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01:31 < nmz787> .wik cfd-ace+
01:31 < yoleaux> "CFD-ACE+ is a commercial computational fluid dynamics solver developed by ESI Group. It solves the conservation equations of mass, momentum, energy, chemical species and other scalar transport equations using the finite volume method." — http://en.wikipedia.org/wiki/CFD-ACE%2B
01:33 < nmz787> .title https://www.youtube.com/watch?v=IWKXChpTbqg
01:33 < yoleaux> Lava Lamp simulation with ACE+ - YouTube
01:33 < nmz787> this obviously must become the hello world of physics simulators
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01:41 < nmz787> .wik parabolos
01:41 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
01:42 < nmz787> .wik palabos
01:42 < yoleaux> "OpenFOAM (Open source Field Operation And Manipulation) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems, including computational fluid dynamics (CFD)." — http://en.wikipedia.org/wiki/OpenFOAM
01:42 < nmz787> hmm, I am watching this https://www.youtube.com/watch?v=I82uCa7SHSQ
01:42 < nmz787> .title
01:42 < yoleaux> Introduction to Lattice Boltzmann Method @ Nasa Glenn 2013 - YouTube
01:42 < nmz787> .title http://www.palabos.org/software/lattice-boltzmann-method
01:42 < yoleaux> Lattice Boltzmann Method
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08:18 < FourFire> Hey, I'd like to bring up the topic of http://sl4.org/shocklevels.html I'm sure I have before, but I'd like to know whether anyone in here thinks there is any purpose to updating them to 2015?
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08:22 < FourFire> I would appreciate reading an updated version of the essay, but I think I remember last time I brought up the topic, it was ridiculed as being old
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08:29 < kanzure> what was the point of trying to measure someone's "shock" anyway
08:30 < FourFire> kanzure, determine whether you can work with them for transhumanist progress plans
08:31 < kanzure> so if they are experiencing "shock" by definition they are incapable of working on related engineering projects ?
08:31 < FourFire> or whether they need more exposure to real hard transhumanist science/ speculative engineering since they're still on the reddit stargazer memespewer level
08:33 < kanzure> you may have more luck starting with people who are already working on transhumanist engineering projects instead
08:33 < FourFire> I see it as a tool for sorting people you interact with into people worth spending time on, and people not worth that time, not so much as a mastabatory measure of elite nerdyness
08:34 < FourFire> but there aren't enough!
08:34 < FourFire> we need more people!
08:37 < eudoxia> this is the one think where i agree with dale carrico
08:37 < eudoxia> >futurists boasting about how much techno-transformative storm-churn their manly meme muscles can take as compared to meek mehum sheeple of the "luddite" herd
08:38 < kanzure> er, what about that boasting?
08:38 < eudoxia> he's talking about the awfulness of shock levels
08:38 < kanzure> so he was saying something like "shock evels are an example of <that quote you pasted>"?
08:39 < eudoxia> yes
08:39 < kanzure> ah
08:42 < kanzure> there's probably some sort of social benefit to giving people some way of discriminating against out-group
08:42 < kanzure> especially if your social group sucks at maintaining friendships on its own
08:42 < maaku> i am remined of the the Little Prince and a certain picture of a snake eating an elephant
08:42 < kanzure> but this particular social in-group/out-group discrimination is totally broken because people who think "other shock levels are silly" are still capable of doing interesting engineering work
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08:43 < maaku> kanzure: +1
08:44 < kanzure> maaku: http://diyhpl.us/wiki/dna/projects/#igem
08:44 < kanzure> maaku: also https://groups.google.com/group/enzymaticsynthesis has some ideas for enzymatic synthesis of dna and proteins (e.g. aiming for $1/genome or less)
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10:09 < heath> man, purescript is where it's at
10:16 < kanzure> why's that?
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10:21 < kanzure> .wik mothers against decapentaplegic homolog 3
10:21 < yoleaux> "Mothers against decapentaplegic homolog 3 also known as SMAD family member 3 or SMAD3 is a protein that in humans is encoded by the SMAD3 gene. SMAD3 is a member of the SMAD family of proteins. It mediates the signals from the transforming growth factor beta (TGF-β) superfamily ligands that regulate cell proliferation, differentiation and death." — http://en.wikipedia.org/wiki/Mothers_against_decapentaplegic_homolog_3
10:24 < heath> see the fanboyism section at https://gist.github.com/heath/b1525f4c87d104546f65#some-fanboyism
10:26 < heath> static typing, pure functions, and property-based testing makes me feel a bit more comfortable when refactoring large code bases
10:27 < heath> also, immutable data structures plus a virtual dom is generally faster than whatever you would get in angular or pure react.js
10:29 < heath> http://elm-lang.org/blog/Blazing-Fast-Html.elm
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11:04 < QuadIngi> "<maaku> i am remined of the the Little Prince and a certain picture of a snake eating an elephant" in what way?
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11:11 < heath> https://s3.amazonaws.com/static.noisetrade.com/w/91c80015-cd39-49d4-8dd1-bfee3914a790/the_8bit_hymnal_2_christmas.zip?AWSAccessKeyId=1JYYXR88GV8RGYAXTHR2&Expires=1420139484&Signature=FkGrJoKQI4yyJ20032qfc%2Bu42U8%3D
11:11 < heath> 8bit hymnal
11:12 < heath> (music)
11:21 < kanzure> insect flight muscle (protein) http://www.pdb.org/pdb/explore/sequenceCluster.do?structureId=2W49&entity=4&cluster=1403&seqid=30
11:21 < kanzure> no wait, i mean http://www.rcsb.org/pdb/explore.do?structureId=2W49
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11:28 < kanzure> cool you can search proteins by subcellular location http://www.uniprot.org/locations/
11:29 < kanzure> "fimbrium"
11:29 < kanzure> http://www.ebi.ac.uk/QuickGO/GSearch?q=Click%20for%20example%20search
11:34 < nmz787> paperbot: http://link.springer.com/article/10.1007%2Fs10404-010-0720-2
11:42 < nmz787> http://diyhpl.us/~nmz787/pdf/Culture_and_chemical-induced_fusion_of_tobacco_mesophyll_protoplasts_in_a_microfluidic_device.pdf
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11:50 < kanzure> i am not sure why this protein looks the way it does
11:50 < kanzure> .wik apoptosome
11:50 < yoleaux> "The apoptosome is a large quaternary protein structure formed in the process of apoptosis. Its formation is triggered by the release of cytochrome c from the mitochondria in response to an internal (intrinsic) or external (extrinsic) cell death stimulus." — http://en.wikipedia.org/wiki/Apoptosome
11:56 < yashgaroth> shit man that's the last structure the cell's gonna form, it might as well look cool
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12:15 < kanzure> .wik chaperonin
12:15 < yoleaux> "Chaperonins are proteins that provide favourable conditions for the correct folding of other proteins, thus preventing aggregation. Newly made proteins usually must fold from a linear chain of amino acids into a three-dimensional form. Chaperonins belong to a large class of molecules that assist protein folding, called molecular chaperones." — http://en.wikipedia.org/wiki/Chaperonin
12:16 < kanzure> http://people.cryst.bbk.ac.uk/~ubcg16z/cpn/elmovies.html
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12:24 < kanzure> .wik ferritin
12:24 < yoleaux> "Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including algae, bacteria, higher plants, and animals. In humans, it acts as a buffer against iron deficiency and iron overload." — http://en.wikipedia.org/wiki/Ferritin
12:25 < kanzure> "Cavities formed by ferritin and mini-ferritins (Dps) proteins have been successfully used as the reaction chamber for the fabrication of metal nanoparticles (NPs).[30][31][32][33] Protein shells served as a template to restrain particle growth and as a coating to prevent coagulation/aggregation between NPs. Using various sizes of protein shells, various sizes of NPs can be easily synthesized for chemical, physical and bio-medical ...
12:25 < kanzure> ... applications"
12:25 < kanzure> .wik transferrin
12:25 < yoleaux> "Transferrins are iron-binding blood plasma glycoproteins that control the level of free iron in biological fluids. Human transferrin is encoded by the TF gene." — http://en.wikipedia.org/wiki/Transferrin
12:43 < kanzure> http://www.rcsb.org/pdb/explore/explore.do?structureId=4DNU "The Arabidopsis thaliana protein UVR8 is a photoreceptor for ultraviolet-B. Upon ultraviolet-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, which triggers a signalling pathway for ultraviolet protection. The mechanism by which UVR8 senses ultraviolet-B remains largely unknown. Here we report the crystal structure of UVR8 at 1.8 Å resolution, ...
12:43 < kanzure> ... revealing a symmetric homodimer of seven-bladed β-propeller that is devoid of any external cofactor as the chromophore."
12:43 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnature10931
12:47 < kanzure> what?
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12:50 < eudoxia> paperbot has achieved sentience, and is trying to communicate using DOI codes
13:20 < kanzure> "The 2003 Nobel Prize in Chemistry was awarded jointly to Peter Agre for the discovery of aquaporins,[4]"
13:21 < kanzure> "In most cells, water moves in and out by osmosis through the lipid component of cell membranes. Due to the relatively high water permeability of some epithelial cells it was long suspected that some additional mechanism for water transport across membranes must exist. But it was not until 1992 that the first aquaporin, ‘aquaporin-1’ (originally known as CHIP 28), was reported by Peter Agre, of Johns Hopkins University.[11]"
13:22 < kanzure> hehehe "However the first report of protein mediated water transport through membranes was by Gheorghe Benga in 1986.[14][15] This publication that preceded Agre's first publication on water membrane transport proteins has led to a controversy that Benga's work was adequately recognized by neither Agre nor the Nobel Prize Committee.[16] There is a long history of water pores, starting in 1957.[17] There have been many reviews of the ...
13:22 < kanzure> ... history.[18]"
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13:29 < Evoril> hi all :)
13:29 < Evoril> is this channel devoted to nootropics exclusively?
13:30 < Evoril> or other brain enhancment methods as well?
13:30 < heath> meanwhile in a war room: https://github.com/ecomfe/echarts#%E7%82%AB%E5%85%89%E7%89%B9%E6%95%88
13:30 < Evoril> like self-hypnosis, speed/photoreading etc.
13:31 < eudoxia> it's about transhumanism in general, nootropics sometimes, i don't think i've ever heard of those outside of some speedreading apps
13:31 < heath> https://github.com/isohuntto/openbay
13:32 < heath> https://github.com/gorhill/uBlock a more efficient adblock
13:33 < eudoxia> hmm someone should port openbay to a more reasonable language
13:35 < nmz787> Evoril: all that and a bag of chips!
13:36 < nmz787> .ud all that and a bag of chips!
13:36 < yoleaux> To mean that a person is all that and more. Usually it is an opinion and the only one who thinks it is that person. Other people usually don't believe the person is "all that and a bag of chips." The
13:37 < nmz787> 'Adj. 1) A superlative form of all that; something or someone which possesses all desired qualities PLUS unimagined or unforseen bonuses.'
13:38  * nmz787 hplusroadmap: all that, and a bag of chips (fried in tallow)
13:42 < eudoxia> but for real though
13:43 < kanzure> if people really want bioplastics then someone should sell them a bioplastic functionalized with gfp or something
13:43 < Evoril> alri im looking for some good torrents
13:44 < Evoril> collections or individual books
13:44 < kanzure> lobotomies are easier than self-hypnosis
13:44 < Evoril> all about nootropics,memory enhancement etc.
13:44 < Evoril> soo?
13:44 < Evoril> any recommendations?
13:44 < Evoril> like a private tracker i might not have heard of yet or smth?
13:44 < kanzure> hydrolases and methyltransferases look weird
13:47 < kanzure> dehydrogenases too
13:48 < kanzure> and there's a bunch of crab-shaped enzymes like thymidylate synthases http://www.rcsb.org/pdb/explore/explore.do?structureId=1VZE
13:50 < kanzure> and space invaders http://www.rcsb.org/pdb/explore/explore.do?structureId=3JQR
13:58 < kanzure> spinach aquaporin looks pretty different from human epithelial aquaporin http://www.rcsb.org/pdb/explore/explore.do?structureId=3CN5
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14:05 < Evoril> look im not a noob so i know how this works, anonimity is essential and its these type of questions are generally to be avoided so ill accept if u dont answer
14:05 < Evoril> but which private trackers are the best
14:05 < Evoril> for biohacking/brain-boosting type of content?
14:05 < Evoril> the ones im active on have verly little on the subject
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14:15 < archels> we are not unwilling to answer
14:15 < kanzure> paperbot: http://www.nature.com/nature/journal/v510/n7503/full/nature13404.html
14:15 < kanzure> .title
14:15 < yoleaux> Accurate design of co-assembling multi-component protein nanomaterials : Nature : Nature Publishing Group
14:15 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnature13404
14:16 < kanzure> "Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number ...
14:16 < kanzure> ... and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications."
14:16 < archels> Evoril: there are some repositories related to bootstrapping modern society... never really come across anything close to what you're asking for
14:17 < archels> I mean, kanzure hosts some PDFs, I host some PDFs... but that's probably going to be very underwhelming
14:17 < kanzure> the best source of biohacking information are scientific journals
14:18 < kanzure> also: i have now visually inspected the vast majority of all known proteins with more than 300 residues
14:18  * kanzure folds up and dies
14:18 < archels> league; out of
14:19 < archels> not everyone has a level 3 biohazard lab in their garage
14:19 < kanzure> you don't need a biohazard lab to read papers
14:19 < archels> reading is boring. what about the doing part
14:19 < kanzure> i'm gonna go find some food. looking at all those proteins has made me hungry.
14:20 < archels> sounds good
14:20 < nmz787> there are special biohacking torrent trackers? news to me!
14:20 < Evoril> im a first year biopharmacuticals undergrad
14:21 < Evoril> how can i contribute?
14:22 < nmz787> do you know anything about protein catalytics?
14:22 < nmz787> active site design would be a hit here
14:22 < nmz787> or are you more of an enzyme hunter?
14:22 < Evoril> well
14:22 < nmz787> or biologics extraction/purification?
14:22 < Evoril> as i said
14:23 < Evoril> first year undergrad only
14:23 < nmz787> or actually working toward a tech in a pharmacy?
14:23 < nmz787> *toward being a tech
14:23 < Evoril> so am a bit limited in terms of scientific expertise
14:23 < nmz787> like you started 3/4 months ago?
14:23 < nmz787> or you've already completed a year?
14:23 < Evoril> but will gladly participate in above mentioned projects
14:23 < Evoril> no
14:23 < Evoril> just started in september
14:24 < Evoril> but i am highly devoted to chem/bio
14:24 < Evoril> do lots of extra study on my own
14:24 < nmz787> by that time in my biotech program I think I new I wanted a 'genome compiler' device
14:24 < Evoril> and im a fast learner
14:24 < nmz787> but I didn't know much
14:25 < nmz787> just check out diyhpl.us
14:25 < nmz787> if you spend a good hour there scanning you can get an overview of what's available here
14:25 < Evoril> i was thinking about genetic sequencing
14:25 < nmz787> there are a bunch of pdfs and books
14:25 < Evoril> so would do postgrad bioinformatics
14:25 < poppingtonic> see igem.org
14:25 < Evoril> or post grad medicinal chemistry
14:26 < Evoril> not sure yet but still have 3 more years to decide :)
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14:26 < nmz787> no one really likes degrees in here, though we immensely value education, self or institutional. We mainly care about focus.
14:26 < nmz787> I think.
14:26 < nmz787> :)
14:28 < nmz787> I wanted to drop out during my first quarter of school, and now with 2 classes left, I feel pretty much the same
14:28 < nmz787> 6 years later
14:28 < nmz787> :P
14:30 < Evoril> ok so the communitys primary focus is on what? research or enhancing metabolism/cognitive skills for personal 'pleasure'??
14:31 < nmz787> 'advancing' humanity
14:31 < catern> hacking! the hacker spirit!
14:31 < nmz787> we basically talk about all forms of science, tech, math
14:31 < Evoril> yeah, well you are responsible for your studies, you won't become an expert just bc you attend college
14:31 < Evoril> and like i said, i do lots of self-teaching
14:33 < Evoril> memorizing structural formulas from the rubber bible is my idea of fun&relaxation xd :D:D
14:34 < nmz787> I am working on lab-on-a-chip stuff, always looking towards DNA synthesis, but doing lots of stuff from the ground up, so there are plenty of 'stepping stone' projects.
14:35 < Evoril> ok lets start w/ smth simple ok? :)
14:36 < Evoril> gimme an assignment all ill get back to you when its completed :)
14:40 < kanzure> nmz787: instead of saying humanity just link to http://diyhpl.us/wiki/declaration
14:41 < kanzure> humanity is highly ambiguous and usually made up of rude automatons
14:42 < kanzure> Evoril: i need a cheap design for a ct scanner
14:42 < nmz787> check out this paper and try to figure out if any of the promoters that were up/down regulated are unique and potentially useful for being hacked into turning on some other gene, say GFP... so that when the organism is pulsed with electricty it starts making GFP. http://diyhpl.us/~nmz787/pdf/Diversity_of_promoter_elements_in_a_Geobacter_sulfurreducens_mutant_adapted_to_disruption_in_electron_transfer.pdf
14:42 < nmz787> Evoril: ^
14:42 < kanzure> igem already did that
14:43 < kanzure> really what you need is that function in a single protein
14:46 < nmz787> where?
14:46 < nmz787> igem?
14:47 < kanzure> one of the 2014 projects http://diyhpl.us/wiki/dna/projects/#igem-2014
14:47 < Evoril> already done? still do it regardless (as a first time test of my performance) or do smth else instead?
14:48 < nmz787> I don't think it was done, looking now
14:48 < kanzure> i forget which word it was tagged under
14:50 < nmz787> google shows this http://2009.igem.org/Team:Missouri_Miners/Project and this http://2010.igem.org/Team:Missouri_Miners/Project and http://web.mst.edu/~igem/projects.htm
14:50 < kanzure> right, missouri miners have been doing similar things for a few years now
14:50 < kanzure> but their 2014 project seems unrelated <li><a href="http://2014.igem.org/Team:Missouri_Miners">nitrogen oxide fixation and conversion to ammonia</a></li>
14:50 < kanzure> <li><a href="http://2008.igem.org/Team:Missouri_Miners/Project">yeast sensor of ethanol</a></li>
14:50 < kanzure> <li><a href="http://2011.igem.org/Team:Missouri_Miners/Project">bacterial glucose sensor</a></li>
14:50 < kanzure> <li><a href="http://2012.igem.org/Team:Missouri_Miners/Project">anchoring proteins to cell surface</a></li>
14:50 < nmz787> I think you could do what I said largely in-silico (aka reading and using the online tools)
14:51 < nmz787> anyway, g2g help a farmer load hay into a trailer
14:52 < nmz787> lata
14:59 < Evoril> ok so do it or not?
15:04 < kanzure> do whatever you want
15:05 < fenn> go fighting doctors, rah rah rah
15:06 < juri_> completed my talk at the CCC.
15:06 < Evoril> ok will get to in the morning
15:06 < fenn> juri_ you should be schmoozing
15:06 < fenn> schmooze damn you, schmooze like your life depended on it!
15:07 < juri_> i'm hanging with reprap folks.
15:09 < kanzure> you should go find petertodd and absorb his powers
15:09 < kanzure> nsh is also there
15:09 < kanzure> you should go find nsh
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15:13 < kanzure> fenn: thoughts about the ribosome/tRNA scheme for protein synthesis?
15:14 < kanzure> also extropy-chat recommended this http://en.wikipedia.org/wiki/Dr._Zeus_Inc.
15:15 < poppingtonic> yorick should be there too
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15:19 < poppingtonic> Dr. Zeus seems like an engaging story/universe.
15:19 < poppingtonic> to the Library!
15:20 < kanzure> ehh, i predict a stereotypical annoying ending about ai tautology stuff
15:20 < kanzure> this alone makes it worth not reading
15:23 < poppingtonic> did you read Diaspora?
15:24 < kanzure> a very long time ago
15:24 < kanzure> maybe around 2001
15:24 < kanzure> was this the one that began with the long sequence of mind maps and random chance?
15:25 < kanzure> ah yes "Diaspora begins with a description of "orphanogenesis", the birthing of a citizen without any ancestors (most citizens descend from fleshers uploaded at some point), and the subsequent upbringing of the newborn Yatima within Konishi polis. Yatima matures within a few real-time days, because citizens' subjective time runs about 800 times as rapidly as flesher and gleisner time. Early on, Yatima and a friend, Inoshiro, use ...
15:25 < kanzure> ... abandoned gleisner bodies to visit a Bridger colony near the ruins of Atlanta on Earth."
15:25 < Evoril> ok gtg
15:25 -!- yashgaroth [~ffffff@2606:6000:cb85:6a00:d953:9ec3:aaa9:fc73] has joined ##hplusroadmap
15:25 < poppingtonic> no, it started with the birth of an AI. Orphanogenesis was the first chapter's title.
15:26 < Evoril> will be back once i sorted out those promoters (which were already done by someone else but whatever) :)
15:26 < Evoril> take care
15:27 < poppingtonic> I think the "random chance" one was Schild's Ladder
15:28 < kanzure> "Twenty-thousand years in the future, Cass, a humanoid physicist from Earth, travels to Mimosa orbital station and begins a series of experiments to test the extremities of the fictitious Sarumpaet rules, a set of fundamental equations in "Quantum Graph Theory," which holds that physical existence is a manifestation of complex constructions of mathematical graphs. However, the experiments unexpectedly create a bubble of something more ...
15:28 < kanzure> ... stable than ordinary vacuum, dubbed novo-vacuum, that expands outward at half the speed of light as ordinary vacuum collapses to this new state at the border, hinting at more general laws beyond the Sarumpaet rules. The local population is forced to flee to ever more distant star systems to escape the steadily approaching border, but since the expansion never slows, it is just a matter of time before the novo-vacuum encompasses any ...
15:28 < kanzure> ... given region within the Local Group (and ultimately the whole universe)."
15:28 < kanzure> hmm. no, i didn't read this one back then.
15:28 < kanzure> the thing i was remembering was definitely orphanogenesis.
15:29 -!- Evoril [~Evoril@95.45.65.212] has quit [Quit: Leaving]
15:31 < kanzure> poppingtonic: you have seen orionsarm right?
15:31 < poppingtonic> No.
15:32 < kanzure> http://orionsarm.com/
15:32 < kanzure> this was a scifi world building group originally started by a few transhumanists including anders sandberg
15:32 < kanzure> they started with a somewhat strict (although in my opinion, lax) set of rules for what gets to be included
15:33 < kanzure> and then they pillaged basically everything from existing scifi and various as-of-yet(at the time) unused stuff like from forward and freitas and stuff
15:33 < poppingtonic> cool
15:37 < poppingtonic> goodness they have a 'geek code'
15:38 < catern> excellent
15:39 < poppingtonic> :D
15:45 < kanzure> i'd suggest hiring a scifi author to go through hplusroadmap logs but at this point there's very few authors i don't have an immune reaction to
15:45 < kanzure> let's hire greg egan
15:46 < poppingtonic> ^
15:48 -!- ebowden [~ebowden@CPE-60-231-182-230.lns4.dav.bigpond.net.au] has joined ##hplusroadmap
15:48 < kanzure> http://gregegan.customer.netspace.net.au/
15:48 < kanzure> hmm.
15:49 < kanzure> gregegan@gregegan.net
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16:06 < kanzure> "Hat-throwing fungi fire their spore capsules up to 2m,[31] and the cannonball fungi of the genus Sphaerobolus, such as S. stellatus, the Artillery Fungus can throw sticky spore sacs up to 6 m horizontally.[32][33] This species is phototropic, and propels spores towards the nearest source of direct or reflected light, like the sides of brightly colored houses.[34]"
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16:15 < fenn> i don't get the point of doing cell-free protein synthesis
16:16 < fenn> you have to produce, purify, and assemble a bunch of stuff that any cell would do on its own
16:17 < fenn> you have to add linear amounts of bio-reagents vs product, whereas any cell culture reproduces exponentially
16:21 < kanzure> "CFPS has many advantages over the traditional in-vivo synthesis of proteins. Most notably, a cell free reaction, including extract preparation, usually takes 1 –2 days, whereas in-vivo protein expression may take 1–2 weeks. (Carlson ED, et al.)"
16:21 < kanzure> "Cell-free protein synthesis (also called in-vitro protein synthesis or abbreviated CFPS), is the production of protein using biological machinery without the use of living cells. The in-vitro protein synthesis environment is not constrained by a cell wall or homeostasis conditions necessary to maintain cell viability. Thus CFPS enables direct access and control of the translation environment which is advantageous for a number of ...
16:21 < kanzure> ... applications including optimization of protein production, optimization of protein complexes, to study protein synthesis, incorporating non-natural amino acids, high-throughput screens, and synthetic biology."
16:21 < kanzure> "CFPS is an open reaction. The lack of cell wall allows direct manipulation of the chemical environment. Samples are easily taken, concentrations optimized, and the reaction can be monitored. In contrast, once DNA is inserted into live cells, the reaction cannot be accessed until it is over and the cells are lysed." (meh this is a lie)
16:21 < kanzure> toxicity is an okay claim
16:21 < kanzure> "A major application of CFPS is incorporation of non-natural amino acids into protein structures" but this works in vivo so this is not valid
16:22 < fenn> cells can secrete proteins with certain tags
16:22 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Ex-Chat]
16:22 < fenn> i dont see the point of incorporating non-natural amino acids
16:23 < fenn> also you can do this in a cell too
16:23 < kanzure> one major reason is to increase the available types of mutations
16:23 < kanzure> yes you can definitely do nonnatural amino acids in vivo
16:23 < fenn> ok but then you lose the ability to incorporate this protein into a cell culture
16:23 < fenn> so it's going to be super duper expensive forever
16:24 < fenn> gah don't listen to me, nevermind
16:24 < fenn> my brain is running at a sentence and a half behind
16:24 < kanzure> just change your frequency
16:25  * fenn hums a D minor chord
16:26 < kanzure> anywho cell culture scale-up sounds like a valid claim to me
16:26 < fenn> something about aptamers and rna-bound proteins
16:27 < fenn> why can't people just reverse engineer the protein sequence to optimize proteins for whatever
16:27 < kanzure> did you previously know about cell-free protein synthesis?
16:27 < fenn> vaguely
16:27 < kanzure> protein optimization is hard yo
16:27 < kanzure> that's usually left for directed engineering projects
16:27 < fenn> you still need to get your ribosomes from somewhere, so it's not really "cell free"
16:27 < kanzure> and then you look at the results and scratch your head when you compare it to the original protein sequence and protein structure
16:28 < kanzure> whoops i meant directed evolution
16:28 < fenn> evolutionary engineering
16:28 < kanzure> utility function spamming
16:29 < fenn> spam spam spam spam spam spam spam spam
16:29 < fenn> .py while(1): print "spam"
16:30 < kanzure> i had no idea that merrifield's chemical peptide synthesis was limited (by yield of each coupling reaction?) to ~70 amino acid residues
16:30 < kanzure> that's very short
16:30 < yoleaux> <html><head><meta http-equiv="content-type" content="text/html;charset=utf-8"><title>500 Server Error</title></head><body text=#000000 bgcolor=#ffffff><h1>Error: Server Error</h1><h2>The server encountered an error and could not complete your request.<p>Please try again in 30 seconds.</h2><h2></h2></body></html>
16:31 < kanzure> essentially both oligo synthesis and peptide synthesis is limited to very short things
16:31 < kanzure> so my ribosome/tRNA method might work for arbitrarily long sequences
16:31 < kanzure> the downside is that it is only a protein, and not a genome
16:33 < kanzure> i bet chemical peptide synthesis is also limited because of folding thta might happen in the reverse direction that breaks the sort of folding that usually happens
16:34 < kanzure> when amino acid chains are extruded out of the butt pore of a ribosome
16:39 < kanzure> this would be especially useful if we had ideas for rational protein engineering that required very long sequences that are too expensive to make with oligo synthesis + ligations or w/e
16:39 < yashgaroth> ehh you can usually refold it, the problem is purifying out a protein from a mixture of other proteins that look extremely similar minus one amino acid
16:40 < kanzure> talking about why cell-free is yuseful?
16:40 < yashgaroth> why chemical synthesis isn't, so I suppose yes
16:41 < yashgaroth> gotta say I mostly agree with fenn, cell-free of any type is mostly useful for either toxic proteins or niche directed evolution/array stuff
16:41 -!- shubhamg_ [~shubhamgo@118.189.209.93] has quit [Remote host closed the connection]
16:42 < yashgaroth> I just find the aaaggg solution very elegant, assuming you can get a tolerant ribosome
16:43 < yashgaroth> also non-natural amino acids, which is doable in vivo but a lot easier cell-free; but that's a solution without a problem for now
16:45 < kanzure> we have no way of writing long synthetic sequences, cell-free sounds like the only way to me
16:45 < kanzure> i mean, gibson assembly i guess
16:45 < kanzure> and ligation stuff
16:46 < kanzure> but that feels like cheating for some reason
16:47 < kanzure> oh right, you need 20-40 bp overlaps on both sides, and 80 bp is already like 80% of your available space
16:48 -!- yashgaroth [~ffffff@2606:6000:cb85:6a00:d953:9ec3:aaa9:fc73] has quit [Ping timeout: 258 seconds]
16:49 < kanzure> http://www.csbio.com/peptide-synthesizers/
16:49 < kanzure> "and our industrial scale systems (CS936) can handle syntheses >5.0 mol"
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16:51 < yashgaroth> agh ffs
16:52 < kanzure> i was just complaining about gibson assembly for some reason
16:52 < yashgaroth> hey what happened to the logs btw
16:52 < kanzure> i forgot how to use dtach and i've been stuck in a staring contest with jrayhawk for like three weeks
16:53 < kanzure> i guess i just lost
16:53 < yashgaroth> alrighty
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16:56 -!- kanzure changed the topic of ##hplusroadmap to: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA, banned by the Federal Death Administration (4 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki
16:56 -!- mode/##hplusroadmap [-o kanzure] by kanzure
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17:03 < yashgaroth> yay
17:04 < fenn> does it make sense to add logs for 11-26 to 12-26
17:04 < kanzure> i'm fixing that
17:05 < fenn> tales from the dark side: when logs go bad
17:06 < fenn> stories to scare children with
17:06 -!- ebowden [~ebowden@CPE-60-231-182-230.lns4.dav.bigpond.net.au] has joined ##hplusroadmap
17:09 < yorick> poppingtonic: true, but who are you?
17:09 < kanzure> lazyweb wins https://github.com/kaiju/miscellany/blob/master/log2logdir.py
17:09 < yorick> poppingtonic: or did you find it because of the irc channel?
17:10 < poppingtonic> yes.
17:14 < fenn> heath eudoxia "openbay" is missing torrent descriptions, comments, file lists, quality votes, date uploaded, etc etc etc which turn out to be pretty important
17:15 < heath> i never read the comments
17:15 < heath> mostly just look at the pics and number of seeders
17:15 < fenn> there's a "rich.xml" from 2013 which i believe has this stuff, but i haven't been brave enough to unzip it as i estimate the size is around 35GB
17:15 < heath> i usually only use torrenting for videos
17:16 < heath> i once used it at oink and what.cd as well at some point
17:16 < fenn> description is still pretty important because people suck at naming things
17:16 < heath> that's true
--- Log opened Sat Dec 27 17:27:05 2014
17:27 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap
17:27 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA, banned by the Federal Death Administration (4 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki
17:27 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Sat Dec 27 16:56:22 2014]
17:27 [Users ##hplusroadmap]
17:27 [ altersid_] [ comma8      ] [ FAMAS    ] [ kenju254    ] [ Qfwfq      ] [ ThomasEgi ] 
17:27 [ andytoshi] [ crescendo   ] [ fenn     ] [ kragen      ] [ rigel      ] [ TMA       ] 
17:27 [ archels  ] [ cuba_       ] [ gnusha   ] [ maaku       ] [ rk[ohio]   ] [ Urchin    ] 
17:27 [ augur    ] [ Daeken      ] [ heath    ] [ nArkos_     ] [ saurik     ] [ Viper168  ] 
17:27 [ balrog   ] [ delinquentme] [ helleshin] [ nickjohnson ] [ sheena2    ] [ Vutral    ] 
17:27 [ bbrittain] [ docl        ] [ HEx1     ] [ night       ] [ shubhamg_  ] [ yashgaroth] 
17:27 [ bkero    ] [ DonnchaC_   ] [ ivan`    ] [ nmz787      ] [ sivoais    ] [ yoleaux   ] 
17:27 [ blueskin ] [ dpk         ] [ JayDugger] [ nsh         ] [ smeaaagle  ] [ yorick    ] 
17:27 [ BobaMa   ] [ drazak      ] [ JonTitor ] [ paperbot    ] [ soylentbomb] 
17:27 [ Boscop   ] [ drewbot     ] [ jrayhawk_] [ ParahSailin ] [ strages    ] 
17:27 [ Burninate] [ dvorkbjel   ] [ juri_    ] [ pasky       ] [ strangewarp] 
17:27 [ catern   ] [ ebowden     ] [ juul     ] [ poohbear    ] [ streety    ] 
17:27 [ cluckj   ] [ EnabrinTain ] [ kanzure  ] [ poppingtonic] [ superkuh   ] 
17:27 -!- Irssi: ##hplusroadmap: Total of 73 nicks [0 ops, 0 halfops, 0 voices, 73 normal]
17:27 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010
17:27 -!- Irssi: Join to ##hplusroadmap was synced in 11 secs
17:27 < kanzure> you will just have to live without those 15 minutes of logs
17:28 < fenn> good, now heath won't be able to guilt me into vitrifying him
17:29 < fenn> there's also http://hyse.org/irssi-log-merge/  but local time zones would probably mess everything up
17:29  * heath submits a patch to the log file
17:29 < kanzure> patching was what went wrong 18 minutes ago in the first place
17:29 < kanzure> patch reected
17:29 < kanzure> *rejected
17:29 < kanzure> unless it's for some day other than today
17:29 -!- ebowden [~ebowden@CPE-60-231-182-230.lns4.dav.bigpond.net.au] has quit [Remote host closed the connection]
17:31 < kanzure> oh... http://gnusha.org/logs/split_log.py
17:31 < kanzure> that's certainly a simple way to do that
17:31 < kanzure> compare to https://raw.githubusercontent.com/kaiju/miscellany/master/log2logdir.py
17:36 -!- eudoxia [~eudoxia@r190-134-41-185.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap
17:40 < fenn> eudoxia: logs are back up so you can go away now :P
17:40 < kanzure> .title https://news.ycombinator.com/item?id=8803389
17:40 < yoleaux> Ask HN: How to use small chunks of time productively | Hacker News
17:40 < eudoxia> fenn: oh cool, didn't notice
17:40 < kanzure> i think there are some limits on task breakup but this is hard to describe
17:41 < kanzure> ultimately you are always doing things that must be broken down into motor actions
17:41 < kanzure> but the amount of effort to write down and serialize some tasks surely must be greater than execution effort
17:42 < fenn> isn't "product manager" the job description of "that jackass who handles all the little things that come up and have to be dealt with, so i don't have to"
17:42 < kanzure> one of the posters describes his method of breaking everything up into 5 minute tasks
17:42 < kanzure> naturally, all of the interesting stuff is in his backlog since he can't figure out how to split those up
17:45 < kanzure> effort-of-breaking-task-up exceeding task-execution-effort or something
17:45 < kanzure> that must be a threshold that exists somewhere
17:46 < fenn> 200% overhead is still better than 0% progress
17:46 < kanzure> and thus fenn decided to vote big government
17:47 < fenn> go fightin bureaucrats, rah rah rah!
17:47 < fenn> whats all this bitcoin bowl stuff about
17:47 < kanzure> bitpay sponsored a football game
17:47 < fenn> is it like an hour long advertisement for... bitcoin?
17:48 < fenn> do they even play football in st. petersberg?
17:48 < kanzure> there is a giant indoor stadium there
17:48 < kanzure> this was florida not russia
17:48 < fenn> oh!
17:48 < fenn> important distinction
17:48 < eudoxia> 20:39 < kanzure> i bet alcor has corny videos that go like, "Hi, I'm Max More, and today I am going to show you emergency procedures for maintaining dry ice. In the event that this facility has been abandoned, please see the containers to your right..."
17:48 < eudoxia> i think during mike darwin's tenure they had some kind of prepper basement
17:49 < fenn> i was picturing guys in furry hats in the stands trying to use their smartphones with leather gloves
17:50 < kanzure> didn't help that their commercials had eastern block thugs https://www.youtube.com/watch?v=Rm7wgmwKiAk https://www.youtube.com/watch?v=9uA4KO2EEBU https://www.youtube.com/watch?v=FWJDCLpOnf0
17:50 < fenn> "hotdogs, get yer hotdogskis, only 1,000,000 satoshis"
17:50 < kanzure> from the first one you might think russia
17:51 < kanzure> anyway... https://github.com/bitpay
17:53 < fenn> it's good that they are publishing open source software
17:54 < kanzure> yep
17:54 < kanzure> also they have jgarzik (linux kernel monkey)
17:55 < fenn> copay-cola https://raw.githubusercontent.com/marianorod/copay-brand/master/copay-logo-full-negative.png
17:58 < kanzure> "At halftime of the #BitcoinBowl, ESPN will run down all the scores and the latest on Ben Lawsky's BitLicense."
17:58 < fenn> i thought that was a joke
17:59 < kanzure> no idea, i didn't watch
18:01 < fenn> so are gift cards "virtual currency"
18:01 < fenn> it's really weird that the state of new york uses the phrase "Fiat Currency"
18:02 < kanzure> depends on what your definition of "is" is
18:02 < fenn> thank you, bill clinton
18:03 < kanzure> no really...
18:03 -!- eudoxia [~eudoxia@r190-134-41-185.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving]
18:03 < kanzure> further complications include things like "digital gift cards" and "physical-only gift cards through various mastercard/visa programs"
18:04 < kanzure> usually the physical-only gift cards do not tell you enough information for online spending
18:04 < kanzure> i guess you could look up gyft
18:04 < fenn> you can sell physical gift cards
18:04 < fenn> there's a 15% fee or something
18:04 < kanzure> .wik virtual currency
18:04 < yoleaux> "A virtual currency or virtual money has been defined in 2012 by the European Central Bank as "a type of unregulated, digital money, which is issued and usually controlled by its developers, and used and accepted among the members of a specific virtual community.":13" — http://en.wikipedia.org/wiki/Virtual_currency
18:05 < fenn> actually it's like 15% if you just type the code in, and 10% if you physically mail the card to them
18:05 < kanzure> "In 2013, Financial Crimes Enforcement Network (FinCEN), a bureau of the US Treasury defined virtual currency as "a medium of exchange that operates like a currency in some environments, but does not have all the attributes of real currency".[2]
18:05 < kanzure> haha
18:05 < kanzure> in other words.. nobody has any clue.
18:06 < fenn> i was looking at this https://www.cryptocoinsnews.com/ben-lawsky-nydfs-reveal-proposed-bitlicense-regulations/
18:06 < kanzure> http://diyhpl.us/wiki/transcripts/nydfs-bitlicense-lawsky-update/
18:06 < fenn> ugh i am having diybio self-castration flashbacks
18:07 < fenn> who are these people that want to put everyone else in prison just for existing
18:07 < kanzure> regulators
18:08 < kanzure> incumbents
18:08 < fenn> .wik ben lawsky
18:08 < yoleaux> "Benjamin M. Lawsky (born April 14, 1970) is an American attorney and New York State's first Superintendent of Financial Services and former Acting Superintendent of Banks." — http://en.wikipedia.org/wiki/Benjamin_Lawsky
18:08 < kanzure> once you achieve incumbency, switching strategies to regulatory capture is very rewarding
18:09 < fenn> i think a good principle is to assume freedom/permission unless it has been specifically removed (and for good reason)
18:09 < fenn> this "everyone needs a license" culture is bullshit
18:10 < kanzure> so a few bitcoiners elsewhere have recently informed me that one of the reasons that money transmitter licenses happen is because regulators and government agencies often demand the ability to directly meddle with your internal ledger
18:10 < catern> copyleft
18:10 < catern> (oh, you're not talking about software licenses)
18:10 < kanzure> heh
18:10 < catern> let's extend copyleft to business licenses
18:11 < kanzure> these licenses are different
18:11 -!- lichen [~lichen@c-50-139-11-6.hsd1.or.comcast.net] has joined ##hplusroadmap
18:11 < fenn> copyright also applies; you used to have to apply for a copyright, and the default was permissiveness. now it's all locked away even if you don't know who owns the automatically granted copyright
18:11 < fenn> for example you are not legally allowed to copy logs with the words i am typing in right now
18:12 < kanzure> ah right public performance at least
18:12 < fenn> (well actually i think i put all future posts by me in public domain a couple years ago)
18:12 < catern> you can probably repudiate that
18:12 < fenn> it would be meaningless if i could
18:13 < fenn> "no take-backsies"
18:13 < fenn> kanzure: i dont get it; meddle with your ledger? is this like defining pi=3 again?
18:13 < kanzure> er, i believe that exact example was used
18:13 < fenn> if you've spent the money it's gone
18:14 < kanzure> haha no
18:14 < fenn> they can't just edit the ledger and make it reappear
18:14 < kanzure> ledger can say anything
18:14 < fenn> huh?
18:14 < kanzure> *most ledgers can say anything
18:14 < fenn> well then it's just wrong
18:14 < kanzure> of course it's wrong
18:14 < fenn> okay
18:14 < fenn> "government votes to do the wrong thing"
18:14  * kanzure dumps the related logs
18:16 < fenn> i wonder what the FBI is doing with all their "seized bitcoins"
18:16 < kanzure> they sold them to tim draper and second market
18:17 < fenn> was there like an auction, with a pallet of bitcoins
18:17 < kanzure> https://blockchain.info/tx/9e95c3c3c96f57527cdc649550bf8e92892f7651f718d846033798aee333b0c3
18:17 < kanzure> and yes, http://www.usmarshals.gov/assets/2014/dpr-bitcoins/
18:19 < fenn> i bet in 20 years they are going to be regretting that decision
18:19 < kanzure> i believe they were legally required to sell them or something
18:19 < fenn> nah it's "evidence"
18:20 < kanzure> as for the "pi = 3" stuff, see http://gnusha.org/bitcoin-wizards/2014-12-21.log
18:20 < kanzure> 12:45 < petertodd> kanzure: see, I'm saying that there are incentives to make centralized ledgers *insecure* even within conventional finance
18:20 < kanzure> 12:46 < petertodd> yeah, and the smartest regulators get that security lets you bypass the need for identity
18:20 < kanzure> 12:46 < petertodd> gmaxwell: also, note that "unbounded reversability" is also coupled with a desire to make it possible for that reversibility to be *secret*
18:21 < kanzure> 12:51 < petertodd> nsh: it's not that level of conspiracy stuff - you literally have to be able to accomodate courts ordering you to remove things off your ledgers in secret, among many other crazy requirements
18:22 < fenn> i dont understand why there isnt more public outcry about all this secret law stuff
18:22 < fenn> how can you even pretend to have a democracy when you dont even know what the law is, in principle
18:22 < kanzure> also, didn't silent circle stop updating their secret court order canary the other day
18:22 < fenn> "i pledge of allegiance, to honor the constitution and all the secret laws i don't know about"
18:23 < kanzure> https://canary.silentcircle.com/
18:23 < kanzure> ah they updated on december 25
18:23 < kanzure> for a few days before they were 3 weeks late
18:23 < kanzure> "Silent Circle LLC will also make available, weekly, a "warrant canary""
18:23 < fenn> what if they force you to say "i'm turning off this canary because it's a lot of work"
18:24 < kanzure> they could probably argue that it would cause lots of harm to their core business, etc
18:24 < fenn> or just force you to continue "business as usual" which includes updating the canary
18:26 < kanzure> i don't actually see any message that they have not received a warrant on this page
18:26 < fenn> wtf they shut down their encrypted email service because " it was not possible to sufficiently secure email data."
18:26 < fenn> that's pathetic
18:26 < kanzure> well they had courts ordering them to not do that
18:26 < kanzure> (because of edward snowden- i think this was suspected at first, and then it was revealed later?)
18:27 < kanzure> i mean, they had courts ordering them to become less secure
18:27 < fenn> right, if you look at the original source article it is because they didnt want to be forced to reveal keys or whatever
18:27  * fenn fixes wikipedia
18:28 < kanzure> there were multiple things being said back and forth, hard for me to reconstruct the timeline correctly
18:28 < kanzure> the government was claiming that they only wanted headers from emails, and then later they wanted the private key, and silent circle was claiming they wanted the private key the whole time? something something
18:29 < kanzure> where's mah spooks
18:30 < fenn> Silent Circle said specifically that it hadn’t actually received any “subpoenas, warrants, security letters, or anything else by any government” before shutting down, which leads to the troubling conclusion that the threat of action alone was enough to take an option off the market.
18:31 < fenn> all the spooks are in germany
18:31 < kanzure> hm
18:36 < fenn> wow that was literally the next day, after the lavabit shutdown
18:39 < kanzure> they were pretty mad
18:40 < fenn> Levison wrote that after being contacted by the FBI, he was subpoenaed to appear in federal court, and was forced to appear without legal representation because it was served on such short notice; in addition, as a third party, he had no right to representation, and was not allowed to ask anyone who was not an attorney to help find him one. He also wrote that in addition to being denied a hearing
18:40 < fenn> regarding the warrant to obtain Lavabit's user information, he was held in contempt of court. The appellate court denied his appeal due to no objection, however, he wrote that because there had been no hearing, no objection could possibly have been raised. His contempt of court charge was also upheld on the ground that it was not disputed; similarly, he was unable to dispute the charge because
18:40 < fenn> there had been no hearing to do it in. He also wrote that "the government argued that, since the 'inspection' of the data was to be carried out by a machine, they were exempt from the normal search-and-seizure protections of the Fourth Amendment."
18:41 < fenn> this is straight out of a kafka story
18:43 < fenn> The court records show that the FBI sought Lavabit's SSL private key. Levison objected saying that the key would allow the government to access communications by all 400,000 customers of Lavabit. He also offered to add code to his servers that would provide the information required just for the target of the order. The court rejected this offer since it would require the government to trust Mr.
18:43 < fenn> Levison and stated that just because the government could access all customers' communication did not mean they would be legally permitted to do so. Lavabit was ordered to provide the SSL key in machine readable format by noon, August 5 or face a fine of $5000 per day. Levison closed down Lavabit 3 days later.
18:43 < fenn> this "a machine did it" argument is pretty dangerous
18:44 < fenn> "oops we blew up your house, but a drone did it so it's okay"
18:48 < kanzure> oh right, the reason why gibson assembly isn't an answer is because it increases your costs dramatically
18:49 < fenn> how's that
18:49 < kanzure> at a milion pixes with that much overlap you get maybe 20-30 unique bp per pixel
18:49 < nmz787> fenn: up for finishing that laser etcher parts list? I really don't have an intuitive idea of what parts were missing... currently I think the easiest solution for lasers is an optical sled directly from a blu-ray drive... close working distance (around a millimeter) but the spot size is near diffraction limit and they're available.
18:49 < kanzure> especially if you need 20 to 40 bp overlap per pixel
18:49 < kanzure> *pixels
18:49 < nmz787> gibson doesn't seem too expensive
18:49 < kanzure> at a million pixels you only get 20-30 bp per pixe
18:49 < fenn> nmz787: i think the mandate for that laser etcher has long since expired; the original parameters were way too ambitious anyway
18:49 < kanzure> so at most 30 million bp
18:50 < nmz787> fenn: what do you mean? I was looking at it a few nights ago and it seemed reasonable still
18:50 < kanzure> *pixel
18:50 < nmz787> I even found a class paper that used the same rod
18:50 < nmz787> the threaded one
18:50 < kanzure> it was superceded by dmd
18:50 < nmz787> so you chose well!
18:50 < nmz787> nah
18:50 < fenn> nmz787: there's really no need to etch a 100mm x 100mm microfluidics chip, or whatever it was
18:50 < nmz787> no way
18:51 < nmz787> I just bought this 38mm x 38mm CNC laser etcher for $120 but you can't easily change the threaded rods or motors
18:51 < nmz787> also it would be useful for microscopy or something
18:52 < nmz787> you were only a few parts from it being complete i thought
18:52 < nmz787> something about pillow blocks maybe
18:53 < nmz787> kanzure: dmd was deprecated because of inter-pixel noise
18:54 < nmz787> we'd need a piezo vibrator to jiggle the stage with DMD to smooth out the inter-pixel dead zones
18:55 < fenn> what's with cellphones and the camera lens sticking out
18:55 < nmz787> $5 rail to rail i2c DAC for controlling the laser sled focus http://www.adafruit.com/product/935
18:55 < nmz787> I got an S4 Zoom for my dad a few weeks ago
18:56 < nmz787> it has a 10X optical zoom
18:56 < nmz787> http://axeetech.com/wp-content/uploads/2013/06/galaxy-s4-zoom_0.jpg
18:56 < fenn> is that a camera or a phone
18:57 < fenn> where's bill clinton
18:57 < kanzure> neither, it's a computer
18:57 < fenn> and korzybski
18:58 < nmz787> he has a nokia candybar tracfone now which is his, like, second cell phone ever
18:58 < fenn> i like the design of the sony QX100, it's too bad sony had to be the first one to do it though...
18:59 < nmz787> yeah I think I read it wasn't as good
18:59 < nmz787> maybe something about dust?
18:59 < fenn> dust?
18:59 < kanzure> the other problem with gibson assembly is that it doesn't get the price down far enough anyway
19:00 < fenn> the point of the QX10 and QX100 is they are just the lens and image sensor; all the UI stuff is an android app
19:00 < fenn> this means the sensor is matched to the lens, and you never have "lens compatibility" issues
19:01 < nmz787> gibson is basically just cooperative ligation though
19:01 < nmz787> what sounds so expensive about that?
19:01 < fenn> like nikon vs canon lens mount, what a stupid problem
19:01 < kanzure> source material
19:01 < kanzure> is what is expensive in this case
19:01 < nmz787> hmm, maybe I didn't see the QX100 before
19:01 < nmz787> hrmp
19:02 < kanzure> moo
19:02 < nmz787> kanzure: I aim to have them right next to each other on the chip
19:03 < fenn> the way you connect to it is kinda dumb; it acts like a wifi access point and you choose it from the phone as your internet, so you can't use the internet while using the lens
19:03 < fenn> instead of bluetooth, which would actually make sense
19:03 < nmz787>  oh
19:03 < nmz787> that's weird
19:04 < nmz787> wi-gig going forward maybe?
19:04 < fenn> is that a thing
19:04 < fenn> .wik wi-gig
19:04 < kanzure> i am still upset about our differences in engineering estimation
19:04 < yoleaux> "The Wireless Gigabit Alliance (WiGig) was a trade association that developed and promoted the adoption of multi-gigabit speed wireless communications technology operating over the unlicensed 60 GHz frequency band. The alliance was subsumed by the Wi-Fi Alliance in March 2013." — http://en.wikipedia.org/wiki/Wi-gig
19:04 < kanzure> also i have no idea what you are talking about re: "next to each other"
19:04 < nmz787> i saw a demo day with a bunch of stuff a few months ago
19:04 < fenn> wouldnt 60GHz have line of sight issues
19:04 < nmz787> HD displays and such
19:04 < nmz787> yeah
19:05 < nmz787> but like in your livingroom or studio apt, no prob they suppose
19:05 < fenn> a lot of new stuff has dual band wifi, so maybe one antenna can handle multiple connections on different bands
19:06 < nmz787> and for things like public high def multimonitor workstations
19:06 < fenn> existing phones have no reason to do that though (at least according to the manufacturers that be)
19:06 < nmz787> where you bring your machine
19:06 < fenn> is existing miracast not fast enough?
19:07 < fenn> 802.11n is like 50MB/s
19:07 < nmz787> hmm, this qx100 might be good for self surgery of something you can't see well but can get your hands around
19:07 < kanzure> "Panamanian biologist Aradio Rodaniche first reported the Pacific striped octopus in 1991 off the coast of Nicaragua, noting its strange behavior—living in groups of possibly up to 40, laying multiple egg clutches, and mating face-to-face and sucker-to-sucker. Most other octopus species, for instance, come together only to mate. But scientists didn't see another one of these curious octopuses for another 20 years, when Richard Ross, a ...
19:07 < kanzure> ... biologist at the California Academy of Sciences, came across one in 2012. Through a commercial collector, he acquired several wild specimens to study in the lab."
19:07 < nmz787> or cutting your own hair
19:07 < kanzure> commercial collector?
19:07 < kanzure> also: 20 years is too long
19:07 < kanzure> can't a dolphin be trained to find them or some shit?
19:08 < fenn> nmz787: or taking selfies
19:08 < nmz787> fenn how many btc per hour of laser etcher work do you want?
19:08 < fenn> what
19:08 < nmz787> do you have use for that?
19:08 < fenn> i dont know what you're talking about
19:08 < kanzure> usually when fenn disagrees he has a good reason
19:08 < kanzure> paying him to do something he thinks is stupid is not a good plan
19:09 < nmz787> it doesn't seem stupid to me, and he seemed to understand what it needed
19:09 < kanzure> yes but we've already established that you have bizarre engineering standards
19:09 < kanzure> grumble grumble
19:09 < nmz787> so
19:09 < nmz787> :/
19:10 < nmz787> why can
19:10 < nmz787> why can't i be me?
19:10 < fenn> 1) i don't want to build a microfluidic dna synthesizer 2) a chip requried to do so wouldn't be nearly so big 3) microscope stages have adequate performance for the task 4) DMD masks are adequate for the task
19:10 < kanzure> just because something does not seem stupid doesn't mean it's not stupid, obviously
19:10 < nmz787> $500 for a DIY stepper is not unreasonable
19:10 < nmz787> fenn DMD masks are not sufficient
19:11 < nmz787> I can show you the paper if you want
19:11 < fenn> "interpixel noise" doesn't seem like a good excuse; you can blur the lines between pixels anyway
19:11 < fenn> link plz
19:13 < kanzure> http://diyhpl.us/~bryan/papers2/optics/photolithography/Development%20of%20microfabrication%20technology%20with%20maskless%20photolithography%20device%20using%20LCD%20projector%20-%20Itoga%20-%202010.pdf
19:13 < kanzure> probably that
19:13 < kanzure> page 2 figure 2
19:14 < nmz787> no that's not it
19:14 < nmz787> hold on
19:14 < nmz787> grep didn't work for me
19:14 < fenn> kanzure: that's the answer to the problem he's proposing, not the problem
19:14 < kanzure> whoops
19:15 < nmz787> well ok
19:15 < nmz787> if you reduce with a scope enough the DMD image
19:15 < nmz787> and over-represent the size of the minimum feature size you aim for with multiple pixels
19:16 < nmz787> then DMD works
19:16 < fenn> yay
19:16 < nmz787> but you need to step around
19:16 < nmz787> but I still don't have a proceter to scope adapter
19:16 < nmz787> projector*
19:16 < nmz787> btc for that?
19:16 < fenn> is like $50 on ebay
19:17 < kanzure> he's going to mail you a pvc pipe with a passive aggressive sticky note or something
19:17 < fenn> make sure it's a black pvc pipe
19:17 < nmz787> well I would like a share-able CAD for CNC or 3D printing
19:17 < nmz787> or  CAD of the PVC pipe
19:18 < nmz787> I have the projector kanzure mailed me all ready to go except for a blue laser with focusable optics
19:18 < nmz787> that has been ready for like a year and a half
19:19 < fenn> oh another thing to think about is using a cellphone screen as the light source
19:19 < nmz787> but I literally didn't know what to do to get it on my scope
19:19 < fenn> it's slower but more obtainable
19:19 < kanzure> there's something to be said for not encouraging nmz787 to be doing one-offs
19:19 < nmz787> I have an HD cellphone
19:20 < fenn> well phones are mostly the same shape, and there's going to be some bodging no matter what shape it is
19:20 < nmz787> apparently a screen is around $50 on ebay
19:20 < fenn> so you can design around a general phone shaped flat thing
19:20 < kanzure> fenn: i meant for an overall engineering artifact
19:20 < kanzure> "i bought this shit on ebay that you're never going to be able to find again" is not a good strategy
19:20 < fenn> oh, hm
19:20 < nmz787> and I have o get mine replaced tomorrow, I am going to ask to keep the old screen (shattered the glass, though touch and pixels are all good and working)
19:20 < fenn> i dont know how to deal with that problem
19:21 < fenn> microscopes and projectors don't come in standard shapes and optics
19:21 < kanzure> acme threaded stuff are a good example of an okay part
19:21 < nmz787> yes
19:21 < kanzure> microscopes are highly standardized
19:21 < kanzure> apparently they all come out of the same factory
19:21 < fenn> dud there are a bazillion optics threads
19:21 < kanzure> hrm
19:21 < fenn> there's a guy who makes a living just making custom adapters for cameras and microscopes
19:22 < kanzure> that's because of the camera side, right?
19:22 < fenn> i doubt it
19:22 < kanzure> unfortunate
19:22 < fenn> i don't have a pile of microscopes to go check either
19:22 < nmz787> also cell phones aren't 405nm, and the cheap photoresist are often sensitive to 365nm
19:22 < nmz787> or as close to that as possible
19:23 < fenn> Royal Microscopical Society (RMS) thread, also known as society thread, is a special 0.8" diameter x 36 thread-per-inch (tpi) Whitworth thread form used for microscope objective lenses.
19:23 < fenn> yuck
19:23 < nmz787> a CNC with laser is more standard I think
19:23 < fenn> what is the goal here again?
19:24 < kanzure> $1/genome
19:24 < nmz787> fenn: I bought this, just CD-ROM drives I think http://www.ebay.com/itm/Mini-Laser-200-250mW-Engraving-Machine-DIY-Carving-Logo-Picture-Marking-Printer/261591526091
19:24 < fenn> kanzure: synthesis?
19:24 < kanzure> custom genomes
19:24 < kanzure> yes
19:24 < nmz787> I am thinking I can make a manifold for macro to micro, which can interface with a silicon chip with nanochannel and electrodes.
19:25 < nmz787> or other substrate
19:25 < kanzure> but also, a general method of cheaply making microfluidic devices would be useful
19:25 < nmz787> but I read PDMS isn't easy to add electrodes to
19:25 < kanzure> and a dmd setup would be useful for planar "micro"electronics
19:25 < nmz787> I was thinking maybe using DNA to form DNA-sized nanochannels
19:26 < nmz787> because you could "etch" it somewhat afterward with acid/base
19:26 < fenn> prettyworthshop needs a higher resolution test pattern and image of suchlike
19:27 < nmz787> yeah I hope their 0.01mm number is near true
19:27 < nmz787> or maybe that is with microstepping
19:27 < nmz787> grbl seems configurable too
19:27 < fenn> a circle would be good to check for backlash, parallel lines to check repeatability, so a spiral would be a good compromise
19:28 < fenn> you know there's a difference between accuracy and "output resolution" right
19:28 < fenn> huh i didnt expect that to be made in shenzhen
19:29 < nmz787> https://github.com/grbl/grbl/blob/615093ccd2a9bd63f1ecd29c464f032000f5e626/defaults.h#L50
19:29 < fenn> it's all open source hardware modules
19:29 < nmz787> I think that is the relevant line for resolution
19:30 < nmz787> yeah
19:30 < nmz787> the other option was some weird possibly windows only software
19:32 < fenn> nmz787: accuracy depends on the entire machine, from positioning mechanics to optics to CAM software
19:32 < fenn> output resolution is just an arbitrary number
19:34 < nmz787> fenn: fig 5 http://www.intelligentmp.com/Downloads/Technical%20Papers/SF-100%20Greyscale%20Paper.pdf
19:36 < fenn> hmm these projectors are so cheap now it might even make sense to just use them as monitors
19:38 < fenn> it would be cool to have a fiber optic heliostat that pipes light through an lcd projector playing some content-free pictures like 'sunrise earth'
19:38 < fenn> er s/lcd/dlp/
19:39 < nmz787> but then there is this paper, which is almost an order of magnitude in scale, so if the optical system didn't change, the features are over-represented (and they also don't show AFM here) http://www.intelligentmp.com/Downloads/Technical%20Papers/3D%20Structures%20Patterning%20In%20SU8.pdf
19:40 < fenn> nmz787: was i supposed to get something out of this paper
19:41 < kanzure> https://www.tonmo.com/community/threads/larger-pacific-striped-octopus.16101/
19:41 < kanzure> "Two San Francisco Bay Area scientists, Dr. Roy Caldwell of UC Berkeley and Richard Ross of the Steinhart Aquarium in the California Academy of Sciences (working from his home lab), are studying this long ignored and little studied [social] Central American octopus."
19:41 < kanzure> hmm someone with a home octopus lab in sf
19:42 < kanzure> "Until Caldwell and Ross began studying the Larger Pacific Striped Octopus, the creature was virtually ignored. In 1991, Arcadio Rodaniche published a short abstract “Notes on the Behavior of the Larger Pacific Striped Octopus, An Undescribed Species of the Genus Octopus”, providing a tantalizing glimpse of this intriguing animal based on observations he made at the Smithsonian Tropical Research Institute in Panama in the late ...
19:42 < kanzure> ... 70’s. Unfortunately, detailed information contained in a full manuscript documenting the Larger Pacific Striped Octopus’s unique social and reproductive behavior was never published. According to Caldwell, Rodaniche’s descriptions of the behavior of this species were so outside the norm of what biologists at the time thought octopuses did, they were dismissed by other cephalopod biologists. Unable to pass peer review, the ...
19:42 < kanzure> ... manuscript was never published and the animal was forgotten. Living LPSOs weren’t seen again until they were rediscovered last year. According to Ross “We are thrilled to confirm many of Rodaniche’s observations”."
19:42 < kanzure> oh come on
19:42 < fenn> california academy of sciences is not exactly a home lab
19:43 < fenn> they have a 3 story geodesic bio-sphere
19:43 < kanzure> i think they mean he is affiliated with them but has a home lab
19:43 < kanzure> and for some reason they felt it necessary to mention this
19:43 -!- ebowden [~ebowden@CPE-60-231-182-230.lns4.dav.bigpond.net.au] has joined ##hplusroadmap
19:43 < kanzure> that's one really excited octopus https://www.youtube.com/watch?v=voTpUH9Ok4c
19:44 < kanzure> (watching a hatching)
19:45 < kanzure> actually nevermind. that may not be a hatching.
19:45 -!- shubhamg_ [~shubhamgo@118.189.209.93] has quit [Remote host closed the connection]
19:47 < kanzure> ah richard ross hangs out on that forum http://www.stickycricket.com/cuttle/articles/index.html https://www.tonmo.com/community/members/thales.462/
19:47 < nmz787> kanzure: what is the thing juri is iat?
19:47 < nmz787> is at*
19:47 < nmz787> CCC doesn't google well
19:48 < nmz787> ah, 31C3
19:48 -!- ebowden [~ebowden@CPE-60-231-182-230.lns4.dav.bigpond.net.au] has quit [Ping timeout: 264 seconds]
19:50 < nmz787> do you know which is juri_ ? http://events.ccc.de/congress/2014/Fahrplan/speakers.html
19:50 < nmz787> the casting aluminum one?
19:51 < fenn> yes
19:51 < nmz787> ah ya https://gitorious.org/~juri
19:52 < kanzure> http://www.stickycricket.com/cuttle/oc/oc_babies.html
19:52 < kanzure> "Hatchling #23 found dead, dried above the water line."
19:52 < fenn> it's a conspiracy
19:52 < kanzure> "6 left from the first clutch, and 20 or so from the second."
19:54 < fenn> i thought they died after laying eggs
19:55 < kanzure> this subspecies lays multiple eggs and even travels in groups
19:55 < kanzure> or lives in groups, rather
19:55 < kanzure> of 40
19:56 < fenn> why was the paper never published?
19:57 < kanzure> "Rodaniche’s descriptions of the behavior of this species were so outside the norm of what biologists at the time thought octopuses did, they were dismissed by other cephalopod biologists. Unable to pass peer review, the manuscript was never published and the animal was forgotten."
19:57 < kanzure> lolz
19:57 < fenn> facepalm
19:58 < kanzure> so much is wrong with this
20:02 < poppingtonic> huuh?
20:02 < fenn> this projector was designed by Batman http://www.ebay.com/itm/Sony-SRX-R105-4K-HD-CineAlta-SR-Projector-w-KRL-Z125-2-5X-Zoom-Lens-3x-Boards-/331089192951
20:02 < kanzure> batman stole all of his designs from morgan freeman
20:03 < fenn> you mean God?
20:03 < kanzure> that was jim carrey
20:03 < fenn> wow that thing is huge
20:07 < poppingtonic> has juri_ already done her talk?
20:14 < nmz787> huh http://diagenetix.com/smart-dart-platform/
20:15 < fenn> "DNA isothermal amplification method"
20:17 < fenn> https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification
20:19 < kanzure> "loop primers"
20:19 < kanzure> "LAMP has been observed to be less sensitive than PCR to inhibitors in complex samples such as blood, likely due to use of a different DNA polymerase (typically Bst DNA polymerase rather than Taq polymerase as in PCR)."
20:19 < fenn> its like phage rolling replication
20:20 < kanzure> "LAMP is useful primarily as a diagnostic or detection technique, but is not useful for cloning or myriad other molecular biology applications enabled by PCR. Because LAMP uses 4 (or 6) primers targeting 6 (or 8) regions within a fairly small segment of the genome, and because primer design is subject to numerous constraints, it is difficult to design primer sets for LAMP "by eye". Free, open-source[16] or commercial software packages ...
20:20 < kanzure> ... are generally used to assist with LAMP primer design, although the primer design constraints mean there is less freedom to choose the target site than with PCR."
20:20 < kanzure> hmm
20:22 < fenn> beats the hell out of trucking ebola samples back to "the lab" because they don't have electricity in rural liberia
20:22 < fenn> (nevermind that batteries exist)
20:22  * fenn facepalms again
20:23 < fenn> make it stop!
20:24 < fenn> this article really needs an infographic
20:24 < kanzure> a story about an octopus on a genocide mission https://www.tonmo.com/community/pages/tankmates/
20:24 < fenn> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102748/figure/gnd064f1/ not the best graphic ever...
20:25 < nmz787> it seems like you need at least 6 to 12 primers
20:27 < fenn> ok i was wrong, it's not like rolling replication
20:28 < nmz787> I wonder if the rRNA sites are stable enough to support that many probes
20:28 < nmz787> I guess you would want more specific probes to identify different species
20:30 < fenn> i dont get why DLP megapixels arent keeping pace with camera megapixels or even LCD megapixels
20:33 < fenn> a <$1k iPad has 2048*1536 = 3MP  vs a $8k projector with the same resolution
20:35 < fenn> meanwhile cameras are pushing 40MP
20:37 < kanzure> probably limited market pressure
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20:39 < fenn> the silly thing is you an just put a LCD screen in front of a big fresnel lens and a light bulb
20:39 < fenn> and tada 3MP projector, or whatever resolution LCD panel you have
20:41 < fenn> i got a flashlight and some magnifying glasses from the dollar store...
20:48 < nmz787> they're MEMS
20:48 < nmz787> they're MEMS
20:48 < fenn> so?
20:49 < nmz787> different fab process
20:53 < kanzure> here's a possibly evil thing.... if commercial schools exist, why isn't there commercial buying/selling of degrees?
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20:57 < kanzure> also, even with gibson assembly, venter's genome still cost $40 million
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21:02 < kanzure> "The Vatican has not condemned the discovery, but claims it is not a new life. [a 2]"
21:02 < kanzure> "It is estimated that the synthetic genome cost US$40 million to make and took 20 people more than a decade of work.[b 5]"
21:02 < kanzure> reference is Pennisi E (May 2010). "Genomics. Synthetic genome brings new life to bacterium". Science 328 (5981): 958–9. doi:10.1126/science.328.5981.958. PMID 20488994.
21:03 < kanzure> http://www.sciencemag.org/cgi/reprint/328/5981/958.pdf
21:05 < kanzure> oh they didn't even synthesize it in house?
21:05 < kanzure> "The researchers started building their synthetic chromosome by going DNA shopping. They bought from a company more than 1000 1080-base sequences that covered the whole M. mycoides genome; "
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21:07 < kanzure> so i guess that's really only $330,000 in synthesis costs
21:07 < kanzure> if they were paying $0.30/bp
21:07 < kanzure> which sounds right for the time
21:08 < kanzure> so what was the other $40 million for
21:09 < kanzure> definitely wasn't paying everyone $200k/year
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21:18 < kanzure> 1995 sequenced mycoplasma genitalium, 2003 finishe deleting 100 genes out of the 500 genes, 2007 demonstrated insertion of chromosomes, 2008-2009 actual results and synthesis
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21:19 < kanzure> also this pdf claims venter was only thinking about genome synthesis since 1995ish, which sounds insane to me
21:19 < kanzure> timeline doesn't ad up
21:19 < kanzure> *add up
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21:19 < kanzure> *finished
21:20 < kanzure> surely he was thinking about synthesis as soon as he was thinking about sequencing
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--- Log closed Sun Dec 28 00:00:05 2014