--- Log opened Mon Apr 08 00:00:00 2013
--- Day changed Mon Apr 08 2013
00:00 < nmz787> there was a paper about doing it, said optimal distance was 2mm
00:00 < nmz787> so the laser head would need separated from the spindle motor mount, but that should be about it
00:00 < nmz787> i'd like be use the existing motor, and just add power control to the laser (which is what the paper did)
00:07 < nmz787> http://anusf.anu.edu.au/Vizlab/drishti/index.shtml
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00:18 < nmz787> "Drishti is a real-time interactive volume rendering and animation tool"
00:48 < eleitl> which materials can you process with a bluray laser?
00:49 < eleitl> kanzure, you in austin?
00:51 < eleitl> google fiber is coming to town, if yes
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02:01 < nmz787> eleitl: i believe the paper used SU-8 with a photoinitiator added since it's normally processed with deeper UV
02:01 < nmz787> but you could probably ablate PDMS realitically
02:01 < nmz787> or acrylic
02:02 < nmz787> but i specifically want to use it to raster photoresist of some kind
02:02 < nmz787> eleitl: know of a way to move hazardous chems from britain to U.S. ?
02:04 < nmz787> "The embargo is by the UK postal service who are refusing to carry small quantity liquids destined for the US. I will see if we can provide a price to supply 1kg of the resin via alternative transport means."
02:05 < eleitl> what kind of chemicals? organic peroxides?
02:05 < eleitl> so you're using a violet laser to polymerize monomer in the bulk?
02:05 < nmz787> "I have got an approx pack and despatch quote for 100kg of resin which is circa 375.00 sterling - this is excluding all destination costs, import taxes, duties and customs clearance - at least this gives you a rough guide to work on.  The Resin is 213.75 sterling per 25kg container - so obviously the carriage cost is based on 4 of these, so total cost for the resin would be 855.00 sterling."
02:06 < nmz787> photoresin
02:06 < eleitl> try alibaba?
02:06 < nmz787> hmm
02:06 < eleitl> how much power does the violet laser have? 500 mW, more?
02:07 < nmz787> if 4 kg of that == a gallon
02:07 < nmz787> then that's $50 USD / gallon not including shipping
02:07 < nmz787> yeah something like that
02:07 < eleitl> sounds cheap. what are you going do build with it?
02:07 < nmz787> depends how long you want the diode to last
02:07 < eleitl> what's the nominal output?
02:07 < nmz787> in the drive sled it's not sufficient cooling to really blast it
02:08 < eleitl> you can watercool it
02:08 < nmz787> urmm
02:08 < nmz787> /in/ the drive sled?
02:08 < nmz787> mmmaaaaybe oil immersion
02:08 < eleitl> no, outside
02:08 < eleitl> you're building a rapid protyper with bluray diode, right?
02:08 < eleitl> or are you using the whole linear motor assembly?
02:09 < nmz787> yeah, but i'd like to simply move the spindle a bit further away and still use polar coords
02:09 < eleitl> ah, ok
02:09 < nmz787> since the lens is usually <500 microns away from the b;uray disc exterior
02:10 < nmz787> but this paper said for photoresin with su-8 they found best to be 2mm
02:10 < nmz787> http://www.lg.com/ae/products/documents/What%20is%20Blu-ray.doc
02:11 < nmz787> some interesting specs in there about the distances
02:12 < eleitl> I wish they would make metal powder sintering finally
02:13 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S0143816611003617
02:13 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/High%20resolution%2C%20low%20cost%20laser%20lithography%20using%20a%20Blu-ray%20optical%20head%20assembly.pdf
02:14 < eleitl> that's a nice paper
02:15 < eleitl> what are you going to use it for?
02:15 < eleitl> not Si photolitho like in the paper?
02:20 < nmz787> they werent using them for photolith masks afterward
02:21 < nmz787> they were just making gratings in the resist
02:21 < eleitl> yeah, I read that
02:22 < nmz787> i'd be doing the same process, but then laying PDMS on top and curing that, to then peel away
02:22 < nmz787> possibly with a fuming of anti-stick layer first
02:23 < nmz787> this is the company that might have decent 3D modelling photoresin http://www.suscomp.com/Applications.htm
02:23 < nmz787> 3D modelling/microlith :D
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05:31 < wrldpc> Ahoy.
05:31 < wrldpc> What's a good site for books, I need Computable Universe by Zenil.
05:31 < archels> libgen.info
05:31 < archels> ebookee.org
05:35 < wrldpc> gracias
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05:52 < eleitl> libgen doesn't have it
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06:48 < wrldpc> neither does ebookee.
06:48 < wrldpc> brb
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08:55 < kanzure> excellent, nytimes wrote up a thing about the scholarlyoa.com guy http://www.nytimes.com/2013/04/08/health/for-scientists-an-exploding-world-of-pseudo-academia.html
08:56 < kanzure> "Steven Goodman, a dean and professor of medicine at Stanford and the editor of the journal Clinical Trials, which has its own imitators, called this phenomenon “the dark side of open access,” the movement to make scholarly publications freely available."
08:56 < kanzure> hmm i don't think it's fair to attribute this scammy shitness to open access.
09:01 < kanzure> ... what? "This has been normal practice for a good decade or more. There are no more "invited" speakers at conferences. You usually get asked to pay a "sponsorship" and your rank in the the conference goes up the more you pay. $20,000 - $50,000 is not uncommon"
09:11 < kanzure> "It should be noted that some of these conferences, at least in the humanities, are actually organized by tourism offices."
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09:52 < yeastwest> In answer to an earlier question, I still get serious memory leaks in Firefox 15.0.1, which lead to its being recycled about once a week. Viewing Flash videos seems to accelerate the leakage.
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10:20 < EnLilaSko> Uhm, isn't 15.0.1 quite old?
10:25 < yeastwest> I don't know, probably less than a year. Is there some reason to think the memory leaks were fixed more recently?
10:26 < kanzure> i think when they said "we are fixing memory leaks" they provided a good reason to think that they were fixing memory leaks. wtf?
10:26 < kanzure> however, i still posit that they are fixing the wrong/uninteresting leaks.
10:27 < kanzure> flashplugin-nonfree leaks are not mozilla-related so i wouldn't really hold those against them
10:28 < yeastwest> I don't really have any way of distinguishing what's eating the memory in the Firefox address space, I just recycle Firefox when things get slow.
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11:24 < kanzure> google scholar is weird
11:24 < kanzure> http://scholar.google.com/scholar?cluster=14291426330781296140&hl=en&as_sdt=0,44
11:24 < kanzure> gnusha.org and diyhpl.us are served from the same host
11:24 < kanzure> but both virtual hosts are listed as different sources for the same file from /home/nmz787/public_html/
11:25 < kanzure> google is usually really good at detecting situations where different domains are serving the same content (especially when the ip address is the same)
11:26 < kanzure> this is for "Magnetic nanoparticles as gene delivery agents: enhanced transfection in the presence of oscillating magnet arrays"
11:29 < chris_99> i thought it normally counts domains as being separate regardless of IP
11:29 < kanzure> if that was true then link farms would be far more dangerous
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11:41 < kanzure> here are the papers that i've been asked to remove:
11:41 < kanzure> http://diyhpl.us/~bryan/papers2/iop/
11:41 < kanzure> superkuh: let me know when.
11:42 < ParahSai1in> rename them to hash random crap
11:42 < ParahSai1in> simple solution
11:42 < chris_99> who asked you to remove them
11:45 < kanzure> the science police.
11:47 < kanzure> i've also included http://diyhpl.us/~bryan/papers2/iop/movelog.txt
11:47 < kanzure> i'll be removing these in the next few days so let me know
11:48 < archels> kanzure: I would suggest to chmod ga-r. This way they would remain indexed, so if anyone wants them they can just ask you for it
11:49 < superkuh> http://superkuh.com/library/MiscText/backup/ and as soon as rsync is done, http://erewhon.superkuh.com/library/MiscText/backup/
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11:54 < archels> is the audience listening?
11:54 < kanzure> probably not, why?
11:55 < kanzure> 49.212.213.159 is the offender this time but it looks like this is just a random proxy
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11:59 < kanzure> there have also been some strangely specific queries from google.co.uk (near their offices)
11:59 < kanzure> like for q=pf_oiunderbarinit+copyright&ei=qgRjUeGDLM6_PK7dgdgI&usg=AFQjCNGx4XNXd4VmA4DNDOcTguJSmNBCoQ
11:59 < kanzure> "pf_oiunderbarinit copyright" refers to a javascript file..
11:59 < kanzure> but the results are only paperbot things
11:59 < kanzure> http://oi-underbar.ifactory.com/underbar/js/pf_oiunderbarinit.js
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12:42 < archels> paperbot: http://www.nature.com/nrn/journal/v7/n4/pdf/nrn1885.pdf
12:42 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/5e80e242c2ff32625d203fcbbe647dcb.txt
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14:31 < kanzure> "His effort to patent the whole human genome wasn't termed the "Human Genome Project": That label generally applies to the efforts of the Human Genome Consortium that spared at least a large fraction of our genetic heritage from Venter's grasp."
14:31 < kanzure> "Although, it's highly debatable whether Venter could even have sequenced the genome successfully using the methods Celera were attempting to push at the time; his successes with Bacterial chromosomes didn't translate well over to redundant, repeat-rich, massive human genomes."
14:31 < kanzure> "Suffice to say, if you're willing to leverage potential ownership over something critical to scientific advancement in human biology and medicine, you can get plenty of business-before-ethics people on board to pay for your big projects. And, likewise for the concept of "minimal cells", which will no doubt be very broadly patented by Venter & co, too as soon as they succeed in making a reference implementation. Given the amount of big oil ...
14:31 < kanzure> ... money being lavished on their work, I don't doubt they'll beat the better intentioned labs around the world to that goal, as there's no "minimal cell consortium" to save the day this time."
14:31 < ParahSailin> where?
14:37 < kanzure> an email from cathal about craig venter
14:41 < ParahSailin> makes sense
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14:42 < brownies> "minimal cells"?
14:42 < klafka> minimal viable cell that would be living
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14:43 < kanzure> smallest genome, etc.
14:43 < klafka> http://en.wikipedia.org/wiki/Mycoplasma_laboratorium
14:43 < ParahSailin> minimal cell was the one where venter synthesized and assembled mycobacterium genome from scratch
14:43 < kanzure> not quite
14:43 < klafka> http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/home/
14:43 < kanzure> minimal cell was the idea of an even smaller genome
14:45 < ParahSailin> kanzure: ah, i'd forgotten that they were going to go even smaller
14:46 < brownies> can't you just find those hanging out in nature?
14:46 < kanzure> no, most cells have a huge genome
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14:49 < kanzure> i wonder if you could make a selective pressure for smaller genomes by making some of the dna replication mechanisms dissociate more regularly
14:49 < kanzure> i guess that will just incentivize smaller fragments more frequently
14:52 < brownies> dissociate?
14:53 < brownies> perhaps one could engineer a metabolic pathway used in DNA replication to require additional energy, so that the cost function pushes the organism towards doing less of it
14:54 < kanzure> no you want dna replication to be abundant because otherwise you don't get much for your selection process to work off of
14:54 < kanzure> also that just incentivizes mutations towards making dna replication less costly
14:54 < brownies> hm, fair point.
14:55 < ParahSailin> dna replication is already a pretty high metabolic load
14:56 < ParahSailin> enough that with a high copy number plasmid, the difference between the blank plasmid and the one with an insert will make a visible different in colony size
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14:57 < kanzure> also it's difficult to predict the right environment for a minimum genome
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14:57 < kanzure> for instance, membrane maintenance proteins aren't /entirely/ necessary
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15:02 < brownies> probably a dumb question, but isn't a virus technically a minimum genome already?
15:02 < brownies> it wanders around, it replicates, and... that's it.
15:04 < kanzure> by definition they need to infect cells to replicate
15:05 < kanzure> "The smallest viral genomes – the ssDNA circoviruses, family Circoviridae – code for only two proteins and have a genome size of only 2 kilobases."
15:05 < kanzure> http://en.wikipedia.org/wiki/Circoviridae
15:05 < kanzure> "The genome is monopartite, circular, single-stranded DNA of between 1.8 to 3.8 kilobases. There are two main open reading frames arranged in opposite directions that encode the replication (Rep) and capsid (Cap) proteins. Alternative start codons are common in the avian species."
15:07 < brownies> i see. so the quest is for a minimal bacterial genome
15:08 < kanzure> doesn't have to be bacteria but yes.
15:08 < brownies> non-viral
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16:28 < abetusk> Does anyone else think the Mu Thermal Camera is a scam?
16:28 < kanzure> wrong wavelengths?
16:29 < abetusk> hows that?
16:40 <@fenn> doesn't seem like a scam to me; i've always wondered why thermal cameras were so expensive
16:40 < ParahSail1n> because you cant use a cct
16:40 < ParahSail1n> the microbolometer chips are super expensive because they are actual mems i think
16:41 < ParahSail1n> maybe even involving microfabricated cantilevers or something crazy like that
16:41 <@fenn> so what; DLP chips are the same and they don't cost $2k each
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16:42 < ParahSail1n> yeah http://en.wikipedia.org/wiki/File:Cross-sectional_microbolomter.jpg
16:42 < ParahSail1n> well then the question of economies of scale pops up
16:44 < ParahSail1n> i think a microbolometer is significantly more difficult to fabricate than mems gyroscopes, pressure sensors, and dlps
16:49 <@fenn> from the wikipedia page it seems most of the manufacturers are military contractors
16:49 <@fenn> that would explain the inflated price
16:52 <@fenn> wow these military imagers have stirling cryocoolers built in
16:53 < ParahSail1n> there might be a lot of patents on them too
16:56 < ParahSail1n> the business model of finance your research completely off darpa grants, then get patent monopolies to everything is guaranteed win
16:57 < superkuh> Tangential: http://www.beilstein-journals.org/bjnano/single/articleFullText.htm?publicId=2190-4286-2-22
16:58 < superkuh> "Infrared receptors in pyrophilous (“fire loving”) insects as model for new un-cooled infrared sensors"
16:58 < ParahSail1n> paperbot, http://www.beilstein-journals.org/bjnano/single/articleFullText.htm?publicId=2190-4286-2-22
16:58 < superkuh> It's free full text.
16:58 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Infrared%20receptors%20in%20pyrophilous%20%28fire%20loving%29%20insects%20as%20model%20for%20new%20un-cooled%20infrared%20sensors.pdf
16:58 < ParahSail1n> are the infrared receptors in this case just temperature receptors?
16:58 < ParahSail1n> or photon excitation
16:58 < superkuh> They are bolometers.
16:59 < ParahSail1n> ah, well we knew snakes could do that too
16:59 < superkuh> Golay cells.
16:59 < ParahSail1n> the lensing is always a challenge too
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18:37 < nmz787> individual cells would be like microlenses though, right?
18:38 < nmz787> like, throw the temp sensitive ion channel in a synthetic vesicle that has some ion sensitive receptor or enzyme that makes a pigment
18:38 < nmz787> or breaks down xgal
18:39 < nmz787> paperbot: http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2012.128.html
18:39 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Printing%20colour%20at%20the%20optical%20diffraction%20limit.pdf
18:39 < ParahSail1n> its tough to make enzymes sensitive to the tiny deltaT that it would require
18:40 < nmz787> umm
18:40 < nmz787> i think i saw something not too long ago about self-adjusting enzymes
18:40 < ParahSail1n> and ion channels require a whole bunch of other machinery that would be difficult to interface
18:41 < ParahSail1n> nmz787, sure, i researched the same papers a while ago too
18:41 < nmz787> like how our neurons stop feeling our socks after we put them on
18:41 < nmz787> or something
18:42 < nmz787> ParahSail1n: seems like the main limitation is temp_sensitive_pixel = new vesicle()
18:42 < nmz787> i haven't seen anything on synthetic vesicles
18:42 < nmz787> like, where they were doing microchemistry
18:42 < nmz787> though i haven't looked in probably a few years
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19:02 < Juul> nmz787, cool paper
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20:44 < nmz787> http://3dprintingindustry.com/2013/04/08/bioprinting-3d-printing-liquids-that-stay-liquid/
20:44 < nmz787> the video if prety friggin sweet
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21:54 < kanzure> elsevier has bought mendeley
21:54 < kanzure> https://news.ycombinator.com/item?id=5515526
21:54 < kanzure> http://techcrunch.com/2013/04/08/confirmed-elsevier-has-bought-mendeley-for-69m-100m-to-expand-open-social-education-data-efforts/
21:59 < kanzure> welp there goes that..
22:00 < kanzure> it's amazing that people used mendeley. getting data out of mendeley is really painful. you have to physically use their website to download pdfs.
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22:30 < brownies> whoa, that is something.
22:30 < brownies> 70 million dollars? goddamn.
22:31 < brownies> "Mendeley — which was founded in 2008 and has raised just under $12 million in funding"
22:31 < kanzure> yeah the exit seems a little low to me
22:31 < brownies> doesn't seem like a high price when put in perspective.
22:31 < kanzure> mendeley was reporting some really stellar growth figures just last year
22:31 < kanzure> they were pivoting into "alternative metrics" and selling dashboards to grant agencies and university offices
22:32 < kanzure> for monitoring the impact of their science workers and what their school is reading on average etc.
22:32 < nmz787> hmm
22:33 < nmz787> good thing i never used it much
22:33 < brownies> i thought they'd always been about laternative metrics
22:33 < nmz787> never trusted it, guess my gut did me well
22:33 < kanzure> their original product was just pdf organization
22:33 < brownies> ah i see
22:33 < kanzure> "download our proprietary software, which uploads your pdfs to our servers so we can run our fancypants proprietary OCR to figure out what metadata applies to the document"
22:34 < kanzure> and now they have this massive pdf collection that i can't get access to
22:34 < brownies> could you get access to it before?
22:34 < kanzure> huh? no. it's a company. why would they just give away their 70 million pdfs?
22:35 < nully> kanzure: Ugg that sounds horrible.
22:35 < kanzure> .. are you katsmeow?
22:35 < nully> Negitory.
22:35 < kanzure> juri?
22:36 < nully> Nope, but i know Juri
22:36 < kanzure> fascinating
22:37 < nully> Heh, you're not the first person to ask me about juri on this conner of freenode =P
22:38 < nully> Dont worry, i'm a hopeless freesoftware nut, just like juri_ =P
22:38 < kanzure> "Do you really not understand how fundamentally anti-open-access Elsevier is? Have you not seen what happens to the other companies they absorb? Many of us have experience in this particular field and it's not a pleasant one. Your official blog post is inane marketing-speak that has no basis in the reality of the damage Elsevier has done and continues to do to the fabric of science publishing. Mendeley should be ashamed, and you personally ...
22:38 < kanzure> ... should be ashamed for perpetuating this nonsense. Within a year your company will be effectively dismantled and anyone left over who actually cares about open access can start over from scratch. I wish them luck."
22:38 < kanzure> "I have a feeling people aren't going to wait a year to start on an open replacement given the cartoonishly awful reputation Elsevier has."
22:38 < kanzure> "Cartoonish is right. Not only are they horribly exploitative towards the academics and librarians who by and large both write and purchase what Elsevier publishes, they also ... sponsor arms fairs! whee!"
22:38 < brownies> it's $100M
22:39 < kanzure> still not 10x
22:39 < brownies> let the peanut gallery navel-gaze about the supposed morality
22:39 < kanzure> well, it's because mendeley has often claimed they are about "open access"
22:39 < brownies> are they? what do they have to do with access of any sort, though?
22:40 < kanzure> their marketing says so! that's all, really.
22:40 < brownies> thought so.
22:41 < kanzure> mom is moving, so she is trying to get rid of junk by giving it to me, including this box of old school stuff
22:41 < kanzure> back from when i was going to waldorf
22:41 < kanzure> the teachers apparently wrote these elaborate reports about their experiments on me
22:42 < kanzure> http://diyhpl.us/~bryan/waldorf/stuff.txt
22:44 < kanzure> be amused!
22:46 < brownies> wild.
22:46 < brownies> all they did in public school was give us crackers to munch on and worksheets to muddle through.
22:48 < nully> In public schools you're lucky if they remeber to give you a report v.v
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23:12 < kanzure> it wasn't a public school
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23:18 < nully> Sadly that is obvious, too much attention to detail.
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