--- Log opened Mon Jun 02 00:00:08 2014
--- Day changed Mon Jun 02 2014
00:00 < kanzure> here's one... "A high numerical aperture, polymer-based, planar microlens array" http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-22-19908
00:00 < kanzure> "We present a novel microfabrication approach for obtaining arrays of planar, polymer-based microlenses of high numerical aperture. The proposed microlenses arrays consist of deformable, elastomeric membranes that are supported by polymer-filled microchambers. Each membrane/microchamber assembly is converted into a solid microlens when the supporting UV–curable polymer is pressurized and cured. By modifying the microlens diameter (40-60 ...
00:00 < kanzure> ... μm) and curing pressure (7.5-30 psi), we demonstrated that it is possible to fabricate microlenses with a wide range of effective focal lengths (100–400 μm) and numerical apertures (0.05-0.3)."
00:02 < kanzure> and:
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00:02 < kanzure> http://infoscience.epfl.ch/record/178092/files/charbon11omex.pdf "Hybrid polymer microlens arrays with high numerical apertures fabricated using simple ink-jet printing technique"
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00:07 < kanzure> "Direct-writing of complex liquid crystal patterns" http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-22-10-12691&id=286314
00:07 < kanzure> "Downloading of the abstract is permitted for personal use only."
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00:21 < kanzure> gene_hacker: that nasa paper sounds like they want an excuse to blast up a large vat of photoresist
00:22 < kanzure> cool paper
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03:34 < poppingtonic> paperbot: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1539-6924.2007.00960.x
03:35 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/479617625f547c822610788969f661fa.txt
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03:38 < poppingtonic> paperbot: http://www.onlinelibrary.wiley.com/doi/10.1111/j.1539-6924.2007.00960.x/pdf
03:38 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/11b2fce3dfede6790e1d3e1b5b843299.txt
03:39 < poppingtonic> paperbot: http://onlinelibrary.wiley.com/store/10.1111/j.1539-6924.2007.00960.x/asset/j.1539-6924.2007.00960.x.pdf
03:39 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/ed0346d10cdb475d53eff1327a9016c1.txt
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07:31 < kanzure> fda banned easter eggs: http://en.wikipedia.org/wiki/Kinder_Surprise
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07:53 < kanzure> 23:50 < narmno> sorry kanzure but i ended up using lua
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08:13 < kanzure> "These lenses often appear on the surplus market, many of which were made for cathode-ray ("tube type") big screen televisions but are often sold as "fire starters" or solar ovens.  Typically made using flexible optical plastic, many of these lenses measure around 1 meter diagonally.  To use these lenses effectively they must be mounted in a rigid frame as it is imperative that they remain as flat as possible in order to accurately focus.  In ...
08:13 < kanzure> ... other words, you cannot "hand-hold" them and expect any reasonable performance - they must be mounted in a frame!"
08:13 < kanzure> "Flexible lenses.  Stamped in clear vinyl, these are flexible and are usually mounted in some sort of flexible plastic frame to allow them to be kept in a 3-ring binder."
08:14 < kanzure> "One potential source of Fresnel lenses for experimenters have been overhead projectors.  Typically, these lenses are built into the plate onto which the transparency is laid, with the Fresnel lens being used to direct the light upwards toward the right-angle mirror or lens assembly and onto the screen. Unfortunately, these lenses are NOT usually suitable for purposes of collimation or the focusing of a distant light source onto a detector as ...
08:15 < kanzure> ... they may not be designed to focus at infinity.  Since their main purpose is usually that of concentrating the light from the projection bulb and not forming an image directly, they do not function as needed and often blur and/or scatter light should they be attempted to be used.."
08:15 < kanzure> http://modulatedlight.org/optical_comms/fresnel_lens_comparison.html
08:16 < kanzure> oh hm.... " As noted before, the imprecise nature of a Fresnel lens precludes their efficient use to efficiently collimate coherent light (such as that from a laser) as an inexpensive, molded Fresnel lens may not practically be made to be accurate enough to be diffraction-limited.  In other words, attempts to use a Fresnel lens for laser light will likely result in a significant percentage of that light being scattered rather than being ...
08:16 < kanzure> ... collimated."
08:19 < kanzure> this is an unusual site
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08:26 < kanzure> "In 1984, Robert Forward suggested another conceptual technique to improve the performance of an interstellar laser sail. As shown in figure 7.7, Forward would position a thin-film refractive optical element - a Fresnel lens - between the laser and the starship. If the position of these three optical elements (laser, lens and starship) can be accurately maintained for decades or centuries (no mean task!), the light-years distant starship ...
08:26 < kanzure> ... could be presented with a very well collimated beam, at a distance measured in liht years.... If the lens radius is 500 km and the lens focal length is 15 AU, about 110,000 Fresnel zones are required for 1 micron laser light. A well-collimated beam from the lens would completely fill the 500 km radius sail of a very distant starship if the laser were to be positioned 15 AU from the lens, as shown."
08:26 < kanzure> "Exercise 7.4: Jones (1985) proposed a maser propelled light sail pushed by a well-collimated 3 m wavelength microwave beam. How many Fresnel lens zones would be required for this wavelength if the maser lens separation (lens focal length) is 15 AU and the lens radius is 3000 km?"
08:26 < kanzure> this is from "Deep Space Probes: To the outer solar system and beyond"
08:28 < kanzure> *distance measured in light years
08:40 < kanzure> interventional astronomy
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08:44 < eudoxia> >...a very distant starship
08:44 < eudoxia> how distant? over how many AU would you be able to maintain constant acceleration?
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10:02 < kanzure> publicknowledge.org emailed a pdf to openmanufacturing re: patent system reform, https://groups.google.com/d/msg/openmanufacturing/vS4ju1VqXb0/e3AB5NvvgsAJ
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10:28 < kanzure> .title http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm399335.htm
10:28 < yoleaux> FDA launches openFDA to provide easy access to valuable FDA public data
10:28 < kanzure> hmm http://open.fda.gov/
10:29 < gradstudentbot> Oh that's interesting, do you want to write a paper together?
10:30 < chris_99> sure gradstudentbot, what on
10:30 < gradstudentbot> I am sponsored by the Beijing Genomics Institute.
10:30 < kanzure> list of us government api endpoint thingies http://18f.github.io/API-All-the-X/data/developer_hubs
10:32 < chris_99> "Bureau of Alcohol, Tobacco, Firearms, and Explosives" interesting combination
10:32 < eudoxia> bureau of fun things
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10:32 < chris_99> haha
10:39 < kanzure> i'm skeptical of curved optics now
10:39 < kanzure> what's all that matter for
10:43 < kanzure> "The Gran Telescopio Canarias is a 10.4 m (410 in) reflecting telescope... The GTC began its preliminary observations on 13 July 2007, using 12 segments of its primary mirror, made of Zerodur glass-ceramic by the German company Schott AG. Later the number of segments was increased to a total of 36 hexagonal segments fully controlled by an active optics control system, working together as a reflective unit.[4][7]"
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10:46 < sheena> kanzure: i pm'd you
10:46 < kanzure> i see it
10:48 < kanzure> .title https://www.youtube.com/watch?v=PVXQUItNEDQ
10:48 < yoleaux> Ray Kurzweil: Get ready for hybrid thinking
10:48 < kanzure> blah nevermind
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11:01 < kanzure> huh, didn't know about photoresist tape
11:02 < kanzure> "I think you are refering to what is called Dry Film Resist. Dry film resist is commonly used in printed circuit board industry and can cover a much larger area than spin photoresist. However, thickness is needed to hold the film together so film photoresist typically comes in thickness of around 50 microns, and is applied to a planar area by hot roll lamination. Resolution is also lower. The smallest line/space that a state of the art PCB ...
11:02 < kanzure> ... company can mass produce are 100 micron/100 micron."
11:02 < kanzure> http://www.dupont.com/pcm/techinfo/laminate/optimize.html
11:02 < kanzure> http://www.dupont.com/pcm/techinfo/laminate/hotroll.html
11:02 < nmz787_i1> yep
11:02 < nmz787_i1> you can get it on ebay too
11:03 < kanzure> sounds easier than spincoating all the time
11:03 < chris_99> you can get a spray apparently
11:03 < kanzure> how would you guarantee thickness with the spraw?
11:03 < kanzure> *spray
11:03 < chris_99> no idea, probably not v. well
11:03 < kanzure> or surface finish, rather
11:05 < chris_99> mm
11:06 < kanzure> nmz787_i1: it would be nice to not need bulky lenses for everything (photolithography, micromachining, spectroscopy, etc)
11:08 < ||0_-_0||> paperbot http://brain.oxfordjournals.org/content/early/2014/04/22/brain.awu107.abstract
11:09 < paperbot> XMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)
11:11 < kanzure> hmm
11:11 < kanzure> ||0_-_0||: file bug reports https://github.com/kanzure/paperbot/issues
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11:24 < delinquentme> http://www.genomeweb.com//sequencing/roche-acquires-nanopore-sequencing-firm-genia-technologies-350m
11:24 < delinquentme> damn. biotech everywhere.
11:25 < kanzure> i have a mole there.. i should ask him for things.
11:25 < delinquentme> "Genia, based in Mountain View, Calif., has been developing a single-molecule sequencing-by-synthesis technology that uses nanopore-based electrical detection and employs a semiconductor integrated circuit."
11:26 < kanzure> yeah it's this one:
11:26 < kanzure> http://211.144.68.84:9998/91keshi/Public/File/49/30-4/pdf/nbt.2147.pdf
11:28 < kanzure> "An emerging DNA sequencing technique uses protein or solid-state pores to analyze individual strands as they are driven in single-file order past a nanoscale sensor1–3. However, uncontrolled electrophoresis of DNA through these nanopores is too fast for accurate base reads4. Here, we describe forward and reverse ratcheting of DNA templates through the α-hemolysin nanopore controlled by phi29 DNA polymerase without the need for active ...
11:28 < kanzure> ... voltage control. DNA strands were ratcheted through the pore at median rates of 2.5–40 nucleotides per second and were examined at one nucleotide spatial precision in real time. Up to 500 molecules were processed at ~130 molecules per hour through one pore. The probability of a registry error (an insertion or deletion) at individual positions during one pass along the template strand ranged from 10% to 24.5% without optimization. This ...
11:28 < kanzure> ... strategy facilitates multiple reads of individual strands and is transferable to other nanopore devices for implementation of DNA sequence analysis."
11:29 < kanzure> and then it's a matter of using a dsp and doing lots of funky stats to figure out the right sequence for molecules going through a large nanopore array
11:34 < kanzure> .tell gene_hacker the valveless microfluidic dna synthesizer is also interesting because it shoves all of the complicated equipment outside the realm of microfluidics (like the valve train). in fact, with a large enough array and micromirror array, you could have a 1024x1024 well microfluidic dna synthesizer that you could even operate manually (using manual dna synthesis), which although time-consuming has the advantage of building a million ...
11:34 < yoleaux> kanzure: I'll pass your message to gene_hacker.
11:34 < kanzure> ... separate dna fragments simultaneously.
11:35 < kanzure> blah yoleaux probably doesn't do multi-line .tell does it?
11:35 < kanzure> .tell gene_hacker http://diyhpl.us/~bryan/papers2/DNA/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf
11:35 < yoleaux> kanzure: I'll pass your message to gene_hacker.
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11:59 < nmz787_i1> kanzure: diffractive optics via self-assembled nanostructures would probably be pretty nice
11:59 < nmz787_i1> otherwise they're expensive if not made in bulk
12:03 <@fenn> https://en.wikipedia.org/wiki/Magnetic_refrigeration  neat stuff
12:03 < delinquentme> nmz787, what material are you suggesting to use for the assembly?
12:04 < delinquentme> fenn, that sounds like the "Cells alive system"
12:04 < kanzure> fenn, why were we thinking of a bluray led micromachiner cutter thing instead of dmd? was there a good reason?
12:05 < kanzure> was it something about avoiding lenses?
12:05 < kanzure> iirc i was annoyed about curing times, but that's not a good enough reason
12:05 < delinquentme> You know about these freezers right? magnetic agitation of fluids while dropping the temperature
12:05 <@fenn> continuous channel length is higher with a continuous process like a single laser
12:05 <@fenn> also smoother side walls because no aliasing
12:06 < kanzure> that's a marginally okay reason
12:06 <@fenn> also it could be used as a laser cutter?
12:07 <@fenn> also i've never actually used a DMD chip and the unknowns associated with that
12:07 < kanzure> so with a photolithography system you get dna synthesis (partially), microelectronics, microfluidics, and 3d printing
12:07 < kanzure> fwiw dmd documentation from texas instruments is reasonably thorough, i mean the instruction set looked like something usable, and they probably have application notes about throwing it into an apparatus/device/thing
12:08 <@fenn> i wouldn't use a bare chip if at all possible
12:08 <@fenn> things that take digital video as input are somewhat scarce tho
12:09 <@fenn> banned by RIAA
12:09 < kanzure> what scarcity are you referring to
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12:09 <@fenn> it's hard to find a simple DVI to parallel adapter
12:10 <@fenn> i recently found a chinese LED panel with HDMI in for $40
12:10 < kanzure> i thinkthe lack of optics required for micro led cutting/curing is a neat benefit, but ultimately spatial light modulation or micromirrors sound better.. argh.
12:11 <@fenn> it still needs optics, no?
12:11 < kanzure> i think it just needs a pinhole slit?
12:11 <@fenn> i mean, someone has done all the hard work to make the optics to read bumps on a DVD
12:12 <@fenn> and DMD projectors have the optics needed to use the chip
12:12 < kanzure> if that was true then why does everyone make hilariously complex setups with microscopes and micromirror arrays
12:13 <@fenn> because they are looking at the newport catalog with specs and cad drawings
12:14 < kanzure> take a gander at figure 1,
12:14 < kanzure> http://diyhpl.us/~bryan/papers2/optics/photolithography/A%20maskless%20photolithographic%20prototyping%20system%20using%20a%20low-cost%20consumer%20projector%20and%20a%20microscope.pdf
12:14 <@fenn> do i have to
12:14 < gradstudentbot> Wasn't that a Nature paper?
12:14 < kanzure> it's a projector taped to a microscope with a bunch of other optical elements
12:15 < kanzure> hm maybe that's not so bad
12:16 <@fenn> notice the ~5 degree angle the projector is mounted at on the bracket
12:17 < kanzure> argh what a terribly stupid picture. where's your diagrams..
12:17 <@fenn> anyway yes, that would be one way to do photolithography
12:17 <@fenn> do microscopes commonly have numerically controlled stages?
12:18 <@fenn> i've heard of "motorized stage" but that could mean anything
12:18 < delinquentme> South Korea’s Electronics and Telecommunications Research Institute (ETRI)
12:18 < kanzure> these guys used linuxcnc so i assume yes http://diyhpl.us/~bryan/papers2/optics/photolithography/Low%20cost%20UV%20laser%20direct%20write%20photolithography%20system%20for%20rapid%20prototyping%20of%20microsystems.pdf
12:18 < delinquentme> has done something like what you're talking about ... with a maskless curing of photo resists at microscales
12:18 < delinquentme> LCD based
12:20 <@fenn> i dont understand what is going on in that image
12:21 <@fenn> why is the monitor mounted on a micometer slide?
12:22 <@fenn> i guess the objective is connected to the monitor by a big bracket
12:24 < kanzure> on a related note, this one claims something about 20 million separate dna fragments built in parallel with a micromirror array projector glued to a microscope:
12:24 < kanzure> http://diyhpl.us/~bryan/papers2/optics/photolithography/Step-and-scan%20maskless%20lithography%20for%20ultra%20large%20scale%20DNA%20chips.pdf
12:25 <@fenn> if you have a belt of magnetocaloric material and feed it through a magnetized region, it will give off heat. does it require force to feed the belt in? and does that mean a heat differential can cause the belt to turn?
12:25 < gradstudentbot> That's beyond the scope of my research.
12:26 < kanzure> i wonder if laser cutting and micromirror array modulation could be interchanged on the same device. i mean, the xy stage is certainly the same component in both cases. (i think a micromirror array is the way to go since it's cheap and an lcd is slightly more hacky?)
12:26 < kanzure> and it sounds like these guys are just shining a uv led through a regular microscope
12:26 <@fenn> yes a micromirror array lets you tune the wavelength, is higher power, and is smaller
12:27 <@fenn> smaller is important when dealing with precision optics
12:27 < kanzure> and shining a regular micromirror array through a regular microscope too
12:27 < kanzure> in the low cost direct uv led write paper, there's no line item in the BOM for "crazy optics"
12:27 < kanzure> oh, lens $50
12:27 < kanzure> hm.
12:28 <@fenn> it's worth mentioning that you can do "spatial dithering" with a high resolution stage, to smooth out pixel aliasing
12:28 < kanzure> well that's not bad. if you know which lens.
12:28 <@fenn> the pixel center can be moved around
12:29 <@fenn> yeah i'm not at all impressed with their level of documentation
12:29 <@fenn> this is not even instructables grade
12:29 <@fenn> it's a talk abstract?
12:30 <@fenn> "Honolulu PRiME 2012" the 222nd meeting of the electrochemical society
12:31 < kanzure> "the 310th meeting of weird wizards nobody will ever hear of"
12:31 <@fenn> seems like there is a lot of optics stuff in hawaii
12:32 < kanzure> i'm curious why i don't see microscope setups for microelectronics photolithography reasons
12:33 < cpopell> I'm pretty sure that's how azonenberg does it
12:33 < cpopell> but I don't remember that much detail on his lab
12:33 < kanzure> he's in hibernation mode
12:33 < kanzure> (spending his time elsewhere)
12:33 < cpopell> yeah, he's trying to wrap up his PhD
12:33 < cpopell> and got a girlfriend :V
12:33 < kanzure> what a loser
12:33 < kanzure> about the phd thing, i mean
12:33 < gradstudentbot> I wasn't able to find any references.
12:34 < kanzure> also, i'm concerned about how cheap this system is ($1k in parts) compared to how few have bothered
12:35 < kanzure> microelectronics, microfluidics, dna synthesis, and 3d lithography-printing-something, for the price of one, and nobody is doing it??
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12:41 <@fenn> "A major breakthrough came 2002 when a group at the University of Amsterdam demonstrated the giant magnetocaloric effect in MnFe(P,As) alloys that are based on earth abundant materials."
12:41 < kanzure> nmz787_i: i would be willing to do continuous-flow valveless microfluidic dna synthesis
12:42 <@fenn> paperbot: http://www.nature.com/nature/journal/v415/n6868/full/415150a.html
12:42 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2F415150a
12:45 < kanzure> fenn, did you look at gene_hacker's nasa link? http://www.nasa.gov/sites/default/files/files/Quadrelli_2012_PhI_OrbitingRainbows_.pdf
12:48 < kanzure> actually, i mean, it is an interesting thing to look at
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12:55 < kanzure> "Forty six clumps [from Project West Ford] are known to remain in orbit as of 2013.[13]"
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13:05 < justanotheruser> kanzure: please describe your attack on maidsafe
13:06 < kanzure> the attack is just an accumulation of their currency/money/tokens- you can do a sybil attack, host only a single version of the file, and earn a disproportionately larger amount of credit than the well-behaving actors
13:07 < kanzure> *single copy of the file
13:08 < justanotheruser> yeah, I assumed PoR (really Trust in Resource because there is no such thing as a proof of resource) either needed a central authority or was vulnerable to sybil
13:09 < kanzure> i think my attack only works if they are storing redundant copies of data
13:09 < kanzure> not sure
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13:14 < kanzure> ParahSailin: are there any dna synthesis bead-based protocols where you use light to attach/detach beads (perhaps even selectively with maskless light arraying)
13:15 < kanzure> or, some other method of starting strands in particular regions on a well array, and later decoupling them to wash them into a collection chamber
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13:16 < nmz787_i> kanzure: if you've seen a support-free synthesis method (for any kind of polymer) I'm looking for refs
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13:18 < dbolser> anyone want a post doc in Korea working on biomedical engineering?
13:18 < dbolser> My friend is hireing
13:19 < kanzure> i'll take one, but i'm only paying $25k/year at the moment
13:19 < dbolser> the university teaches all courses in english
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13:19 < kanzure> nmz787_i: dbolser might know
13:19 < kanzure> dbolser: oh, you're not offering me a postdoc person?
13:19 < dbolser> kanzure: no, sorry
13:20 < dbolser> 'support free'?
13:20 < kanzure> nmz787_i: yeah wait, be more specific.. obv. there are in-solution synthesis methods.
13:21 < dbolser> Jong is hiring post-doc's here:
13:22 < dbolser> http://www.unist.ac.kr/index.sko
13:22 < [nsh]> <--- free money goes here kthx
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13:27 < nmz787_i> most in-solution are liquid-phase supports... i.e. grown on PEG
13:29 < kanzure> welp you can always look through the dark corner http://diyhpl.us/~bryan/papers2/DNA/
13:29 < dbolser> nmz787_i: are you looking for something like emulsion PCR?
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13:33 < heath> https://github.com/heath/treemap
13:34 < heath> now onto the frontend
13:34 < kanzure> oh i forgot about this paper,
13:34 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Light-directed%20synthesis%20of%20high-density%20oligonucleotide%20arrays%20using%20semiconductor%20photoresists%20-%201996.pdf
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13:36 < nmz787_i> dbolser: nope, no PCR, it would all be in solution, so not emulsion
13:37 < kanzure> "Once the resist has been applied to the substrate and patterned, a nucleotide is added to the surface in the exposed areas using standard solid-phase oligonucleotide synthesis protocols. The glass surface is initially derivatized with hydroxyl-terminated linker molecules protected with acid-labile DMT (or "trityl") groups. In the image-transfer step, exposed regions of the substrate are selectively deprotected ("detritylated") by treatment ...
13:37 < gradstudentbot> I am busy researching.
13:37 < kanzure> ... with acid, revealing hydroxyl groups that are then reacted with a 5'-DMT-protected deoxynucleoside phosphoramidite. By repeating this sequence of steps in conjuniction with an appropriate series of masking patterns and nucleotide additions, a large matrix of oligonucleotide sequences can be constructed in a relatively small number of steps (18, 19)."
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13:38 < nmz787_i> i found a paper using water-resistant chemistry, using modified 5'-DMT group chemistry
13:38 < nmz787_i> the keyword was NBS n-bromo-succinimide
13:38 < nmz787_i> that is also worth looking further into
13:39 < nmz787_i> water is a major PITA for any of this
13:39 < kanzure> does your car have a valve train
13:42 < nmz787_i> yes
13:42 < nmz787_i> all except electric would
13:42 < kanzure> i really like gene_hacker's idea of not including the valves in the microfluidic device
13:43 < nmz787_i> which specifically?
13:43 < kanzure> and we can get away with not having any at first (manual insertion of liquids by syringe pump or syringe)
13:44 < kanzure> well he was referencing that picoarray dna snythesizer paper.. they were doing continuous flow-through valveless microfluidics with a micromirror array for photogenerated acid dna synthesis. they had it plugged into a column on a conventional dna synthesizer (expedite 8909) to use its existing valve train.
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13:45 < kanzure> valveless means less parts means less engineering effort
13:45 < nmz787_i> but that's only part of the problem
13:45 < nmz787_i> you need to then cleanup the dna and insert it
13:45 < kanzure> fragment selection?
13:45 < nmz787_i> which, I'm pretty sure, you're going to want some valves for
13:46 < nmz787_i> yeah basically
13:46 < kanzure> wasn't there at least one version of dna synthesis that had cleavable fluorophores
13:46 < kanzure> or was that only in sequencing.. ugh.
13:46 < nmz787_i> and if you use a solid support, or even a liquid-phase support, you're going to have to cleave the constructs from the supports every time you want to purify
13:46 < nmz787_i> yeah
13:46 < nmz787_i> i think that was  the single molecule guys
13:47 < nmz787_i> i always forget their name, even though their process is kickass
13:47 < nmz787_i> Helicos
13:47 < nmz787_i> http://www.google.com/patents?id=TfEAAgAAEBAJ
13:47 < nmz787_i> but yeah who knows what their chemistry is
13:47 < nmz787_i> that's why i figure its easier to do valves than chemistry
13:48 < kanzure> how would the valves do sequencing?
13:48 < kanzure> what?
13:48 < nmz787_i> (i've been thinking lately about how to manage getting a chem PhD)
13:48 < nmz787_i> you sequence the order they open/close
13:48 < kanzure> if you're going to go for a phd you should study with gene_hacker or jmil
13:49 < kanzure> yeah but you still have to verify and sequence eventually either way
13:49 < nmz787_i> jmil isn't a polymer chem guy afaik
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13:49 < nmz787_i> i've been planning on simply having a reporter that i always synthesize
13:49 < nmz787_i> to work as a  sort of CRC
13:49 < gradstudentbot> That's not really surprising since they did it ex vivo.
13:50 < nmz787_i> GFP or something 'if it glows it goes' or the banana smell gene 'if it gasses it passes
13:50 < nmz787_i> '
13:50 < kanzure> how long is gfp anyway?
13:50 < kanzure> 500 amino acids?
13:50 < nmz787_i> nah
13:50 < nmz787_i> prob 300ish
13:51 < kanzure> 238 amino acids according to wikipedia
13:51 < nmz787_i> 238
13:51 < kanzure> hm
13:51 < kanzure> not the smallest
13:51 < kanzure> oh that would be worth looking up, directed evolution of shorter gfp molecules
13:51 < kanzure> *gfp sequences
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13:53 < kanzure> close..
13:53 < kanzure> .title http://peds.oxfordjournals.org/content/22/5/313.short
13:53 < yoleaux> Directed evolution of an extremely stable fluorescent protein
13:53 < kanzure> "eCGP123 could not be denatured by a standard thermal melt, preserved almost full fluorescence after overnight incubation at 80°C and possessed a free energy of denaturation of 12.4 kcal/mol. It was created from CGP by a recursive process involving the sequential introduction of three destabilizing heterologous inserts, evolution to overcome the destabilization and finally ‘removal’ of the destabilizing insert by gene synthesis. We ...
13:53 < kanzure> ... believe that this approach may be generally applicable to the stabilization of other proteins."
13:53 < gradstudentbot> Anyone else think pol II looks like a butt?
13:53 <@fenn> paperbot: http://www.opticsinfobase.org/ao/viewmedia.cfm?uri=ao-28-5-976&seq=0
13:53 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/93514aa9aede1d8ae0a80250a240a40.txt
13:54 <@fenn> paperbot: http://www.opticsinfobase.org/DirectPDFAccess/AF98D35B-DA55-98A8-EAC0DE8800362C8D_32231/ao-28-5-976.pdf?da=1&id=32231&seq=0&mobile=no
13:54 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/141d3bf3c08a1cd0f424219ebc3e032d.pdf
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13:54 < kanzure> who the hell names their folder "Direct PDF Access"
13:55 < kanzure> also: i wonder if that nasa paper considered orbital clouds of protein for their electromagnetic aerosol devices
13:55 <@fenn> lots of hieroglyphics in this paper
13:56 < kanzure> it seems to be some kind of code
13:56 <@fenn> i just want to know what a kinoform is
13:56 < kanzure> .d kinoform
13:56 < yoleaux> Sorry, I couldn't find a definition for 'kinoform'.
13:57 <@fenn> "Kinoform lenses, a type of refractive lens similar to those found in lighthouses  are being considered by researchers for their ability to efficiently focus x-ray light down to very small spots. This feature is vital to the study of molecules, atoms, and advanced materials at the nanoscale"
13:57 <@fenn> blah blah diamond heat conduction synchrontron etc
13:57 < kanzure> i thought lighthouses use fresnel lenses
13:58 <@fenn> no
13:58 <@fenn> they look similar
14:02 < kanzure> ParahSailin: minimum viable sequence of a fluorescent protein?
14:05 < kanzure> so that nasa paper wants granular clouds of dust with micron-sized particles.. proteins could probably be made that large if necessary.
14:05 < kanzure> or even dna
14:09 < dbolser> focus xrays?
14:09 < dbolser> if you can do that, you can look at atoms
14:09 < dbolser> how big is a micron in Angstroms?
14:11 < kanzure> dbolser: hm? the paper is about using orbital optical tweezers to manipulate clouds of dust to form kilometer-scale telescopes
14:11 < kanzure> dbolser: http://www.nasa.gov/sites/default/files/files/Quadrelli_2012_PhI_OrbitingRainbows_.pdf
14:11 < dbolser> Interesting
14:12 < dbolser> yeah, big viruses are only a few hundred angstroms, and a micron is 10,000 angstrom
14:12 < nmz787_i> kanzure: those kinoforms look like a specific ruling style for a diffractive optic
14:12 < dbolser> it's not easy to engineer a protein that big
14:12 < kanzure> it was fenn asking about kinoforms btw
14:13 < kanzure> dbolser: i think some of the larger viruses are much bigger
14:13 < dbolser> you can get fibers on that scale, but they prolly aint the right shape
14:13 < dbolser> kanzure: I'd be surprized
14:13 < nmz787_i> but yeah diffraction is how fabs are doing sub-wavelength these days
14:13 < dbolser> based on the physics of protein folding
14:13 < kanzure> mimivirus has a capsid of 0.6 microns
14:13 < kanzure> capsid diameter
14:14 < kanzure> sometimes 0.8 microns
14:14 < dbolser> pretty awesome
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14:18 < dbolser> the biggest virus structure solved is .2 microns
14:18 < dbolser> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137492/
14:18 < kanzure> solved = seen in a microscope?
14:18 < dbolser> yes
14:19 < dbolser> seen at atomic resolution
14:19 < kanzure> oh i see. well that doesn't seem necessary? heh
14:19 < dbolser> I guess you can literally see things on that scale
14:19 < kanzure> i think it should be possible to use directed evolution to get a virus of larger size if necessary
14:19 < dbolser> no, not at all :-)
14:19 < kanzure> for some reason i think virus capsids would be a better substrate than dried dead bacteria or dna for interstellar telescopes
14:20 < dbolser> yes
14:20 < kanzure> dead bacteria will probably collapse in unpredictable ways
14:20 < dbolser> I bet the structures hold up in space better
14:20 < kanzure> i assume a virus capsid stays a virus capsid much longer
14:20 < dbolser> kanzure: if you could stableize em like above
14:20 < kanzure> sure, optical tweezers etc
14:20 < kanzure> other advantage is you could embed stuff into the capsid
14:20 < dbolser> however, there is a trade off between stability and folding efficiency
14:21 < dbolser> indeed... but not sure if they'd fall apart in a vacuum
14:21 < kanzure> i guess if you really wanted a dead substrate you could also just use emulsions or microspheres
14:21 < dbolser> proteins unfold under pressure
14:21 < dbolser> yeah
14:21 < dbolser> http://www.ncbi.nlm.nih.gov/pubmed/23251035 <- folding vs. stability
14:21 < paperbot> http://libgen.org/scimag/get.php?doi=10.1073%2Fpnas.1210180110
14:22  * kanzure pets paperbot
14:23 < kanzure> "Pandoraviruses have a size approaching 1 micrometer and a blob-like shape resembling some types of bacteria. The genome of the larger variant, Pandoravirus salinus, was reported to contain 2556 putative protein-coding sequences, of which only 6% had recognizable relationships with genes from other known organisms."
14:23 < kanzure> doh i forgot about this one. mimivirus isn't the largest.
14:23 < dbolser> some viruses are just weird
14:24 < dbolser> same with bacteria
14:24 < dbolser> fungi
14:24 < dbolser> plants
14:24 < dbolser> paris japonicus has a genome the size of a small village of humans
14:26 < kanzure> does jong have a complete backup of all the ncbi-hosted genomes?
14:29 < kanzure> i am concerned about redactions from ncbi genbank and proteinwhatever
14:33 < dbolser> kanzure: he built a korean version of NCBI in his previous job
14:34 < dbolser> ENA mirror genbank
14:34 < kanzure> but just genbank?
14:34 < dbolser> there is also soemething called biomirror
14:34 < dbolser> genbank, sra, gca, etc
14:34 < dbolser> european nucleotide archive
14:34 < kanzure> i haven't tracked the data but i think that companies might be forcing ncbi to do redactions of certain proteins or genes
14:35 < dbolser> it's possible, but against their guidelines...
14:41 < kanzure> "Fig 28: A simulated raw image of an exo-earth at 10 light years, using a 150 apertures regularly distributed over 150 km."
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14:49 < kanzure> .wik optical lift
14:49 < yoleaux> "Optical lift is an optical analogue of aerodynamic lift, in which a cambered refractive object with differently shaped top and bottom surfaces experiences a stable transverse lift force when placed in a uniform stream of light." — http://en.wikipedia.org/wiki/Optical_lift
14:51 < kanzure> "The experiment began as computer models that suggested when light is incident on a tiny object shaped like a wing, a stable lift force is applied to the particle. Then the researchers decided to do physical experiments in the laboratory, and they created tiny, transparent, micrometer-sized rods that were flat on one side and rounded on the other, rather like airplane wings. They immersed the lighfoils in water and bombarded them with 130 mW ...
14:51 < kanzure> ... infrared laser light from underneath the chamber. Radiation pressure pushes the particles along the direction of propagation, this is called the scatter force, but the excitement came when the particles were forced to the side in a direction perpendicular to the direction of propagating light. The transverse force on the particles is the lift force. The researchers discovered not only that the rods experienced stable lift, but that, ...
14:51 < kanzure> ... depending on refractive index, the rod could have up to two stable angles of attack it rotated to when exposed to the laser light. Symmetrical spheres tested did not exhibit this same lift effect.[2] In optical lift, created by a "lightfoil", the lift is created within the transparent object as light shines through it and is refracted by its inner surfaces. In the lightfoil rods a greater proportion of light leaves in a direction ...
14:51 < kanzure> ... perpendicular to the beam and this side therefore experiences a larger radiation pressure and hence, lift.[2] The 2010 discovery of stable optical lift is considered by some physicists to be "most surprising".[3] Unlike optical tweezers, an intensity gradient is not required to achieve a transverse force. Many rods may therefore be lifted simultaneously in a single quasi-uniform beam of light. Swartzlander and his team propose using ...
14:51 < kanzure> ... optical lift to power micromachines, transport microscopic particles in a liquid, or to help on self-alignment and steering of solar sails,[3] a form of spacecraft propulsion for interstellar space travel. Solar sails are generally designed to harness light to "push" a spacecraft, whereas Swartzlander designed their lightfoil to lift in a perpendicular direction; this is where the idea of being able to steer a future solar sail spacecraft ...
14:51 < kanzure> ... may be applied.[4] Swartzlander said the next step would be to test lightfoils in air and experiment with a variety of materials with different refractive properties, and with incoherent light.[2]"
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14:56 < dbolser> 28 c is nice
15:03 < delinquentme> As far as cellular aging is concerned. We need only to worry about two things: nuclear DNA + mitochondrial DNA right?
15:03 < delinquentme> As far as a *cell* is concerned. Thats everything.  Right?
15:03 < dbolser> no
15:03 < dbolser> cells accumulate mis-folded proteins in 'granules'
15:03 < dbolser> that accumulate with age
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15:05 < kanzure> "Palmer [60] considered using the nonlinear optical index of glass beads or aerosol droplets to organize the particles and trap them into fresnel-like three-dimensional holographic gratings."
15:05 < delinquentme> Ah ok so cytoplasmic junk
15:06 < delinquentme> dbolser, thoughts on how to locate and remove those?
15:06 < delinquentme> Really specific binding proteins.
15:06 < gradstudentbot> Dude, you contaminated my experiment.
15:07 < kanzure> defeat of cellular aging will most likely take longer than whole head life support could theoretically take (why are people always more interested in cryonics? there are perfectly good brains still living that could continue to live if you etc.. etc..)
15:07 < kanzure> i forgot what i was typing about
15:10 < delinquentme> kanzure, you're saying chop the head off and stick it on a robot ... feed it with proper nutrients
15:10 < kanzure> you don't need the robot part
15:13 < ||0_-_0||> delinquentme if you want to remove lipofuscins first you'll need to target the aggregates and then you'll need to do some sort of molecular work to un-clot them
15:13 < ||0_-_0||> problem is they really like being clotted
15:13 < ||0_-_0||> so you've got a fair high barrier to overcome there
15:14 < kanzure> lipofuscins are not the only problem in aging, sigh
15:15 < delinquentme> literally we could just jam probes with the correct antigens for known aggregates and yank them out
15:15 < ||0_-_0||> kanzure we're aware but the discussion was part of "cytoplasmic junk"
15:16 < kanzure> no, he only said that because he doesn't know
15:16 < ||0_-_0||> and delinquentme sure we could try that, but getting an antibody into a cell is not exactly easy and you've still got the problem of induced toxicity when the aggregates break up or you fuck the membrane trying to yank them out
15:19 < delinquentme> Also we've got the whole breeding thing as a way to clean all damage.  Which makes me REALLY take a second look at this:  http://guardianlv.com/2012/10/jd-stem-cell-discovery-will-allow-gay-men-to-create-their-own-eggs-for-surrogate-birth/
15:21 < delinquentme> I'm trying to find the associated paper
15:21 < EnLilaSko> MB + centrophenoxine for dat dere lipo
15:21 < EnLilaSko> Although centro is questionable
15:22 < delinquentme> So these guys are taking somatic cells and coaxing them into eggs.
15:22 < ||0_-_0||> wtf delinquentme biology is not legos; what works in one very limited and simplified system is not the truth
15:23 < delinquentme> ||0_-_0||, specific example?
15:23 < ||0_-_0||> all of it
15:23 < delinquentme> I mean I understand DNA isn't a lego.  But what caused the 'wtf'
15:23 < ||0_-_0||> breeding to clear damage isn't going to rejuvenate anyone
15:23 < ||0_-_0||> I don't know how you've drawn that conclusion
15:24 < gradstudentbot> My project sucks.
15:25 < kanzure> gene_hacker: optical lift is pretty neat
15:25 < gradstudentbot> Blah, I'm going to quit.
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15:27 < delinquentme> ||0_-_0||, Ok so we know that everytime someone makes a whole human from a new embryo ... there is no damage ( per aging is concerned ) IN that organism.
15:28 < delinquentme> yes? Yes. Ok. So in looking at the research statements above they're essentially coaxing asexual reproduction .
15:28 < ||0_-_0||> if epigenetics weren't also a factor, I'd find that possible
15:28 < delinquentme> Cells derived from that cluster ... could be immunologically the same
15:29 < delinquentme> specifics ||0_-_0|| what epigenetic events are giving you reservations here?
15:30 < kanzure> lots of embryos die for all sorts of reasons, including damage
15:30 < ||0_-_0||> stress markers, preserved transcription factors, chromatin patterns
15:30 < gradstudentbot> My labview crashed.
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15:32 < delinquentme> kanzure, sure but we've got a totally novel way of getting cellular material to that pristine state.  With the possibility of them being genetically identical
15:33 < kanzure> what about it
15:33 < delinquentme> ||0_-_0||, so these are all part of that intergenerational process ... but it remains to be determined if any of that matters if all we want are less damaged cells
15:33 < Mokstar> basically he's trying to recreate the system described in A Brave New World
15:33 < Mokstar> and/or solve the Japanese underpopulation problem
15:33 < delinquentme> If the thing identifies the cell as self , thats a step in the right direction
15:33 < ||0_-_0||> Brovansky groups, yes
15:34 < ||0_-_0||> you're aware that there's no real immune system to speak of for quite a while in gestation, right?
15:34 < delinquentme> Sorry ||0_-_0||  Im talking about taking those cells and jamming them into adult persons as therapy
15:35 < ||0_-_0||> OK can we please work on making parameters and context clearer lest we appear to be spouting out our collective anal manifolds?
15:36 < justanotheruser> ||0_-_0||: I don't like your name
15:36 < delinquentme> I think there are a total of like 6 things necessary for total acceptance within the body. 2 of those are MHCs
15:36 < justanotheruser> I don't have any authority here, i'm just stating that
15:36 < ||0_-_0||> justanotheruser it's pronounced "THWB"
15:36 < justanotheruser> thwub?
15:37 < delinquentme> thumpin
15:37 < ||0_-_0||> I should probably reclaim my main nick
15:37 < ||0_-_0||> your feedback has been noted justanotheruser thank you for caring
15:38 < justanotheruser> lol
15:39 < nmz787_i> tubthumper
15:39 < nmz787_i> kanzure: optical lift is indeed neat
15:39 < ||0_-_0||> do you get knocked down nmz787_i ?
15:39 < nmz787_i> i will have to look for some shapes
15:39 < nmz787_i> yes, but I get up again
15:40 < nmz787_i> I have a bad tendency to piss the night away sometimes, though last night I was pretty productive with kicad!
15:41 < kanzure> nmz787_i: pick out a microscope for doing dmd things
15:42 < gradstudentbot> Can I defend with just one aim done?
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16:10 < justanotheruser> kanzure: I assume youve heard of http://www.swarmcorp.com/
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16:14 < kanzure> ugh
16:14 < kanzure> that sounds awful
16:16 < justanotheruser> kanzure: great camera work and dramatic music
16:17 < kanzure> ah, didn't look at the video, because why would i
16:17 <@fenn> why is "optical lift" surprising at all? it's just conservation of momentum, and it's how solar sails work
16:18 < kanzure> no, solar sails work by a different mechanism
16:20 <@fenn> actually no, you're wrong
16:20  * kanzure pouts
16:20 < kanzure> but the author said so
16:21 <@fenn> either way it's force caused by the momentum of light being reflected in some direction or other
16:21 <@fenn> the fact that they used glass rods doesn't change the physics
16:21 < nmz787_i> kanzure: I've got a microscope that is trinocular and supposedly has some fluorescense filters... but if i were to buy one, I've been eyeing the new ones on ebay and/or microscopenet.com
16:21 < kanzure> hook up the dmd projector to the microscope
16:22 < nmz787_i> kanzure: my microscope is ~50 years old though (has good optics)... so its dusty and all the oil is gelled up now so action is hard on control knobs... also power supply/light bulb is gone
16:22 < gradstudentbot> The grant got rejected.
16:23 < kanzure> so why were we doing the lasre cutter xy slide if you already had one
16:23 < kanzure> i guess something repeatable that can be made multiple times is better
16:23 < nmz787_i> kanzure: I had trouble thinking of how to connect the two, and adjust the hell so planes were parallel
16:23 < nmz787_i> yep
16:24 <@fenn> i wish people would stop making terrible websites
16:24 < kanzure> adjust the hell?
16:24 < nmz787_i> well cause if the planes aren't parallel, results could be shitty
16:24 < nmz787_i> so how do you finely adjust the projector relative the the scope
16:24 < kanzure> i think a certain amount of shit is acceptable, ya?
16:24 < kanzure> well according to these articles you don't have to
16:24 < nmz787_i> until you need to start iteratively debugging
16:24 < kanzure> or you get one $50 lense or osmething.. very confused.
16:25 <@fenn> you keep the plane in focus like a camera autofocus
16:25 < nmz787_i> are you looking at DMD photolithography exposure of the photo generated acid?
16:25 < nmz787_i> fenn: that doesn't work for getting them all focused at once
16:25 < nmz787_i> fenn: that also doesn't take into account the adjustment hardware
16:25 < kanzure> dmd photolithography for 3d lithography, microelectronics fabrication, dna synthesis, and microfluidics
16:26 <@fenn> yes it does, the projection plane is short so it can all be in focus (as long as your optics dont suck)
16:26 <@fenn> some optics have spherical abberation or whatever
16:26 < nmz787_i> sure autofocus algos are great, and work if you only need one area in focus at a time, but with that autofocus algo/data you can then feed it back to some adjustment screws or something
16:26 < nmz787_i> but the projector was a few lbs
16:26 < nmz787_i> and I'm apparently bad with fabricating mechanical stuff
16:27 < nmz787_i> kanzure: i'm kinda not so interested in DMD photolith after I saw interpixel noise in some photoresist in one of the pro DMD photolith companies research articles they had posted
16:28 < nmz787_i> (I believe Heidelberg)
16:28 < gene_hacker> you can calibrate for that
16:28 < yoleaux> 18:35Z <kanzure> gene_hacker: the valveless microfluidic dna synthesizer is also interesting because it shoves all of the complicated equipment outside the realm of microfluidics (like the valve train). in fact, with a large enough array and micromirror array, you could have a 1024x1024 well microfluidic dna synthesizer that you could even operate manually (using manual dna synthesis), which although time-consuming has the  …
16:28 < yoleaux> advantage of building a million ...
16:28 < yoleaux> 18:35Z <kanzure> gene_hacker: http://diyhpl.us/~bryan/papers2/DNA/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf
16:28 < kanzure> what is an acceptable amount of noise for you?
16:28 <@fenn> ugh i hate everyone /me goes away
16:29 < kanzure> fenn: what's wronnnnng
16:29 <@fenn> PMS
16:29 < gene_hacker> there is noise and you have to deal with the fact that the illumination isn't uniform
16:29 < kanzure> fenn: the pixels?
16:29 < nmz787_i> tracing around with a laser seems to get around interpixel noise totally
16:30 < nmz787_i> but then you have to have a nice smooth tracing machine
16:30 <@fenn> inertia smooths out steps
16:30 < gene_hacker> then you have laser tracking noise
16:30 < nmz787_i> fenn: idk about that at such microscales
16:31 <@fenn> what "noise" are you all talking about?
16:31 < nmz787_i> fenn: i'm talking about leadscrew variation
16:31 < gene_hacker> oh tracing
16:31 <@fenn> periodic error doesn't matter if it's repeatable; absolute error doesn't matter because hopefully your feature size is small
16:31 < gene_hacker> well whatever works.
16:32 < seba-> hm
16:32 < seba-> i could do sous vide
16:32 < gene_hacker> you could also use use an array of LEDs for a synthesizer, from what i understand a picoarray doesn't have very many pixels
16:32 < seba-> in my incubator
16:32 <@fenn> how do you release the dna once you've synthesized it?
16:32 < seba-> lol
16:33 < kanzure> fenn: probably solid phase support release.. wash away the beads, etc
16:33 < kanzure> or you could have pressure applied to the whole device so that beads are held in place
16:33 <@fenn> but you want to release one well at a time or it will cross contaminate
16:33 < nmz787_i> fenn: i've been planning on a support-free or at least liquid-phase support
16:33 <@fenn> otherwise what's the point of the "array" at all?
16:33 < kanzure> yes you will probably not have single bead release in that design
16:33 < gene_hacker> or use frickin' magnets!
16:33 < kanzure> well you can synthesize lots of dna fragments that are meant to be assembled together
16:33 < gene_hacker> and magnetic beads
16:33 < kanzure> oh yeah, magnetic beads exist
16:33 < gradstudentbot> Who used the last of the buffer?
16:34 <@fenn> this plan doesn't make any sense
16:34 < kanzure> gene_hacker: i dunno why the pico array didn't have lots of pixels, i see no reasons why not
16:34 < gene_hacker> the point of the array is to keep the photogenerated acid separate
16:34 < gradstudentbot> I think I just cured cancer. Wow.
16:34 < kanzure> fenn: you synthesize your library, then you put your library in a pot and you make your super-long protein sequence
16:34 <@fenn> what's the error rate of "picowell photosynth" or whatever they're calling it
16:34 < gene_hacker> well one should start simple first to work out any kinks
16:35 <@fenn> let's say you have one picowell
16:35 <@fenn> there are a million dna strands in it
16:35 <@fenn> what percentage of those strands are "perfect"
16:35 <@fenn> let's say it's 100 bases long
16:36 < kanzure> the picoarray one is 67% yield per 40mer ? http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf
16:36 < kanzure> lol 67%
16:36 <@fenn> .wa e^40 = 0.67 solve for e
16:36 < yoleaux> e⁴⁰ = 0.67 e: False
16:36 <@fenn> bah
16:36 <@fenn> .c 0.67^(1/40)
16:36 < yoleaux> 0.67^(1/40) = 0.99003801...
16:37 <@fenn> so you gotta get a lot of 9's
16:37 <@fenn> or you gotta sequence each strand and then you are cambrian genomics
16:38 < kanzure> well, hm
16:40 <@fenn> oh they were talking about targeting picowells, not etching them
16:42 < nmz787_i> or you have a saner synthesis process
16:42 < nmz787_i> that keeps track for you
16:42 < kanzure> oh yeah, fluorescence-based things that tell you if the reaction happened at all
16:42 < kanzure> but it's not a single strand if it's on a bead- it's probably a few million strands
16:42 < kanzure> maybe you could get single strands to grow in each area
16:43 < nmz787_i> nah there's plenty of interogation methods
16:43 < kanzure> and then make the fluorescence event bright enough
16:43 < nmz787_i> scanned frequency voltammetry is what i want to investigate
16:43 < kanzure> well if some % of your strands on the bead are wrong you're going to get propagating pcr errors
16:43 < nmz787_i> then dont use a bead
16:43 < nmz787_i> so you can get rid of the erroneous (even if length check is the only metric)
16:46 < kanzure> i wonder what the source of the yield problem is in this case
16:47 < kanzure> maybe it's the chemistry
16:47 < nmz787_i> corners that don't get mixed well (microwells dont have this problem)
16:47 < kanzure> what's the point of having a chemical process that only works 1% of the time
16:47 < nmz787_i> chemistry that hurts existing syntecons
16:47 < nmz787_i> or whatever you call the already-synthesized stuff
16:48 < kanzure> i wonder if dna gets tangled on beads and makes certain strands miss out on individual cycles
16:48 < nmz787_i> like the acid can either activate.... OR it can depurinate a sidechain
16:48 < nmz787_i> probably
16:54 < kanzure> there should be a journal of theoretical dna synthesis
16:54 < kanzure> (not just "journal of nucleic acids research")
16:55 < kanzure> *of practical dna synthesis
16:56 < kanzure> paperbot: http://www.mdpi.com/1420-3049/18/1/1063/pdf?y=1
16:56 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/b2d710d98a9d3d35094b393ac7161a84.pdf
16:56 < kanzure> "Frontiers and Approaches to Chemical Synthesis of Oligodeoxyribonucleotides"
16:57 < nmz787_i> that is one i will have to read when i leave work
16:57 < nmz787_i> but maybe find some similar that don't "focusing on large-scale methods"
16:58 < nmz787_i> that is the opposite optimization we want
16:58 < nmz787_i> (solution to the problem could overlap, but my thinking is the end-goals are sufficiently different)
16:59 < nmz787_i> i.e. if you think their target is some small RNA for FDA human trials of some RNA interference crap
16:59 < nmz787_i> (i know it says deoxy)
16:59 < nmz787_i> bbl
17:00 < nmz787_i> try to find that nbs (n-bromo-succinimide) paper
17:00 < kanzure> i'm curious about other complex chemical reactions with yield problems
17:00 < kanzure> surely chemists have done this before in other areas
17:01 < kanzure> i'd be very disappointed if dna synthesis is the most complicated sequence of reactions we've bothered to make
17:01 < kanzure> but also, presumably more complex chemistries would require clever solutions that can be backported, erm, sidewayported
17:01 <@fenn> symported!
17:02 < kanzure> you can't just make up words, you have to use someone's name
17:03 <@fenn> symbionese liberported
17:04 < kanzure> i should go find a chemist and bug them about this
17:04 <@fenn> chemists get to use crystallization
17:04 < kanzure> hm
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17:04 <@fenn> afaik crystallization doesnt  work so well wrt strand mismatch
17:04 <@fenn> it does work but it's tricky
17:05 <@fenn> you linked a paper about it some years ago
17:05 < kanzure> was this dna related?
17:05 <@fenn> yes, maybe it was george church?
17:05 < kanzure> great i'll just look it up in my non-existing tagging system
17:05 <@fenn> slow cooling of pcr products
17:06 <@fenn> the strands with no mismatches would anneal first
17:06 <@fenn> but it was like 0.0001C
17:07 < kanzure> (i'm not digging this up, i have no audible bells ringing)
17:07 < kanzure> i wonder if people really think they're hearing bells whenever they remember things
17:07 < kanzure> (must be loud in there)
17:08 < kanzure> (or silent in my case..)
17:09 < kanzure> hm, i think nate has a point here, "oh we have terrible yields? let's just parallelize it!" is probably not a good idea
17:10 <@fenn> today i was woken up by the doorbell, i roll around and go back to sleep. i'm woken again by the doorbell a couple hours later. whoever's at the door must be back, guess i have to get up and answer it. go to the door, nobody's there. turns out it was the printer making its "paper jam" noise
17:10 < kanzure> during your napyear did you see the printer device that moves itself around on top of the stack of blank paper
17:10 <@fenn> why would i want that
17:11 < kanzure> well i didn't want it
17:11 <@fenn> does it have a laser cutter or something
17:11 <@fenn> or is it just a turtle LOGO bot
17:11 < kanzure> i think inkjet or laser toner transfer (probably inkjet, knowing the world..)
17:11 <@fenn> ok whatever, don't care
17:12 <@fenn> i remember a "paint roller" with a mouse sensor to track position and a print head, you could "roll" a pattern onto a wall
17:13 < ThomasEgi> fenn,  http://theoatmeal.com/comics/printers
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17:14 <@fenn> why are there no open source printers?
17:14 <@fenn> how hard could it be to drill a tiny hole in something
17:15 < kanzure> tiny hole?
17:16 < gradstudentbot> I remember the paper, I just don't remember the details.
17:16 <@fenn> wow the paranoid schizophrenics are going to love this http://www.technologyreview.com/news/527561/military-funds-brain-computer-interfaces-to-control-feelings/
17:17 <@fenn> also it uses the same electrode layout as my piezo sonar array sketch
17:17 < kanzure> an open source printer is worth doing
17:18 < kanzure> and bypassing fingerprinting would be nice
17:19 <@fenn> fingerprinting?
17:19 < kanzure> most inkjet printers have a specific id they make apparent on each printed page
17:19 < kanzure> something about the government
17:20 < kanzure> .title http://boingboing.net/2008/10/23/howto-read-the-secre.html
17:20 < yoleaux> HOWTO read the secret forensic dots in your laser-printer output
17:20 <@fenn> that's only laser printers i guess
17:20 < kanzure> "These dots were long-rumoured, but it wasn't until EFF discovered them that their existence was verified and their code was cracked."
17:20 < kanzure> huh the electronic frontier foundation had to do it? wtf?
17:22 < kanzure> other results from same search include:
17:22 < kanzure> .title http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/c0nr00593b#!divAbstract
17:22 < yoleaux> In situ growth of gold nanoparticles on latent fingerprints—from forensic applications to inkjet printed nanoparticle patterns
17:23 < kanzure> "Latent fingerprints are made visible in a single step by in situ growth of gold nanoparticles on ridge patterns. The chemicals, among the essential components of human sweat, found responsible for the formation and assembly of gold nanoparticles are screened and used as ink to write invisible patterns, using common ball pen and inkjet printer, which are then developed by selectively growing gold nanoparticles by soaking them in gold salt ...
17:23 < kanzure> ... solution."
17:30 < kanzure> .title http://pubs.rsc.org/en/content/articlehtml/2013/cc/c3cc42451k
17:30 < yoleaux> Solid phase click ligation for the synthesis of very long oligonucleotides
17:30 < kanzure> "owever, it remains challenging to achieve clean and efficient chemical ligation of oligonucleotides. An alternative strategy is to design a chemical linkage that mimics the natural phosphodiester and which can be formed efficiently and selectively. This has been achieved through a click chemistry approach4 in which the CuI-catalysed [3+2] azide–alkyne cycloaddition (CuAAC) reaction5,6 is used to synthesise DNA containing biocompatible ...
17:30 < kanzure> ... artificial linkages (Fig. 1a) ....  We now report a solid-phase strategy for ligating oligonucleotides using the CuAAC and SPAAC reactions. This approach has several desirable features; it is simple to carry out, the reaction can be forced to completion by adding an excess of the solution-phase reactant, there is no requirement for a template oligonucleotide, and excess reagents can be conveniently removed and recovered."
17:40 < kanzure> the review paper "DNA-associated click chemistry" says that people have tried this click chemistry technique in vivo. that seems like an unusual thing to do..
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17:41 < kanzure> also, you don't really need dna, you just need something that a polymerase enzyme will recognize correctly, or that a polymerase enzyme can be modified to recognize correctly
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17:54 < kanzure> this link redirects to a weird place: http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300032/full
17:54 < kanzure> it redirects over to http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300032/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+Saturday%2C+7+June+from+10%3A00-15%3A00+BST+%2805%3A00-10%3A00+EDT%29+for+essential+maintenance&userIsAuthenticated=false&deniedAccessCustomisedMessage=
17:55 < kanzure> i wonder if that's an xss vulnerability
17:55 < kanzure> either chrome is stripping my injected html or the server is smart enough to not use it as input
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18:13 < nmz787> kanzure: have you seen the HELP synthesis articles?
18:13 < nmz787> that overview mentioned it
18:15 < kanzure> no
18:15 < nmz787> I think its High Efficieny Liquid Phase
18:20 < kanzure> hm i forgot about this one,
18:20 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Optical%20tweezers%20directed%20one-bead%20one-sequence%20synthesis%20of%20oligonucleotides.pdf
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18:35 < kanzure> yashgaroth: have you visited azco biotech yet?
18:36 < yashgaroth> no, are they affiliated with aztechnology?
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18:49 < kanzure> yashgaroth: they do dna synthesizer equipment refurbishing
18:49 < kanzure> yashgaroth: in san diego
18:51 < yashgaroth> well, san diego county
18:51 < yashgaroth> they have a strange website
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19:10 < nmz787> they make new ones too
19:10 < nmz787> they make the one cambrian uses
19:19 < kanzure> cambrian genomics didn't build their own equipment?
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19:43 < nmz787> well, they put them all in a row and interfaced them with robot arms or something, their big thing is sorting them once they seqquence them
19:56 < kanzure> caruthers historical review of the context of oligonucleotide and dna synthesis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543024/?report=classic
20:01 < kanzure> uhh "I also found myself in the middle of this revolution both in research and as a cofounder of two biotechnology companies, Amgen and Applied Biosystems."
20:01 < kanzure> caruthers co-founded applied biosystems.. so i guess that explains why they have always been one of the few to bother to make dna synthesizers.
20:02 < kanzure> "At our first meeting in Thousand Oaks, Lee and I proposed that this new company, which was to be called Applied Molecular Genetics, should have an instrument division that would sell protein sequencers and DNA synthesizers based upon Lee's and my work, respectively. However, the other scientists were concerned that Applied Molecular Genetics would become primarily an instrumentation company rather than one focused on genetic engineering and ...
20:02 < kanzure> ... molecular biology. As a result, the proposal was dropped, but later that same morning, Lee and I, in discussion with the venture capitalists who were starting Applied Molecular Genetics, decided to move forward with the formation of a new instrument-focused company, which became known as Applied Biosystems."
20:03 < kanzure> "We located Applied Biosystems in Foster City, California, and hired Sam Eletr as our first chief executive officer (spring 1981). Sam proved to be an excellent entrepreneurial choice. We started with only three million dollars but were able to convince a large number of pharmaceutical and biotechnology companies and academic laboratories to advance large deposits (half of the proposed sale price) on future protein sequencers and DNA ...
20:03 < kanzure> ... synthesizers (that had yet to be designed, let alone manufactured) simply so they would be in the queue for the first machines. With this capital, Sam hired two or three scientists each from Lee's and my laboratories to design and build our first instruments. From my laboratory, Bill Efcavitch and Curt Becker were among the first employees (later, Lincoln McBride as well). Bill and Curt started with a series of valves, tubing, small ...
20:03 < kanzure> ... HPLC-grade silica columns, a tank of liquid nitrogen, and a large piece of plywood. Within a few months, they were synthesizing DNA on this platform. Sam asked John Bridger, an engineer hired from Hewlett-Packard, to design a DNA synthesizer, which became known as our 380A machine. By December 1982, Bill installed the first commercial synthesizer in my laboratory (Fig. 5), and Applied Biosystems began shipping the instruments in 1983."
20:04 < kanzure> "Meanwhile, Winston Salser and Bill Bowes recruited George Rathmann as the first chief executive officer of Applied Molecular Genetics, and they raised 18.9 million dollars, which, at that time, was the largest initial private placement ever put together to start a new venture capital-funded company"
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20:41 < kanzure> .title http://www.thingiverse.com/thing:159052
20:41 < yoleaux> Laboratory Pipette by lewisite
21:06 < kanzure> google scholar search results for "intitle:theoretical phosphoramidite": 48
21:06 < kanzure> not promising
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21:38 < aristarchus> i got my dna sequenced!
21:39 < jrayhawk_> post it!
21:40 < aristarchus> i will after i augment it
21:40 < aristarchus> lol
21:41 < ||0_-_0||> whelp, guys
21:41 < ||0_-_0||> today we lost a hero
21:41 < ||0_-_0||> Alexander Shulgin passed away today
21:43 < kanzure> roman lygin replied
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21:44 < heath> http://docs.python-guide.org/en/latest/scenarios/admin/
21:45 < heath> not sure the part about fabric really makes sense
21:47 < kanzure> you know, i've found that fabric is really quite weird
21:48 < kanzure> i don't usually think in the way that fabric expects me to be thinking
21:51 < kanzure> heath: i've been liking fig lately, http://orchardup.github.io/fig/
21:51 < kanzure> service discovery is still a pain though
21:52 < kanzure> and it makes livereload slightly more confusing
21:52 < gradstudentbot> Protip: the lab's attic hasn't been used since 1966. Pretty nice.
21:54 < kanzure> "Peter Glaser died on May 29, 2014. I knew him through SSI because he pioneered the concept of Solar Power Satellites, and was associated with Gerry O'Neill and Bill Brown on beamed power and space settlements. He also worked on Apollo and Space Station missions." http://en.wikipedia.org/wiki/Peter_Glaser
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22:14 < kanzure> .title https://pag.confex.com/pag/xxi/webprogram/Paper6977.html
22:14 < yoleaux> Abstract: true-Single Molecule Sequencing Illuminates the Sequencing of Ancient DNA Molecules (Plant and Animal Genome XXI Conference)
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22:15 < kanzure> "Pleistocene horse bones preserved in permafrost"
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22:19 < heath> hrm, wonder why the hitchhiker's guide doesn't mention httpie
22:20 < kanzure> because you should be using httpretty instead
22:21 < heath> i don't really mock stuff
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22:22  * heath needs to sleep
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22:30 < gene_hacker> sleep is for slackers
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23:15 < kanzure> https://archive.org/details/HackerNewsStoriesAndCommentsDump
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--- Log closed Tue Jun 03 00:00:23 2014