--- Log opened Sat Oct 17 00:00:09 2015
--- Day changed Sat Oct 17 2015
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00:24 < fenn> delinquentme: it almost sounds like you're trolling when you say things like "i'm writing this verbatim into the patent"
00:25 < fenn> anyway, patents are worse than trade secrets because they limit other people
00:25 < fenn> i agree that enzymes are mechanosynthesis
00:25 < fenn> i don't think it's worth anything to try to do DNA mechanosynthesis with an AFM tip
00:25 < fenn> have fun with your patent
00:27 < fenn> try not to rub people's noses in it
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00:50 < delinquentme> nah i was kinda jking just because it would be fun
00:50 < delinquentme> but im with what nmz said
00:52 < delinquentme> fenn, ^
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02:00 < gene_hacker> it's a bit of a stretch to call enzymes mechanosynthesis
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04:31 < JayDugger> No, he must be over in Mountain View. I've have heard if he'd moved to London.
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05:03 < kanzure> picard maneuver https://www.youtube.com/watch?v=x2o77i74T48
05:04 < kanzure> gene_hacker is upset because he's busy working on actual mechanosynthesis
05:07 < kanzure> .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322377/
05:07 < yoleaux> The “Gemini” spinal cord fusion protocol: Reloaded
05:10 < JayDugger> Picard maneuver...that's where everyone pretends an English native sounds French, right?
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05:52 < fenn> bonus points for doing the picard maneuver while simultaneously doing a riker chair straddle http://youtu.be/lVIGhYMwRgs&t=22s
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06:02 < fenn> how about the actual cassini saturn flyby data: http://youtu.be/R2WlXNHaJwY
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06:44 < fenn> http://www.boston.com/bigpicture/2009/04/cassinis_continued_mission.html
06:46 < kanzure> "Swept-source optical coherence tomography powered by a 1.3-μm vertical cavity surface emitting laser enables 2.3-mm-deep brain imaging in mice in vivo" http://biomedicaloptics.spiedigitallibrary.org/article.aspx?articleid=2458790
06:48 < kanzure> "Native proteins trap high-energy transit conformations" http://advances.sciencemag.org/content/1/9/e1501188.abstract
06:49 < fenn> actually wikipedia has much better versions of those images: https://en.wikipedia.org/wiki/Rings_of_Saturn
06:50 < fenn> some of them
06:57 < kanzure> .ttile http://ambermd.org/
06:57 < kanzure> .title http://ambermd.org/
06:57 < yoleaux> The Amber Molecular Dynamics Package
06:58 < kanzure> large email archive too http://archive.ambermd.org/
06:58 < kanzure> .title http://archive.ambermd.org/201510/0088.html
06:58 < yoleaux> [AMBER] Cytochrome P450 with heme simulation from Abelak, Kavin on 2015-10-09 (Amber Archive Oct 2015)
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07:15 < kanzure> On Sat, Oct 17, 2015 at 1:58 AM, Cathal (Phone) <cathalgarvey@cathalgarvey.me> wrote:
07:15 < kanzure> > If I had time, and if you didn't keep meticulous IRC logs *and* present them
07:16 < kanzure> > for consumption on a public web server, then perhaps I'd take part in HPRM
07:16 < kanzure> > more often. ;)
07:26 < poppingtonic> The Marblestone thesis is a surprisingly good read. Thanks for sharing it, kanzure
07:27 < poppingtonic> Way above my current level of skill, but it feeds the imagination in so many ways.
07:29 < kanzure> which parts are above your "level of skill" in particular?
07:29 < kanzure> and which parts are fascinating
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07:46 < poppingtonic> Anything more intensive than what Church covered in Regenesis covers both. I've been pondering the problem of neural data acquisition - in terms of the kind of information that would be enough to enable whole-brain emulation, and the data that cryonicists hope to store via vitrification. I had considered the possibility of capturing that data at the molecular level, but couldn't think of which techniques could be discussed, because
07:47 < kanzure> cutoff at "discussed, because"
07:47 < poppingtonic> ...continues.. "I don't have the vocabulary yet."
07:50 < poppingtonic> "We structured the analysis around three problems: (1) All neurons must be probed at a sufficient
07:50 < poppingtonic> rate, (2) the energy transmitted into the brain must not cause thermal damage and (3) the volume
07:50 < poppingtonic> of instrumentation introduced into the brain must not cause physical damage. We found that all
07:50 < poppingtonic> existing approaches require orders of magnitude improvement in key parameters in order to scale to
07:50 < poppingtonic> whole brain observations."
07:50 < poppingtonic> " Electrical recording is limited by the low multiplexing capacity of electrodes
07:50 < poppingtonic> and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible
07:50 < poppingtonic> light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water
07:50 < poppingtonic> protons, and the implementation of molecular recording is complicated by the stochastic kinetics of
07:50 < poppingtonic> enzymes."
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07:53 < kanzure> smaller brains are easier for whole brain observation
07:57 < poppingtonic> the phrase "stochastic kinetics of enzymes" is interesting. The bigger the brain, the more dimensions you add to an already incredibly high-dimensional space, since every molecule in every synapse has a vector of motion that would need to be captured for accurate state measurement.
08:20 < poppingtonic> .title http://dspace.mit.edu/handle/1721.1/79910
08:20 < yoleaux> DSpace@MIT: Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
08:24 < poppingtonic> What is misincorporation rate gain?
08:25 < poppingtonic> "We found that Dpo4 acts as a DNA recording device for Manganese with a misincor-
08:25 < poppingtonic> poration rate gain of 2%/mM
08:25 < poppingtonic> "
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09:50 < kanzure> iDavid_: greetings
09:56 < iDavid_> kanzure: hello :)
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11:18 < kanzure> "ECS is celebrating Open Access Week this year by making all the content—over 120,000 articles—in the ECS Digital Library freely accessible from October 19 through 25, 2015. The ECS Digital Library is home to the Journal of The Electrochemical Society, the flagship journal of ECS, published continuously since 1902, and to the ECS Journal of Solid State Science and Technology, ECS Electrochemistry Letters, ECS Solid State Letters, ...
11:18 < kanzure> ... Electrochemical and Solid-State Letters, ECS Transactions, ECS Meeting Abstracts, and Interface."
11:18 < kanzure> http://www.openaccessweek.org/
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11:25 < kanzure> http://surgicalneurologyint.com/surgicalint_articles/heaven-the-head-anastomosis-venture-project-outline-for-the-first-human-head-transplantation-with-spinal-linkage-gemini/
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12:13 < delinquentme> hive mind: mention drexler in a patent ... or no?
12:19 < kanzure> thought you said the patent thing was a joke
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12:25 < delinquentme> kanzure, ohh no i meant that writing the innuendos into the actual patent was a joke
12:25 < delinquentme> the patent is real
12:25 < delinquentme> the pokey tip grazing dehydration and affixing
12:28 < kanzure> "Relative equilibria and the stability of the rings of Saturn" http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.26.5176
12:29 < kanzure> delinquentme: i don't think it would be good precedent to poach ideas from hplusroadmap and patent everything
12:29 < kanzure> delinquentme: just doesn't seem like a stable strategy to me
12:32 < delinquentme> only patenting those ideas which pertain to the thing im working on
12:33 < delinquentme> I think the central question which needs to be considered here is will i do more good than harm for transhumanisms by patenting this
12:33 < delinquentme> and since none of us happen to be in the vaulted leagues of thiel-esque money yet and funding more hard research
12:33 < delinquentme> i think we need someone to get there
12:34 < delinquentme> in addition if you're contributing ... as stated many times ... you guys have the option to be pulled into this project
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12:41 < delinquentme> - tip chemistry protocols similar to "surface recharing" mentioned by Mann et al ( http://dx.doi.org/10.1166/jctn.2004.008 ) as applied to DNA adhesion to an AFM or STM probe tip
12:41 < delinquentme> i feel like thats WAY too vague
12:41 < delinquentme> thoughts?
12:42 < Whip__> Nuvigil ?  thoughts
12:42 < Whip__> is it worth the price
12:43 < delinquentme> Whip__, how different from provigil / modafinil
12:43 < delinquentme> i liked my modafinil
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12:51 < Whip__> delinuentme, it's the new provigil, from what i know is that the patent ranout on provigil and then nuvigil came out
12:52 < Whip__> i have no experience with either
12:53 < Whip__> do either of them work or are they just adderall rebranded?
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12:59 < FourFire> ok, so, I just had a rather long talk with the aspiring transhumanist, who calls themselves "Singrana", and am considering reprioritising my goals
13:05 < delinquentme> Whip__, they're def not adderall.
13:05 < delinquentme> much more subtle
13:05 < delinquentme> someting that you could possibly take daily and operate as a good human in society
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13:19 < Whip__> well thats good the price is pretty outrages though
13:23 < FourFire> topic?
13:23 < mgin> FourFire: reprioritizing how?
13:23 < mgin> hey is anyone here interested in AGI / Strong AI?
13:24 < kanzure> er, yes?
13:24 < poppingtonic> yes
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13:25 < poppingtonic> but to quote Hofstadter, "don't use the term Strong AI - it was invented by John Searle, and you're playing his game"
13:25 < mgin> oh
13:25 < mgin> :)
13:26 < mgin> nice quote
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13:28 < FourFire> mgin consdiering altering my goal reaching strategy
13:29 < FourFire> I'm fearing that I'm wasting far too much time, and I've been reminded, recently that I haven't got very much of it
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13:29 < FourFire> main discussion going on in #lw, channel
13:29 < mgin> sorry i got disconnected
13:30 < FourFire> <FourFire> mgin consdiering altering my goal reaching strategy
13:30 < FourFire> <FourFire> I'm fearing that I'm wasting far too much time, and I've been reminded, recently that I haven't got very much of it
13:30 < FourFire> <FourFire> main discussion going on in #lw, channel
13:30 < mgin> i'm banned from #lesswrong
13:30 < FourFire> hmmh
13:32 < mgin> time anxiety is pretty tough
13:33 < mgin> there's a hard deadline for a hard problem... you have to be very wise and efficient
13:34 < mgin> sometimes that means cutting your losses and changing course... and sometimes it means sticking it out and suffering the anxiety
13:36 < kanzure> FourFire: summary of my comments from #lesswrong to you is that you should give up on a focus on intelligence and instead focus on (cap)ability to make things. intelligence wont build you a bridge or fold your laundry.
13:37 < FourFire> kanzure, I'm not too fussed about intelligence, I know i can't make more, I'm concerned with hacking myself to get higher agency
13:37 < FourFire> and most of all, what to spend it on
13:38 < kanzure> yes but they were telling you "focus on rationalitiessss!!!!!" and i don't think that's possibly helpful in any way....
13:38 < kanzure> what did singrana say?
13:38 < FourFire> oh I haven't read the responses yet, trying to find a quote
13:39 < kanzure> FourFire: btw, i was once one of the original members of a goal-oriented cult from ~2006
13:39 < mgin> goal-oriented cult?
13:40 < kanzure> yes, we had a method of brainwashing people into becoming insanely productive goal-obsessed individuals
13:40 < FourFire> ok, I too, have done stupid shit, and thought it was a good idea at the time, but as we live, we encounter more aspects of the world and learn things
13:40 < FourFire> kanzure, you what??
13:40 < kanzure> thought this was common knowledge around these parts
13:40 < FourFire> describe what this brainwashing involved
13:40 < kanzure> tag teaming
13:41 < FourFire> no, I'm a noob, remember
13:41 < kanzure> like, 14 hour pow-wow sessions just convincing someone of a series of statements and such
13:41 < kanzure> (although, looking back, i think that after 14 hours you can convince anyone of almost anything; but this would have to be more thoroughly tested.)
13:41 < mgin> oh that sounds fun!
13:44 < FourFire> kanzure, quote: the history of mathematics is a history of horrendously difficult problems being solved by young people too ignorant to know that they were impossible.
13:44 < FourFire> (some old high IQ guy that lw people like to quote)
13:44 < kanzure> meh
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13:55 < FourFire> ok, you could say I have calmed down and stopped "freaking out"
13:56 < kanzure> heh, now what was it you were trying to do? life extension?
13:56 < FourFire> (also, please explain how I "freaked out", so I am sure your observations match up with my own)
13:56 < FourFire> were? still am afaik, just uncertain of the best way to go about it
13:56 < kanzure> eh? you're reading too much into "freaked out"
13:58 < mgin> a lot goes into defining one's objective in the first place...
13:59 < kanzure> FourFire: most life extension projects would benefit from far cheaper materials, methods, instruments, tools, etc.
13:59 < kanzure> shouldn't have to be a "one project only" sorta ordeal
14:00 < kanzure> but because of limits of resourcefulness that's what most academics have had to suffer with
14:00 < FourFire> mgin, I want to test my insight from a couple of years back that you can use a(n advanced) genetic algorithm in combination with molecular dynamics software, and an intelligently designed utility function to design protein(s) which perform arbitrary biological functions
14:01 < FourFire> I want to make a tool, which integrates automation of the genetic algorithm, and optimized simulation state backup frequencies, and generation population sizes, and simulation resolution/detail levels, and portability between CPU archetectures
14:02 < FourFire> and use this tool, to design one, maybe two proteins(complexes)
14:03 < kanzure> i am not onvined that there is a way to make a theory that would allow you to design arbitrary protein function, other than bruteforce trial-and-error, and even then that has limitations- the energy necessary to overcome large chasms in state-space is greater than available in the universe in many cases
14:03 < mgin> FourFire: isn't that what you told me you were trying to do last time?
14:03 < kanzure> *onvinced
14:03 < kanzure> *convinced
14:03 < kanzure> you would probably have better results focusing on structural nanotechnology using proteins and peptides
14:03 < FourFire> #1, a mechanism which mimics and/or improves upon and impliments the DNA repair ability of Deinococcus radiodurans, and #2, a custom organelle which can store oxygen at high density inside human cells
14:03 < kanzure> like http://diyhpl.us/~bryan/papers2/bio/protein-engineering/Design%20of%20a%20single-chain%20polypeptide%20tetrahedron%20assembled%20from%20coiled-coil%20segments.pdf
14:04 < FourFire> kanzure, yeah, likely my proof of concept protein (replicate human histone) won't work, and i give up on the whole thing in five years
14:05 < kanzure> an hour in the library an save five years in the lab
14:05 < kanzure> *can save
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14:09 < FourFire> kanzure, so you're telling me that it will definitely not work?
14:10 < kanzure> there are physical forces involved that are still not modeled in molecular dynamics software
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14:10 < kanzure> .title https://www.youtube.com/watch?v=khq7xvzb93c
14:10 < yoleaux> Protein Engineering Webinar - YouTube
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14:11 < kanzure> .title https://www.youtube.com/watch?v=JlASigotkVQ
14:11 < yoleaux> Maureen Hanson - Improving photosynthesis by engineering chloroplast proteins - YouTube
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14:12 < kanzure> .title https://www.youtube.com/watch?v=a6TN-czZY60
14:12 < yoleaux> Real Vegan Cheese - Engineering yeast to produce casein [cccamp15] - YouTube
14:12 < kanzure> hmm didn't know they did a presentation there
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14:12 < kanzure> .title https://www.youtube.com/watch?v=UTAQYx4f6sc
14:12 < yoleaux> Strategies for Studying Protein-Protein Interactions - YouTube
14:12 < kanzure> .title https://www.youtube.com/watch?v=zP2GhM3cilM
14:12 < yoleaux> Tuning cell-surface receptor signaling through structure-based ligand engineering - YouTube
14:12 < kanzure> ^last one is probably good
14:13 < FourFire> mgin, yes, This is going to take at least 17 years, probably longer, given my proof of concept works
14:14 < FourFire> wow thanks kanzure I know what I'm doing tomorrow, then
14:15 < mgin> that's an extremely long timeline
14:15 < kanzure> .title https://www.youtube.com/watch?v=TUyo8NFi_3Q
14:15 < yoleaux> Intro to Protein Structure Prediction and Design including Review of Protein Structure - YouTube
14:15 < kanzure> .title https://www.youtube.com/watch?v=0E0a5ZaE6Gk
14:15 < yoleaux> George Church on the Future of Human Genomics and Synthetic Biology - YouTube
14:15 < kanzure> there's not many presentations about state-of-the-art in rational protein design, wut
14:16 < kanzure> .title https://www.youtube.com/watch?v=RBPcKbEvK3U
14:16 < yoleaux> 16. Protein Interaction Networks - YouTube
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14:18 < kanzure> .title https://www.youtube.com/watch?v=JX2MdZX6Bys
14:18 < yoleaux> Ron Vale (UCSF) Part 1: Introduction to Motor Proteins - YouTube
14:18 < kanzure> .title https://www.youtube.com/watch?v=yzSgCD7_jSM
14:18 < yoleaux> Mechanics of the kinesin-based transport -- Dr. Wonmuk Hwang - YouTube
14:18 < kanzure> .title https://www.youtube.com/watch?v=ceQ6Kqz8VoY
14:18 < yoleaux> High Speed Protein Simulations with Anton - YouTube
14:18 < kanzure> .title https://www.youtube.com/watch?v=Hz7oHd1mu8k
14:18 < yoleaux> Protein-Protein Docking - YouTube
14:20 < kanzure> .title https://www.youtube.com/watch?v=aJ8WluU7F3Q
14:20 < yoleaux> ChE Capstone Project: Industrial Scale Spider Silk Production - YouTube
14:20 < kanzure> "spiderx" hehe
14:21 < kanzure> ah here we go, how about this one?
14:21 < kanzure> .title https://www.youtube.com/watch?v=F7qjkQZMlIs
14:21 < yoleaux> David Baker - Design of protein structures, functions and assemblies - YouTube
14:24 < kanzure> oh, just foldit stuff. meh.
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14:45 < kanzure> https://www.youtube.com/user/UWfoldit/videos
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19:10 < kanzure> bloop
19:11 < fenn> blorp
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19:12 < fenn> if people want to be exclusive and hold secret meetings that's fine, but apparently i'm never invited to any secret IRC channels with anything important going on
19:12 < fenn> so i have to work in public apparently
19:13 < fenn> or at least that's what i would say if i were trying to cover up my involvement in secret channels
19:14 < kanzure> well done
19:14 < fenn> how's the anonymity working out for you, justanotheruser?
19:15 < kanzure> hm? we know his name
19:15 < fenn> obviously it's "Justan"
19:15 < kanzure> from his github repo
19:15 < fenn> oh poo that's not fun
19:16 < fenn> tbh i'm more worried about crazies like erasmus watching the logs than any patent poachers
19:17 < fenn> we've certainly had enough over the years
19:18 < kanzure> "why should i spill the beans when everyone else is just lurking the logs?"
19:20 < fenn> i could say something like "there are 90blah people lurking and who the hell are they" but actually most of the names on the list are awesome people i know and wish participated here more
19:20 < kanzure> there's a bunch of log lurkers
19:21 < kanzure> not counting the search bots
19:21 < kanzure> since oct11 about 3932 .log requests
19:21 < fenn> wow
19:21 < kanzure> (which does include the search bots)
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19:21 < fenn> how does that compare to random files?
19:22 < kanzure> haven't looked yet. filtering out known bots at the moment.
19:23 < fenn> i wonder if wget -r -c does a lot of requests
19:23 < fenn> even if you've already downloaded the files
19:25 < fenn>  /join #project_elrond
19:25 < fenn> abort abort!
19:27 < kanzure> 856 requests when i filter out known-bots
19:27 < kanzure> someone is using page2rss
19:28 < fenn> the smoking gun
19:28 < fenn> it's probably eudoxia
19:28 < kanzure> or yashgaroth or eleitl or any of the other losers
19:29 < kanzure> 217 requests to /logs in that time frame
19:30 < yashgaroth> hey I only check the logs once, maybe 50 times a day, tops
19:30 < kanzure> filthy casual
19:31 < yashgaroth> my money's on eudoxia too, unless he is actually just psychic
19:33 < kanzure> i feel like he would use a user-agent string that proudly rants about lisp
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23:03 < maaku> mgin: you're working on AGI?
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23:20 < maaku> kanzure: for fun, try replacing the logs with markov chain text generated from the actual logs
--- Log closed Sun Oct 18 00:00:00 2015