i guess, but they seem prohibitively expensive for most people
07:06 < kanzure> yeah well that's not my fault :p
07:06 < chris_99> heh
07:07 < chris_99> could you isolate the plasmid from something already existing, or is that not possible?
07:10 < kanzure> .wik plasmidome
07:10 < yoleaux> "The term Plasmidome refers to the total plasmids content that is available in a certain environment. The term is a portmanteau of the two English words Plasmid and Kingdom." — http://en.wikipedia.org/wiki/Plasmidome
07:11 < kanzure> .title http://www.youtube.com/watch?v=Ek49JSAiKjY
07:11 < yoleaux> c_elegans.avi - YouTube
07:11 < kanzure> .title https://www.youtube.com/watch?v=mM_C-AkVrDQ
07:11 < yoleaux> caenorhabditis elegans, locomotion model - YouTube
07:11 < kanzure> .title http://www.biomedcentral.com/1471-2202/12/S1/P363
07:11 < yoleaux> BMC Neuroscience | Full text | CLONES : a closed-loop simulation framework for body, muscles and neurons
07:11 < kanzure> history of progress in simulating c. elegans https://docs.google.com/spreadsheets/d/1NclOVMRIqY_hn-aL8MdLlJrfuhDgNJyk_ChsZMjugmE/edit
07:12 < kjskjskjs> "kingdom"? "genome" comes from "kingdom"‽
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07:15 < archels> no, it comes from genus + chromosome
07:15 < archels> .ety genome
07:15 < yoleaux> genome (n.): ""sum total of genes in a set," 1930, modeled on German genom, coined 1920 by German botanist Hans Winkler, from gen "gene" + (chromos)om "chromosome."" — http://etymonline.com/index.php?term=genome
07:15 < archels> .ety gene
07:15 < yoleaux> gene (n.): "1911, from German Gen, coined 1905 by Danish scientist Wilhelm Ludvig Johannsen (1857-1927), from Greek genea "generation, race" (see genus). De Vries had earlier called them pangenes. Gene pool is attested from 1950." — http://etymonline.com/index.php?term=gene
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07:15 < kanzure> gene pool is from 1950?
07:18 < pasky> ah maybe i should add some comments there
07:18 < kanzure> hm?
07:19 < pasky> wrt. nemaload
07:19 < pasky> already did
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07:24 < archels> oh, great. "university branch organisation VSNU in The Netherlands terminates negotiations with Elsevier over open access policies. potential disruptions in the usual way in which you access articles in these journals. we apologize for the inconvenience."
07:25 < kanzure> haha you are boned
07:36 < kjskjskjs> hopefully they were trying to pressure Elsevier for more open access and so the end result will be that we are all less boned
07:37 < kanzure> a $7 billion gorilla like this is really problematic
07:37 < kanzure> i mean, $7 billion can tolerate a lot of er, disruption, or whatever it's called
07:39 < kjskjskjs> yeah.  RIP Aaron.
07:41 < kanzure> it's funny how aaronsw gets all the credit for gmaxwell's monster jstor torrent dump
07:41 < kanzure> i can see how it might seem confusing
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07:44 < kjskjskjs> well, gmaxwell wouldn't have done it without aaronsw to give him the courage or outrage or whatever
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08:43 < heath> augur: :)
08:43 < kanzure> http://datassette.net/content/datashat-businessfunk2.mp3
08:43 < heath> i guess the amount of work is piling up on your end around this time
08:45 < nmz787_i1>  kanzureis there a reason you didn't recommend salome to me? just forgot?
08:47 < kanzure> what was i supposed to recommend it to you for?
08:48 < nmz787_i1> CAD stuff
08:48 < kanzure> lots of salome is just opencascade
08:52 < justanotheruser> If publishers had no incentive to pay their editors then what would scientists end up doing to get published?
08:55 < kanzure> dingo: there should be a thing to make simple summaries of strace log output, like collapsing similar messages or sequences or something
08:55 < kanzure> justanotheruser: most editors are currently not paid anyway
08:56 < kanzure> http://online.wsj.com/articles/mark-wetjen-bringing-commodities-regulation-to-bitcoin-1415060058
08:57 < justanotheruser> kanzure: What do you think of this model? Authors self publish to some set of websites, peers review it and sign a hash of the paper plus their comments, users of these websites construct a WoT for peer reviewers to determine the legitemacy of the paper.
08:58 < justanotheruser> paperbot: http://online.wsj.com/articles/mark-wetjen-bringing-commodities-regulation-to-bitcoin-1415060058
08:58 < kanzure> i very strongly doubt that it is a problem of technology at this point
08:58 < kanzure> it's entirely a problem of reputation
08:58 < kanzure> and career metrics
08:59 < kanzure> there was a whole fad about "alt metrics" that was trying to get launched around 2007-2011 but never went anywhere
08:59 < justanotheruser> alt metrics?
08:59 < kanzure> you know, other than isi web of knowledge impact factor
09:00 < kanzure> btw you can get access by querying google for "wsj wetjen cftc bitcoin" or clicking one of their url redirection link thingies
09:02 < yorrick> kanzure: got a record on gmaxwell's torrent?
09:02 < kanzure> .wik impact factor
09:02 < yoleaux> "The impact factor (IF) of an academic journal is a measure reflecting the average number of citations to recent articles published in the journal. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones." — http://en.wikipedia.org/wiki/Impact_factor
09:02 < kanzure> yorrick: https://thepiratebay.se/torrent/6554331
09:02 < yorrick> kanzure: gracias
09:02 < yorick> oh god why is there a yorrick
09:03 < yorrick> yorick, sorry dude, I'll drop this nick. Didn't realize a "yorick" existed at the time
09:03 < kanzure> i hired him to replace you
09:03 < yorick> yorrick: nah, it's okay
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09:03 < yorick> kanzure: what was my function anyways
09:04 < kanzure> who knows, that's why you're fired
09:04 < justanotheruser> is yorick a bot?
09:04 < yorick> not that I know of
09:06 < justanotheruser> yorick: what is the 2nd derivative of acceleration
09:06 < PoorYorrick> lel
09:07 < yorick> I know the 2nd integration, that's location
09:07 < yorick> is that good enough?
09:07 < PoorYorrick> justanotheruser: the 1st derivative of a jerk? ;)
09:07 < PoorYorrick> 3rd*
09:08 < PoorYorrick> There's supposed to be a pun in there somewhere.
09:08 < yorick> jounce!
09:08 < yorick> https://en.wikipedia.org/wiki/Jounce do people just make this up
09:08 < justanotheruser> PoorYorrick: the guy who shakes hands with the guy who shakes your hand.
09:08 < yorick> "snap", "crackle", "pop"
09:08 < PoorYorrick> kanzure: dem ads on piratebay...
09:10 < justanotheruser> yorick: are you from a former soviet country?
09:10 < yorick> no.
09:10 < justanotheruser> is your name yorick?
09:10 < yorick> yes
09:10 < justanotheruser> are you a descendant of a viking?
09:11 < yorick> probably?
09:11 < justanotheruser> are you > 72 inches tall?
09:11 < yorick> yes
09:11 < justanotheruser> ok
09:11 < yorick> but so is everyone here
09:11 < justanotheruser> really?
09:11 < PoorYorrick> Yeah, I'm like 90 inches soft.
09:11 < yorick> netherlands
09:11 < justanotheruser> oh
09:12 < justanotheruser> I thought you meant ##hplusroadmap
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09:15 < chris_99> http://nextglass.co/beer-census/
09:17 < justanotheruser> If that really works its strange that they limit it to beer
09:17 < chris_99> spectrometize everything!
09:17 < chris_99> can't see why it wouldn't work
09:18 < chris_99> you can get stuff like IBU etc. via mass spectrometery iirc
09:23 < PoorYorrick> Anyone ever read this before?
09:23 < PoorYorrick> http://en.wikipedia.org/wiki/User:Asmodeus/pseudosciencerfarb
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09:31 < kanzure> http://datassette.net/content/datashat-businessfunk3.mp3
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09:48 < heath> "Naples is one of the wealthiest cities in the United States, with the sixth highest per capita income in America,[5] and the second highest proportion of millionaires per capita in the US"
09:48 < heath> seems like we need a startup scene here :)
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10:08 < heath> neat, coworking space downtown has fiber
10:08 < heath> http://zincubate.com/venture-x-coworking-offices
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10:57 < FourFire> PoorYorrick: I'm not going to read all of that
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10:57 < PoorYorrick> FourFire: I have. At least twice. Entertaining stuff. :P
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11:21 < kanzure> .d will
11:21 < yoleaux> kanzure: Sorry, that command (.d) crashed.
11:21 < kanzure> "expressing the future tense."
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11:32 < heath> https://www.kickstarter.com/projects/chaibio/open-qpcr-dna-diagnostics-for-everyone
11:33 < heath> mac cowell
11:35 < heath> hm, schloendorn even?..
11:36 < heath> it doesn't look like opentrons is going to meet their goal
11:52 < delinquentme> heath, what about these guys??
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11:55 < delinquentme> COOL
12:25 < heath> delinquentme: eh?
12:25 < heath> those two are associated with the open-qpcr it looks like from the vid
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12:30 < kanzure> http://opencores.org/project,bluespec-80211atransmitter
12:30 < kanzure> http://opencores.org/project,bluetooth
12:30 < kanzure> https://github.com/RangeNetworks/openbts
12:30 < kanzure> https://github.com/travisgoodspeed/80211scrambler
12:30 < kanzure> https://github.com/ewa/802.11-data
12:31 < kanzure> openbts is curious http://openbts.org/
12:32 < kanzure> "The OpenBTS software is a Linux application that uses a software-defined radio to present a standard 3GPP air interface to user devices, while simultaneously presenting those devices as SIP endpoints to the Internet. This forms the basis of a new type of wireless network which promises to expand coverage to unserved and underserved markets while unleashing a platform for innovation, including offering support for emerging network ...
12:32 < kanzure> ... technologies, such as those targeted at the Internet of Things."
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12:37 < kanzure> that's really unfortunate because i thought 3gpp was an mpeg container format
12:37 < kanzure> .wik 3gp
12:37 < yoleaux> "3GP (3GPP file format) is a multimedia container format defined by the Third Generation Partnership Project (3GPP) for 3G UMTS multimedia services. It is used on 3G mobile phones but can also be played on some 2G and 4G phones." — http://en.wikipedia.org/wiki/3gp
12:38 < kanzure> "OpenBTS-GSM (2.5G) supports SDRs from vendors such as Ettus Research, Fairwaves, and Nuand, as well as Range Networks’ SDR1, which is found in its development kit and base station products, and whose design files have been open-sourced and can be found below and at Github. If you choose a product which connects via Ethernet, make sure your Linux server has a dedicated Ethernet port for the radio."
12:39 < kanzure> "The Range Networks SDR1 consists of two individual PCBs that work in tandem, referred to as the SDR module and the RF module (or board). The SDR module provides signal processing and digital data transfer between the RF signals and the host. The RF module provides the wireless transmission of the data. The SDR and RF module boards are each on a 5.5″ x 3.25″ PCB outline. This is a stacked design with a single interface connector between ...
12:39 < kanzure> ... them. The RF module uses the same PCB layout with different component stuffing options and is capable of supporting the following frequency bands: 850, 900, 1800, 1900 MHz. The SDR1 is based in large part on the USRP1 design."
12:40 < kanzure> pcb stuff https://github.com/RangeNetworks/hardware-designs
12:41 < kanzure> http://openbts.org/site/wp-content/uploads/2014/07/OpenBTS-4.0-Manual.pdf
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13:45 < chris_99> are there any sites specifically for manuals of old random pieces of lab equipment out of interest
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13:58 < kanzure> yes i think it's called hplusroadmap
13:58 < kanzure> drethelin might know, actually
14:01 < jrayhawk_> i am sure if you link to it somewhere, kanzure will compulsively shove it in his papers repository
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14:07 < chris_99> heh, i just found this www.ebay.co.uk/itm/Mass-Spectrometer-Waters-Micromass-Tof-Spec-2E-/281482569637 was just curious to find the manual for it, to see what it could do
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14:20 < kanzure> hello eudoxia
14:20 < eudoxia> hey kanz
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14:47 < kanzure> .tw https://twitter.com/xor/status/529428190729478144
14:47 < yoleaux> Now that Sherlock is in the public domain I guess the FBI is free to make an adaptation where he can't figure out crimes because of crypto (@xor)
14:48 < chris_99> heh
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15:19 < heath> upvotes welcome https://www.reddit.com/r/robotics/comments/2lb63h/opentrons_opensource_rapid_prototyping_for_biology/
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15:21 < chris_99> 'there doesn't seem to be anything here'
15:25 < heath> chris_99: it's a link to the kickstarter page
15:25 < chris_99> oh i thought there was supposed to be a comment
15:25 < chris_99> is that your kickstarter?
15:26 < heath> chris_99: nope
15:26 < heath> i want it to succeed though
15:27 < chris_99> :)
15:47 < nmz787_i> https://www.youtube.com/watch?v=_VFsdPAoI1g
15:48 < nmz787_i> .title
15:48 < yoleaux> Make It Wearable Finalists | Meet Team Nixie - YouTube
15:48 < nmz787_i> 'Team Nixie (http://flynixie.com) is developing the first wearable drone camera, which can be worn around your wrist.'
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15:57 < chris_99> how does it do object detection tho?
16:23 < nmz787_i> https://www.kickstarter.com/projects/chaibio/open-qpcr-dna-diagnostics-for-everyone
16:31 < nmz787_i> 'releasing cad designs and software'
16:35 < nmz787_i> oh, wait, that's just what their video said, the text lower down says "The hardware design, including BOM, SolidWorks files, and Eagle CAD will all be released as open source when the machine ships, and are available sooner as an early access reward."
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17:36 < nmz787> kanzure: know anyone in pdx that would be a lab tech for us?
17:37 < nmz787> I have to assume that the quality of that qPCR machine is good enough now, since they're trying to kickstart it... but I wonder if it isn't for some applications, and whether if I got it, would I even have the time to prep and run the thing
17:42 < kanzure> "fr us"?
17:42 < kanzure> *for
17:42 < kanzure> i would consider pestering lichen, i guess, depending what "us" is
17:44 < kanzure> .title https://github.com/iimarckus/pokered/pull/61
17:44 < yoleaux> Charmaps by stag019 · Pull Request #61 · iimarckus/pokered · GitHub
17:44 < kanzure> there goes my preprocessor. oh well.
17:44 < kanzure> it sucked anyway
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18:18 < nmz787> idk, someone to throw monotonous bio tasks at
18:19 < kanzure> try lichen first
18:20 < nmz787> lichen: hi
18:20 < nmz787> what is a fair rate for bio technicians?
18:20 < nmz787> or range
18:20 < nmz787> for like making media
18:20 < nmz787> and plating cells
18:20 < kanzure> apparently $10-$20/hour
18:21 < nmz787> running qpcr
18:21 < nmz787> mm
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18:51 < ParahSailin_> qpcr is so old fashioned
18:51 < ParahSailin_> some biologists apparently need to be dragged into the ngs age kicking and screaming
18:54 < nmz787> how does it compete with it for on-site diagnostics?
18:55 < nmz787> I could put this in a lab room at my farmers new building and he could use it on-site just after he milks, for example
19:06 < sheena> blah
19:09 < sheena> nmz787: did we talk about my chicken diagnostic problem?
19:12 < nmz787> no, but I think I saw something about it in the logs at one point
19:12 < sheena> there is a chicken disease that can be transmitted through eggs
19:12 < sheena> mycoplasma
19:12 < nmz787> ok, yeah, i've tested for that before
19:12 < sheena> ok
19:12 < sheena> is on-farm testing something that owuld be worth even considering for it?
19:13 < nmz787> qpcr /should/ be able to tell you yes/no
19:13 < sheena> thats an emphatic should...
19:13 < nmz787> well it will, if the primers work
19:13 < nmz787> but i'm not sure how much reagents are these days
19:14 < nmz787> i think i used to get qpcr kits for free
19:14 < nmz787> as samples
19:15 < sheena> oh hm
19:15 < sheena> we'd be needing to test flocks.. would we be able to mix samples?
19:15 < nmz787> but yeah i did qpcr and it's the standard protocol, or was
19:15 < nmz787> you could mix samples, but then you would only know if someone in the mix had it, but not who
19:16 < nmz787> the unit has 8 or 16 wells
19:16 < nmz787> but the description of it is worded a bit strangely
19:17 < nmz787> 'The software supports amplification curve Ct thresholds, presence/absence detection, melt curve analysis, and relative quantification. Software support for absolute quantification may be ready by the shipping date, or will otherwise be made available shortly thereafter as a free downloadable update. It's a bit tricky to do absolute quantification with a 16 well block, but we've got some ideas.'
19:19 < sheena> right, we'd be testing flocks, so if anyone comes back positive, we'd test that flock for individuals?
19:19 < kanzure> you could just assign one well per unit-mammal
19:20 < sheena> the place we sent samples to says they use 3 tests.. ELisa, Hemagglutination inhibition and molecular diagnostic services..
19:20 < nmz787> prices for 'mastermix' (not including primers) from VWR is (t# ests : price) "100 : $187.68 , 500 : $849.66 , 2000 : $3,165.06"
19:20 < nmz787> #tests *
19:20 < nmz787> this would be the latter
19:20 < nmz787> 'molecularz'
19:21 < nmz787> ELISA is a good one too
19:21 < nmz787> always good to have more data, unless you're cheap
19:21 < sheena> indeed
19:21 < sheena> cheap wou ldbe the issue
19:21 < nmz787> but at the prev posted prices, qpcr from VWR isn't too cheap
19:22 < sheena> so less than $2/test, but an initial $1500 outlay for the machine?
19:22 < nmz787> $1300 today
19:23 < nmz787> so one local machine could be running stuff for you and my farmer buddy... now we just need someone to run it and also to get more farmer buddies who need stuff tested
19:23 < nmz787> i wonder if it showed up at one of the hackerspaces, if someone would be enticed into running samples
19:24 < nmz787> $1300 is a lot to drop for me personally right now
19:28 < sheena> we have a hackerspace working on opening up at ht emoment
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19:29 < nmz787> ctrl-h?
19:29 < sheena> at the?
19:29 < sheena> moment
19:29 < sheena> ugh
19:29 < nmz787> is it ctrl-h?
19:29 < nmz787> wait, are you in pdx?
19:30 < sheena> um
19:30 < sheena> i dont think im any of those things
19:30 < sheena> lol
19:30 < sheena> im in kamloops bc
19:30 < sheena> if pdx is a geographical location
19:31 < sheena> brand new "innovation centre" with a modlab (robot things?) and some other stuff in the works here
19:32 < nmz787> it is an airport code
19:32 < nmz787> ah, cool
19:33 < nmz787> i'm in portland OR
19:33 < nmz787> well, just outside there
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19:50 < sheena> YKA is my airport code :)
19:50 < sheena> if that helps
19:51 < nmz787> :)
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19:59 < fenn> pretty awesome military/technical library http://archive.hnsa.org/doc/
20:01 < fenn> the foundry manual is basically the source information for the gingery series
20:03 < kanzure> haha http://www.ultrasound-autism.org/
20:03 < fenn> lame
20:04 < kanzure> an entire web page for every possible idea
20:04 < fenn> "Effects noted in two other research projects are low birth size and increased left-handedness."
20:04 < fenn> cure left-handedness, write the FDA today!
20:05 < kanzure> "it was never proven safe!!!"
20:05 < fenn> your children are at risk of not being able to use scissors
20:10 < kanzure> "Non Structural Closures, 2005"
20:10 < kanzure> "Photography (Advanced), 1995"
20:13 < fenn> "Through synthetic biology, we engineer our yeast to become milk-protein factories. Our milk proteins will then be combined with water and vegan oil to make Vegan Milk, which will ultimately be converted into Real Vegan Cheese through standard cheese-making processes"  once upon a time i might have thought this was a good idea
20:22 < fenn> "Another Soviet contribution to genetics in these years was the concept of gene pool. The Russian geneticist A. S. Serebrovskii first formulated the concept in terms of genofond (gene fund), a word that was imported to the United States from the Soviet Union by Theodosius Dobzhansky, one of the members of Chetverikov’s group, who translated it into English as “gene pool.” Today few people
20:22 < fenn> know that this term, so common in biological discourse the world over, has a Russian origin. Chetverikov, Serebrovskii, Filipchenko, Dobzhansky, Karpechenko, and Romashov were among the many pioneering Russian biologists of the 1920s."
20:24 < fenn> it's true, i read it in a book
20:43 < kanzure> "A cost analysis of intraoperative microelectrode recording during subthalamic stimulation for Parkinson's disease." http://www.ncbi.nlm.nih.gov/pubmed/21674622
20:43 < kanzure> "The average cost for subthalamic nucleus deep brain stimulation implantation with microelectrode recording per patient is $26,764.79 for unilateral, $33,481.43 for simultaneous bilateral, and $53,529.58 for staged bilateral. For unilateral implantation, the cost of microelectrode recording is $19,461.75, increasing the total cost by 267%. For simultaneous bilateral implantation, microelectrode recording costs $20,535.98, increasing the total ...
20:44 < kanzure> ... cost by 159%. For staged bilateral implantation, microelectrode recording costs $38,923.49, increasing the total cost by 267%. Microelectrode recording more than doubles the cost of subthalamic nucleus deep brain stimulation for Parkinson's disease and more than triples the cost for unilateral and staged bilateral procedures."
20:44 < kanzure> "... a mean operating room time of 223.83 minutes for unilateral and 279.79 minutes for simultaneous bilateral implantation."
20:47 < kanzure> i wonder if that means in malaysia or thailand that it's $5,000.
20:47 < fenn> what are they recording?
20:48 < kanzure> not really sure, i was more interested in the stimulation
20:49 < fenn> also how does adding 25% to the operating time increase cost by 267%?
20:50 < fenn> o wait i read that wrong
20:51 < fenn> tangentially related to libraries and gene pools http://genofond.ru
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21:23 < fenn> nmz787 sheena regular PCR would be just fine for detecting presence/absence of pathogen DNA
21:23 < fenn> although that machine is cute
21:24 < fenn> you would have to run a gel for regular pcr, though that's not as hard as it sounds
21:25 < fenn> getting the primers and making sure they work would be a small hurdle for either PCR or qPCR
21:26 < sheena> fenn: cost?
21:26 < fenn> i guess you could use the qPCR dsDNA dye instead of a gel for presence/absence
21:26 < fenn> not sure about cost, to me PCR means anything from buckets of water to a zillion dollar robot
21:27 < fenn> i do think $599 for openpcr is too much; the light bulb pvc pipe thingy looked about right
21:27 < fenn> http://www.russelldurrett.com/lightbulbpcr.html
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21:30 < fenn> i'd say $50 for the materials and electronics, plus $2 per test, and primers are like $30(?)
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21:33 < fenn> you'll also need a p200 micro pipettor and eppendorf tubes
21:35 < fenn> .title http://www.sigmaaldrich.com/catalog/product/sigma/mp0035?lang=en&region=US
21:35 < yoleaux> LookOut® Mycoplasma PCR Detection Kit Optimized for use with JumpStart™ Taq DNA Polymerase, D9307. | Sigma-Aldrich
21:35 < fenn> impossible to get prices on anything
21:37 < fenn> apparently those tubes are "pre-coated with nucleotides, primers, and internal controls"
21:40 < fenn> this is probably intended for testing cell cultures, not chickens; the mycoplasma species may be too different, or it may just be close enough to work
21:43 < nmz787> i see prices for sigma
21:43 < fenn> how much is the kit?
21:43 < nmz787> $253.50
21:44 < fenn> that's a bit much for just one test
21:44 < nmz787> yes but it is more than that
21:44 < nmz787> http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/mp0035bul.pdf
21:45 < fenn> how is it more than just one test?
21:45 < fenn> oh, maybe it's 3 tests
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21:48 < fenn> i wonder why it says "use of the PCR process requires a license"
21:48 < fenn> PCR has been out of patent protection for decades
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21:52 < fenn> After the publication of the first PCR paper, the United States Government sent a stern letter to Randy Saiki, admonishing him for publishing a report on "chain reactions" without the required prior review and approval by the U.S. Department of Energy. Cetus responded, explaining the differences between PCR and the atomic bomb.
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21:52 < fenn> it would be funny if the fate of the entire planet weren't in their hands
22:03 < catern> [citation needed]
22:03 < catern> http://en.wikipedia.org/wiki/History_of_polymerase_chain_reaction
22:03 < fenn> go cite yourself
22:03 < fenn> .title https://xkcd.com/978/
22:03 < yoleaux> xkcd: Citogenesis
22:17 < ebowden> Heh, didn't the guy who developed PCR end up becoming an aids denialist or something like that?
22:18 < fenn> if you read what he actually says, no
22:18 < fenn> if you believe fox news or whatever, yes
22:19 < fenn> basically he's upset that the CDC spends so much money on aids treatment because in the process they end up supporting "the aids establishment" and label things as aids that are really just diseases of the third world
22:19 < fenn> opportunistic infections resulting from weakened immune systems due to aids look mighty similar to opportunistic infections from weakened immune systems due to malnutrition
22:20 < fenn> i'm actually trying to find the book "dancing in the mind fields" if anyone has it
22:21 < fenn> field*
22:34 < fenn> lol "Duesberg proposed his hypothesis that AIDS is caused by long-term consumption of recreational drugs and/or antiretroviral drugs, and that HIV is a harmless passenger virus."
22:34 < fenn> so aids is caused by anti-aids drugs, problem solved
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22:40 < fenn> "although Duesberg and the AIDS denialist movement have garnered support from some prominent scientists, including Nobel Prize winner Kary Mullis, most of this support is related to Duesberg’s right to hold a dissenting opinion, rather than support of his specific claim that HIV does not cause AIDS."
22:42 < sheena> how bout i send you some samples, fenn and you make me a tester machine? :D
22:42 < fenn> wah
22:43 < fenn> i've been trying to get away from biology since 2003
22:46 < fenn> i thought for sure there would be a $50 diybio lab in a box kit by now
22:52 < sheena> make ittttttt
22:53 < sheena> what do you want to do instead of bio?
22:54 < fenn> tech-nomadism and wearable enhancements
23:10 < fenn> sheena: here's a list of documents related to things i'm interested in; it may or may not make any sense http://fennetic.net/irc/stuff
23:11 < sheena> those both sound like biology to me
23:11 < sheena> foam puzzle mats.gnumeric?
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23:14 < fenn> trying to find the cheapest play mat tiles per square foot
23:14 < fenn> i'd rather have the gray ones but it seems colorful alphabet is 20% less, and more widely available
23:17 < sheena> heh we have this same issue
23:17 < sheena> but i suspect not for the same reason
23:17 < sheena> what are you using it for?
23:18 < fenn> floor covering
23:18 < fenn> i've used blue EPS board but it tends to get dinged up
23:19 < fenn> polyurethane foam is tougher and interlocks
23:19 < fenn> basically i hate carpet
23:22 < fenn> it's hard to know if something is a book or a paper, or if this categorization even matters anymore
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23:26 < sheena> carpet hate is reasonable. you want soft/insulating?
23:26 < fenn> right
23:27 < sheena> https://www.facebook.com/5stardogs/photos/pb.221290505558.-2207520000.1415172437./10152679346915559/?type=3&theater
23:27 < sheena> this is what we do with them
23:27 < fenn> i figured it was something to do with dogs :)
23:27 < sheena> there are some INCREDIBLE floors out there
23:28 < sheena> depending what your needs are re insulation, cushion, traction, impact....
23:28 < sheena> cost.. heh
23:29 < fenn> EPS or polyisocyanurate with radiant barrier can provide a good deal of insulation and and impact absorption, if you use it underneath the foam mat
23:30 < fenn> i started using EPS for lost foam metal casting, and started finding lots of other uses for it
23:30 < fenn> there's a white bead board version that's even cheaper and squishier
23:31 < fenn> what's the pole slalom course called? and why isn't it a human sport?
23:31 < sheena> http://dinoflex.com/index.php/product/walk_soft
23:32 < sheena> agility?
23:32 < sheena> pole slalom being the weave poles?
23:32 < fenn> right
23:41 < fenn> http://www.armynavydeals.ca/asp/products_details.asp?SKU=b0923200
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23:42 < fenn> oh sorry here's the spreadsheet http://fennetic.net/irc/foam_puzzle_mats.gnumeric
23:42 < fenn> the background maybe is black so select all
23:49 < fenn> http://n55.dk/MANUALS/BED_MODULES/BED.html
23:49 < fenn> 60 cm triangles, polyethylene foam density 40 kg / m3, 20 mm and 10 mm
23:49 < fenn> Velcro tape 20 mm
23:49 < fenn> seems the velcro would get expensive
23:59 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 265 seconds]
--- Log closed Wed Nov 05 00:00:41 2014