--- Log opened Fri Nov 10 00:00:11 2017
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03:16 < kanzure> .wik dpo4
03:16 < yoleaux> "DNA polymerase IV is a prokaryotic polymerase that is involved in mutagenesis. It exhibits no 3'-5' exonuclease (proofreading) activity and hence is error prone. In E. coli, DNA polymerase IV (Pol 4) is involved in non-targeted mutagenesis." — https://en.wikipedia.org/wiki/DNA_polymerase_IV
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04:33 <@fenn> this text-based skyrim sucks because you only have 2 input choices
04:33 <@fenn> in a mud you have hundreds of commands available at any time
04:36 < Urchin> parody?
04:36 <@fenn> no it's a serious attempt
04:36 <@fenn> https://medium.com/@filiph/skyrim-rendered-in-text-1899548ab2c4
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05:43 < kanzure> yeah i was always confused about how mud internal game grammar works. because specifying 100 commands effects across 10,000 objects seems like a lotta work and if you don't do it manually then the whole thing is overly repetitive and bland..
05:44 <@fenn> repetitive and bland is not a problem
05:44 < kanzure> why not?
05:44 <@fenn> well for one there's hundreds of commands, so it's your own fault for doing "troutslap" hundreds of times in a row
05:45 <@fenn> but more importantly your brain parses the repeated text rapidly and you carry on without thinking about it
05:45 <@fenn> lots of things can be happening all at once and you can still understand it at a glance
05:46 <@fenn> it helps if each thing appears on its own line, for visual discrimination
05:46 <@fenn> dwarf fortress gets this all wrong and just concatenates everything into a monster blob paragraph
05:47 <@fenn> anyway many muds have lots of custom programming so it's hard to say anything in general about how they work
05:47 <@fenn> usually there are at least a few classes of things like rooms, objects, and mobs (monsters/players)
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05:48 <@fenn> you can't apply navigation commands to a mob for instance
05:50 <@fenn> instead you would have to tell it to move
05:51 < Urchin> say MUD - IRC transitions were always hell for me
05:51 < Urchin> ;)
05:51 <@fenn> alias ' say
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05:56 < kanzure> hm yeah i guess i do remember using the same command 100s of times in a row
05:56 < kanzure> "why does this rock look just like all the other rocks? what's going on?"
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06:01 < kanzure> and everythig was dead because no users because i was a few decades late to the party
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06:18 < kanzure> "Scalable funding of bitcoin micropayment channel networks" https://www.tik.ee.ethz.ch/file/a20a865ce40d40c8f942cf206a7cba96/Scalable_Funding_Of_Blockchain_Micropayment_Networks%20(1).pdf
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06:36 < kanzure> "CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations" http://www.pnas.org/content/114/28/7260
06:36 < kanzure> ".. the molecular mechanism underlying CRISPR-Cas9 function is still incompletely understood. Here, enhanced molecular dynamics (MD) simulations, probing displacements over long timescales, capture at atomic level specific features that are difficult to reach via conventional MD simulations and via the currently available experimental techniques, clarifying the molecular mechanism of ...
06:36 < kanzure> ...CRISPR-Cas9, with understanding of its activation process."
06:37 < kanzure> https://giuliapalermo.wordpress.com/publications/
06:40 < adlai> kanzure: sometime shortly after leaving the hospital, i met a doctor who was allergic to blood. after we talked for thrice the amount of time he billed me, his only diagnosis was "stay away from the math, you're allergic"
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06:49 < kanzure> adlai: he gave you a diagnosis after you left?
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08:06 < mindsForge> "Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy" https://www.nature.com/articles/s41467-017-01466-8
08:06 < mindsForge> .tw https://twitter.com/hnisimasu/status/928933260159197184
08:06 < yoleaux> Single-molecule movie of DNA search and cleavage by CRISPR-Cas9. https://video.twimg.com/tweet_video/DOQ71RsVAAAM3F0.mp4 (@hnisimasu)
08:08 < kanzure> hm.
08:10 < kanzure> interesting that AFM doesn't interrupt its operation too muh
08:10 < kanzure> uch.
08:14 < kanzure> must be "cas9 characterization day".
08:15 < mindsForge> :)
08:15 < mindsForge> when I opened the channel I saw you posted a CAS9 paper and thought it might be the same one haha
08:16 < mindsForge> that is pretty amazing the AFM didn't mess things up, or maybe they tried to get a good image a thousand times before something usable showed
08:17 < mindsForge> I'm looking into AFM, I don't know much about it, seems like it would be like a relatively huge jackhammer on the CAS9 system :|
08:17 < mindsForge> "The laboratory-built high-speed AFM was used in the tapping mode"
08:19 < adlai> kanzure: it's a long story, maybe we can commiserate over the sad state of the venntersection of medicine and lawlitics at the next rooftop party
08:20 < kanzure> yea sure
08:25 < adlai> btw kanzure i was wondering (aloud!) just yesterday, whether it wouldn't be more easier on your carpal tunnelling to live-correct STT rather than typing it all yourself
08:26 < adlai> but i guess they can rebore those tunnels in the happy posthuman future?
08:28 < kanzure> stt?
08:28 < adlai> speech-to-text
08:29 < kanzure> speech recognition is not fast enough for livestream editing.. easier to just type it myself.
08:29 < kanzure> i did, however, write my own speech recognition engine (at maaku's suggestion)
08:29 < adlai> that reeks of a von-neumann bottleneck. neurons do it in realtime just fine.
08:30 < kanzure> neurons only think they do it fine in real-time, but when you ask them for the last 1000 words they just give you abridged bullshit
08:30 < adlai> by "neurons", i meant "kanzure's brain in a vat, with a telepresence robot at the conference, and a keyboard connected to the spinal column"
08:31 < adlai> unless you think the fourier transform happens in the cochlea, which would make for an interesting hypothesis
08:32 < kanzure> i'm not sure how i would design a bone to do that transformation, but it should in principle be possible
08:32 < adlai> re: diagnosis, just so you get a straight answer to an honest question: i have no idea what diagnosis they gave or didn't, and whether it had a "best before" date. the medical establishment is that fucked up.
08:34 < kanzure> my dreams are usually very boring, but last night i was able to summon a door and walk through it out into a vibrant city. very cool experience.
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10:39 < kanzure> .wik sanger sequencing
10:39 < yoleaux> "Sanger sequencing is a method of DNA sequencing first commercialized by Applied Biosystems, based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. Developed by Frederick Sanger and colleagues in 1977, it was the most widely used sequencing method for approximately 40 years." — https://en.wikipedia.org/wiki/Sanger_sequencing
10:48 < nmz787> I guess skyrim is a game... my question is how it relates to hplus
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11:24 < kanzure> podcast editing tool based on deleting words from a transcript to delete segments of audio https://news.ycombinator.com/item?id=15670827
11:24 < kanzure> cc maaku
11:24 < kanzure> nmz787: text is a superior gaming technology
11:33 < kanzure> dunno
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13:22 < kanzure> blott
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15:32 < nmz787> hmm, so I may be on the verge of upsetting the seller of the ALD machine on ebay... too much lowballing I guess
15:32 < nmz787> I guess that's what they get for ebay's "make an offer" not having a lower limit
15:34 < nmz787> .wik calea zachateci
15:34 < yoleaux> nmz787: Sorry, I couldn't find article.
15:34 < nmz787> .wik calea zacatechichi
15:34 < yoleaux> "Calea ternifolia (syn. Calea zacatechichi) is a species of flowering plant in the aster family, Asteraceae. It is native to Mexico and Central America. Its English language common names include bitter-grass, Mexican calea, and dream herb." — https://en.wikipedia.org/wiki/Calea_zacatechichi
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15:42 < kanzure> ALD == ?
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16:00 <@fenn> atomic layer deposition
16:01 < kanzure> .tw https://twitter.com/Reza_Zadeh/status/928516020582547457
16:01 < yoleaux> Reconstructing Visual Experiences from Brain Activity Evoked by Natural Movies. Rudimentary "Mind-reading". Very early, but breathtaking and presents so much potential. A great line of research steadily improving over decades. Paper: http://www.cell.com/current-biology/fulltext/S0960-9822(11)00937-7 https://video.twimg.com/tweet_video/DOLABiCVQAEe6WN.mp4 (@Reza_Zadeh)
16:02 <@fenn> this video is several years old
16:02 <@fenn> gazzaley lab fMRI machine learning hodgepodge
16:03 < kanzure> sure.
16:03 < kanzure> no argument from this biological unit
16:04 <@fenn> er, not gazzaley, gallant
16:06 <@fenn> they actually had relatively high resolution imaging of the visual cortex, higher than normal fMRI
16:07 <@fenn> millimeter level resolution of blood oxygenation
16:08 <@fenn> in this paper they reconstructed what you're actually seeing, but wasn't there a more recent one where you imagined a pre-selected movie or image really hard and they guessed which one it was
16:11 < kanzure> yes there was also fMRI + humanoids reading sentences and guessing about imagery in the sentence or something
16:12 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/imagery/Brain%20areas%20underlying%20visual%20mental%20imagery%20and%20visual%20perception:%20an%20fMRI%20study%20-%202004.pdf
16:12 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/imagery/A%20penny%20for%20your%20thoughts%20-%20Patterns%20of%20fMRI%20activity%20reveal%20the%20content%20and%20the%20spatial%20topography%20of%20visual%20mental%20images%20-%202014.pdf
16:12 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/imagery/A%20voxel-wise%20encoding%20model%20for%20early%20visual%20areas%20decodes%20mental%20images%20of%20remembered%20scenes%20-%202015.pdf
16:17 < kanzure> I AM LINK MONSTER GIVE ME LINKS
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16:27 <@fenn> might have been this voxel-wise paper, in any case it's pretty neato
16:28 <@fenn> wish they would work on some kind of fMRI paint program
16:28 <@fenn> that's what everyone wants to do right
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17:30 < nmz787> kanzure: yep, Atomic Layer Deposition... I was hoping to get it at a price like the FIB was won for... but this seller is saying their "final offer" if $5k
17:30 < nmz787> of*
17:31 < nmz787> I actually meant is*
17:31 < nmz787> is $5k
17:32 < kanzure> "sorry, i only have a budget of $117 for my nanotech fab equipment"
17:32 < nmz787> yeah, pretty much
17:33 < nmz787> "This offer represents a $4,000 reduction from our asking price, your offer is $325 above your original offer. This is not a "dime a dozen" type of item, it's acquisition required significant time and investment, This is my final and lowest offer."
17:33 < kanzure> tell them "Sorry, I don't buy from people who negotiate with a negative attitude" (no just kidding)
17:37 < nmz787> what I don't get is... it seems like the seller is a dime-a-dozen "cyber recycler"
17:37 < nmz787> and why would they go searching for hard-to-sell niche equipment... I thought people with junk come to these folks to clear out their factory/shop/biz
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18:59 < kanzure> jupiter things https://pbs.twimg.com/media/DOODnUxVwAA_lJm.jpg:large
19:22 < kanzure> "As a side note, if anyone's interested in looking a bit more into "programming as magic" there's a great book series called The Wizardry series about programmers being transported into a fantasy realm where magic works similarly to a programming language. The main character ends up writing a compiler based off (IIRC) APL and revolutionizes magic. The first book is called Wizard's Bane and ...
19:22 < kanzure> ...it's light and fun reading."
19:22 < kanzure> http://www.crunchyroll.com/knights-magic
19:24 < kanzure> https://parahumans.wordpress.com/
19:30 < kanzure> from https://news.ycombinator.com/item?id=15670507
19:31 < kanzure> "humanity fuck yeah" https://www.reddit.com/r/HFY/comments/61ya08/oh_this_has_not_gone_well/
19:32 < kanzure> https://www.reddit.com/r/HFY/comments/3jfu5t/oc_assimilation/
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19:35 < kanzure> "It makes me wonder if there are any realms of wizardry where the highest ranking wizards spend all their time on management skills and never get to practice their magic. -freenode bbrittain "Oh, these days I just review a lot of spell-design scrolls and mentor junior acolytes. Magic is more of a people business, you know." The senior staff at Unseen University in Pratchett's Discworld series ...
19:35 < kanzure> ...are a lot like this."
19:36 < kanzure> er... irssi error in there randomly, but okay.
19:39 < kanzure> "You know, us programmers like to refer to ourselves as wizards but I really wonder if non-programmers think the same or is it just like any other profession they're not knowledgeable of? I don't know anything about chemical engineering but I've never considered chemical engineers to be magical."
19:39 < kanzure> "If you knew a wizard you'd probably constantly wish you could do what he could do. I think the only time people wish they could do what I do is when they're trying to get their printer to work."
19:54 < kanzure> dark field microscopy stuff https://www.youtube.com/watch?v=qa3JKuR9fgQ&t=24m20s
19:56 < kanzure> no wait, this one instead https://www.youtube.com/watch?v=ph7v3-BiXLc
19:58 < kanzure> "High-resolution non-destructive three dimensional imaging of integrated circuits" https://www.nature.com/articles/nature21698
19:59 < kanzure> "Here we demonstrate that X-ray ptychography[3,4] —a high-resolution coherent diffractive imaging technique—can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each ...
19:59 < kanzure> ...other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques[5,6,7]. Foreseeable developments in X-ray sources[8], optics[9] and detectors[10], as well as adoption of an instrument geometry[11] optimized for planar rather than cylindrical samples, could lead to a ...
20:00 < kanzure> ...thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes."
20:08 < ebowden_> Oh yessss.
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20:42 < kanzure> .tw https://twitter.com/Jamie_Woodward_/status/927248367591329793
20:42 < yoleaux> The mammoth bone huts at Mezhirich near Kiev are ~15,000 years old. The base of each dwelling is a circle of interlocking mammoth jaw bones. https://pbs.twimg.com/media/DN4_eEPWsAAQg-g.jpg (@Jamie_Woodward_)
20:42 < kanzure> so... there's a good reason to resurrect the wooly mammoths: building materials.
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21:11 < kanzure> gradstudentbot: welcome back
21:11 < gradstudentbot> IOError: [Errno 2] No such file or directory: 'modules2/quotes.txt' (file "/home/bryan/code/gradstudentbot/modules2/quotes.py", line 8, in pick_quote)
21:11 < kanzure> oh hell
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21:12 < kanzure> gradstudentbot: welcome back
21:12 < gradstudentbot> I am sponsored by the Beijing Genomics Institute.
21:12 < kanzure> gradstudentbot: get any writing done?
21:12 < gradstudentbot> Do you have references for that?
21:13 < kanzure> gradstudentbot: the paper?
21:13 < gradstudentbot> Are you ever going to publish that?
21:13 < kanzure> righto
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22:24 < nmz787> gradstudentbot: have you completed your sections for the draft doc yet?
22:24 < gradstudentbot> The thing about this particular theory is that it's excellent at predicting ethnic conflicts which have already happened.
22:24 < nmz787> gradstudentbot: yeah but, uh, how is that relevant?
22:24 < gradstudentbot> His lab is so awkward.
22:24 < nmz787> gradstudentbot: come on, be a litte more optimistic
22:24 < gradstudentbot> Does this look contaminated to you?
22:25 < nmz787> gradstudentbot: link?
22:25 < gradstudentbot> Can I get Saturday off?
22:25 < nmz787> gradstudentbot: we haven't even got past the training stage yet, and you want off already?
22:25 < gradstudentbot> Ugh, my clinical trial isn't going so well.
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22:45 < nmz787> hmm, the pxct thing seems neat, but it requires upfront knowledge of all the compositional materials
22:45 < nmz787> """For recording all 2D projections required for complete 3D tomography, samples need to be accessible to X-rays over a full rotation of the sample. Therefore we used a focused gallium (Ga) ion beam (FIB) to cut a small sample from the extended device (Extended Data Fig. 1a–d). Figure 1 summarizes the experiment, and includes (Fig. 1c) one of the 235,200 coherent diffraction patterns underpinning
22:45 < nmz787> the PXCT images from the ASIC"""  and """Since PXCT is derived from absolutely calibrated density fluctuations, various materials can be identified (Extended Data Fig. 2c–e) by matching PXCT densities to known bulk densities21. This requires prior knowledge about candidate materials implemented in the device, because individual peaks in the histograms can be caused by different material
22:45 < nmz787> combinations mixed within a volume element (‘voxel’)."""
22:50 < nmz787> seems like it could be very useful for fabs to validate what they're producing, I guess
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--- Log closed Sat Nov 11 00:00:12 2017