--- Log opened Tue Sep 22 00:00:35 2015
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04:41 < kanzure> http://www.nature.com/news/chinese-scientists-row-over-long-sought-protein-that-senses-magnetism-1.18397
04:41 < kanzure> .title http://link.springer.com/article/10.1007%2Fs11434-015-0902-0
04:41 < yoleaux> Magnetogenetics: remote non-invasive magnetic activation of neuronal activity with a magnetoreceptor - Online First - Springer
04:42 < kanzure> "exogenous magnetoreceptor, an iron-sulfur cluster assembly protein 1 (Isca1)"
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05:49 < superkuh> Eh... we'll see. I'm doubtful.
05:55 < kanzure> wasn't there some non-receptor magnetic sensor in a bunch of other organisms?
05:57 < superkuh> The only ones I can recall are the the bacteria with iron concentrations in their tips and the free radicals recombination effected by local field mechanism proposed for coloration of vision.
05:57 < kanzure> and the bird magnetism stuff?
05:57 < superkuh> That's the latter one.
06:00 < kanzure> ah right, the bacteria stuff are the magnetosomes and magnetite clusters. right.
06:00 < kanzure> http://2014.igem.org/Team:Kyoto/Project/Magnetosome_Formation
06:02 < kanzure> "glial cell symbiosis with a magnetic bacteria (Magnetospirillum magneticum AMB-1) serving as a linker between reception of wireless magnetic field and optogenetic neuro-stimulation output" http://2011.igem.org/Team:NYMU-Taipei
06:02 < kanzure> "gene expression in the presence of a magnetic field, in-vivo magnetite formation in the magnetosome vesicles of the magnetotactic bacteria, Magnetospirillum magnetotacticum strain AMB-1, mms-6" http://2011.igem.org/Team:Toronto/Project
06:02 < kanzure> "construction of a magnetosome membrane in ecoli" http://2013.igem.org/Team:OUC-China/Review
06:02 < kanzure> and another ecoli/magnetism thing (looks similar to the kyoto project??) http://2013.igem.org/Team:Chiba
06:03 < kanzure> "fluorescent magnetosome to visualize magnetic fields w.r.t cells" http://2013.igem.org/Team:UNIK_Copenhagen
06:03 < kanzure> "magnetic remote control of ecoli, production of various magnetic nanoparticles" http://2014.igem.org/Team:Berlin/Project
06:03 < kanzure> all i got.
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06:11 < kanzure> http://2011.igem.org/Team:NYMU-Taipei/optomagnetic-design "We chose the original BRET method using coelenterazine (luciferin) as substrate in BRET 1 method (See Figure 1). What we do is anchoring the YFP on the N-terminus of Mms13 and r-Luciferase on the C-terminus. We expect that when the magnetic force applied on the membrane and changed the conformation of Mms13 would lead to the close proximity between YFP and r-Luciferase and thus ...
06:11 < kanzure> ... induce fluorescent phenomenon by BRET method)(See Figure 1)."
06:11 < kanzure> "theoretically, BRET will be an constitutive phenomena, leading to uninhibited excitation / unregulated inhibition of target neurons"
06:12 < kanzure> "In our BiFC-based BRET design, we anchored a half of a YFP fragment (with YFP C-terminus) on the inter-helical inhibitor (the CHAMP peptide design). By using the inhibitor, we can affect the tight interaction between Mms13’s two helices, and the constant light induced form BRET phenomenon can also be blocked. The rest of the design is to get the other half of the YFP (with YFP N-terminus) anchored on the N-terminus of Mms13 and ...
06:12 < kanzure> ... anchored the r-Luciferase on C-terminus of Mms13. The result is that when there is no magnetic force applied to Mms13, two helices of Mms13 will have further inter-helical distance due to the inhibitor (CHAMP design) and the BRET phenomenon will not perform due to the lack of close proximity between two helices. When we apply magnetic force to Mms13, the helices of the transmembrane protein will be pulled together and will induced ...
06:12 < kanzure> ... the BRET phenomenon to emit fluorescence."
06:13 < kanzure> lolz http://2011.igem.org/wiki/images/a/a7/Electromagnet.png
06:14 < kanzure> oh weird their pic for "Tensile Force-Dependent Neurite Elicitation via Anti-b1 Integrin Antibody-Coated Magnetic Beads" is pretty awesome, http://2011.igem.org/wiki/images/6/6a/Cell_NYMU.png
06:14 < kanzure> "Fig. 5: Neurite initiation and elongation in response to applied force of only 450 pN. (Joseph N. Fass, et al., 2003)"
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07:37 < maaku> justanotheruser: yeah the David Allen book, which it looks like you found
07:37 < maaku> kanzure: you have a system that works. don't change it
07:39 < maaku> justanotheruser: GTD is an exhaustively engineered (no holes) organizational system, so some of the people who find it and are in need of it tend to become fanatical
07:41 < maaku> the relevance to this channel is that you need some sort of organization framework and planning procedures in order to turn yourself into a planning and ruthless execution machine to achieve your goals
07:42 < maaku> there are many systems that would work, but GTD is simply the most effective of the accessible ones
07:42 < kanzure> i spent many months in high school with a per-minute todo list and schedule, and all i got was an overdeveloped sense of hatred
07:43 < maaku> haha that is most definately doing it wrong
07:43 < kanzure> (it was definitely my own fault, but it's not like anyone pointed out "hey a schedule like that is fucking insane you know")
07:44 < maaku> kanzure: btw do you have a writeup of how diyhpl.us works? i saw you work at scaling bitcoin and it seems to be very low friction. automatic mirror of some local repository you have?
07:45 < kanzure> blame jrayhawk because he wrote a pile of software called piny, which is very minor posix-compliant glue between ikiwiki (git-based wiki) + cgit + some other stuff i'm forgetting.
07:45 < kanzure> http://piny.be/piny-hosting/
07:46 < maaku> i'll look into that
07:46 < maaku> thanks
07:46 < kanzure> git server plus some hooks to recompile statically generated wiki
07:50 < kanzure> maaku: actually one of my weaknesses is non-interrupt-based work scheduling, been trying to figure out what the non-interrupt model is like
07:58 < kanzure> .title https://news.ycombinator.com/item?id=10255821
07:58 < yoleaux> Syrian war spurs first withdrawal from 'doomsday' Arctic seed vault | Hacker News
08:01 < maaku> kanzure: that's exactly where list management is most effective, in my experience. honestly maybe you should give GTD a look, at least as a framework for building your own system
08:02 < kanzure> my problem isn't remembering lists of things to do, my problem is more related to a hatred of habits or something
08:02 < maaku> when I'm executing well, it's cause I'm drilling down a list picking things I'm motivated to work on, while trusting that my prior project-planning self put those things on a list for a reason
08:03 < maaku> well you seem to have developed some really productive ones with respect to systemizing knowledge
08:03 < kanzure> thanks, although some of it is just "has anyone actually checked if they can read all of this content? let's see..."
08:05 < maaku> what I'm saying is -- having seen you at work, briefly -- you seem to be executing on habits that keep such knowledge from being lost, even if it is just self-hosted piny, typing really fast, and an assortment of bots
08:05 < kanzure> yep, lots of that is low-friction stuff as you noticed. just type commands -> stuff happens.
08:05 < maaku> so i take that as proof-point that you could do the same for organizing non-interrupt work via lists or whatever
08:06 < maaku> man low-friction is key
08:06 < kanzure> i was also able to convince andytoshi to start using jotmuch (the bookmarking tool i use)
08:07 < kanzure> https://github.com/davidlazar/jotmuch
08:07 < maaku> that's the #1 insight I've had regarding everything involving humans. make doing the desired action less friction than doing anything else. that's the only way you'll convince anyone (including future self) to do it
08:08 < kanzure> maaku: did you ever see fenn's sleeplog (activity log)? http://fennetic.net/sleep/
08:08 < maaku> nice, thanks i'll use that too
08:08 < maaku> and no, i havne't thanks for th elink
08:09 < kanzure> some things are just not going to be low friction
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08:11 < maaku> building a habit gives other things a friciton disadvantage
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08:12 < kanzure> actually i guess i still can't come up with examples of non-interrupt getting-things-done. how sad.
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08:13 < kanzure> fenn: your sleeplog link to http://www.lauriefrick.com/time-slices/ is broken now, and it's not on the wayback machine.
08:14 < kanzure> perhaps it is this one https://www.artsy.net/artwork/laurie-frick-daily-time-slices-apr-23
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09:21 < archels> "Perhaps a better phrase than artificial intelligence would be “intelligent artifice”"
09:26 < maaku> kanzure: so you work on a firefighting model?
09:30 < kanzure> sorta... hard to explain. hm.
09:31 < maaku> justanotheruser: I sent StealerofSuns here. he/she made a "I just realized my expected lifespan is too small to do everything I want, how do I fix that? (ps: I'm an engineer)" post on reddit
09:31 < maaku> they need to get a bouncer though
09:32 < kanzure> it's firefighting but the fires are used as reminders to go refactor some broken crap or whatever
09:34 < kanzure> and sometimes i have enough "carry-over" bandwidth to sustain something for days but a lot of that is interrupt-driven too.
09:34 < maaku> justanotheruser: I'll go find him on reddit again and send him instructions for a proper IRC client ;)
09:34 < maaku> kanzure: there are lots of people who are quite successful that way. i've had some as managers (ugh).
09:35 < JayDugger> Heh. My sympathies.
09:35 < kanzure> not all fires need to be fought individually, but often they are good indicator of deeper problems
09:35 < JayDugger> "Ugh" strikes me as polite.
09:36 < kanzure> and why focus on 1-on-1 firefighting when you can invent stuff like the firetruck or the extinguisher
09:36 < maaku> JayDugger: you learn how to not look like a fire. it also kills you a little bit as ahuman being
09:37 < kanzure> ... or chemical propellant, for that matter.
09:38 < maaku> kanzure: well to use the healthcare analogy, doing triage has its place. there are people whose only job is to fix trauma that comes in the door. but prevention is also important and takes planning
09:38 < JayDugger> Heh. That's all too familiar too.
09:38 < maaku> eh, screw analogies
09:39 < kanzure> yes one way to fix triage is to make a better bullet. er, wait..
09:39 < JayDugger> Good thing we aspire to something better.
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09:40 < kanzure> maaku: yep, a lot of my planning is also interrupt-driven.
09:41 < kanzure> for example, i came up with my next-generation cryonics plans when i was yelling at gwillen in here earlier this year hehe
09:43 < kanzure> crap that was seven months ago
09:43 < maaku> and you havne't implemented it yet? get on it man!
09:43 < JayDugger> Hooray for timestamped logs!
09:45 < kanzure> well i expected that sort of project to take a few hundred years for humans, but much less for other animals
09:45 < kanzure> so what's a few months in the scheme of things? that's only what, 3^^^^^^^^3 human lives according to trollkowsky, right?
09:46 < maaku> actually I've just made the Significant Realization that for me it changed when I had kids -- a toddler is a human tornado, and managing two of them of non-stop firefighting
09:46 < maaku> if I am to get anything done in work or in off-work hplus projects, it is by non-interrupt planned execution
09:46 < kanzure> and before you were not firefighting?
09:46 < kanzure> habitual planned execution?
09:47 < maaku> i started GTD around the time we had our first kid. i'm mostly habitial now although prolonged fires (i.e. bitcoin block size...) have pulled me out from time to time
09:47 < maaku> also corresponds with my least productive time periods, at least by memory
09:47 < kanzure> i'm gonna hate life even more if it's really just habits vs. firefighting, that sounds so incredibly lame and boring
09:48 < maaku> eh, i'm not sure you have an accurate view of what you call 'habits'
09:48 < kanzure> elaborate
09:49 < maaku> it's more about decoupling planning from executing. so when I'm in-the-flow-state planning, I'm all vision-y and trying to architect something grand, while reducing to executable tasks
09:50 < kanzure> flow-state planning is completely unrelated to actually doing things
09:50 < maaku> and during the week, if it is a good week, I'm freeing myself from worrying about priorities and just looking at the output of that planning and saying 'hey, that looks interesting right now; i'll do that'
09:54 < kanzure> "hey, that looks interesting right now; i'll do that" sounds suspiciously similar to interrupts :-)
09:54 < kanzure> "server is dying, pull up pull up" "hmm that looks interesting"
09:55 < maaku> kanzure: the difference is whether you are looking at what the world presents to you, or what you purposefully aranged to be presented to your future self
09:55 < maaku> but I suspect we are 90% talking past each other
09:56 < kanzure> no, you're right, i missed the planning part
09:56 < kanzure> "and now i shall plan for some magic to happen" alas..
09:57 < maaku> well that's what GTD is, ultimately, just an intricate scheme for scheduling future reminders to yourself
10:00 < maaku> whose achilles heel is IRC. time to get back to work dammnit
10:01 < kanzure> maaku: i have been tracking every conversation since 2009, and my highest code output days (both in quality and quantity) are also the days with the highest amount of irc. so you shouldn't necessarily assume high irc is equivalent to low productivity.
10:02 < kanzure> er, highest amount of unique-people conversations
10:02 < kanzure> (net only, doesn't hold for in-person)
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10:36 < justanotheruser> kanzure: a per-hour todo list plus another list for dated todos is my current system... I don't think I could conform to a per-minute todo list
10:36 < justanotheruser> maaku: okay, I'll go and find the audiobook
10:36 < kanzure> builds character, yo
10:36 < kanzure> minute by excruciating minute
10:37 < maaku> justanotheruser: if you fail to find the audiobook I can get it to you
10:37 < justanotheruser> I'm not good enough at estimating time to get minute-by-minute right, I usually fail with hour-by-hour
10:37 < kanzure> wasn't estimations, was just pre-allocated
10:38 < maaku> kanzure: were you running through a checklist, in order?
10:38 < kanzure> nah more like calendar plus todo list, lots of reserved chunks on calendar in very tiny blocks
10:38 < justanotheruser> "IRC for 10 minutes"
10:38 < kanzure> yes :-(
10:39 < maaku> sounds excruciatingly boring
10:39 < kanzure> yup
10:39 < kanzure> but on the bright side i have developed an immunity to calendars, so that's something
10:39 < maaku> calendar is only for things that have to happen at a very specific time (e.g. meeting, drop kid off at school)
10:40 < maaku> everything else is 'I'll work on it when I damn well feel like it, but i'll keep a reminder to get it done so I don't forget'
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10:40 < maaku> i made that mistake once of micromanaging time. didn't even work because I spent more time making the todos than executing
10:45 < kanzure> yeah i had like 1-2 hours of todo maintenance/day
10:51 < maaku> hrm jot / urlsnap doesn't seem to be able to fetch titles
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10:54 < kanzure> yeah i haven't used that part
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11:37 < ujjwalt> Hi guys anyone here?
11:37 < ujjwalt> Heard enough of why biology is like software. I want to know why biology is not like software
11:39 < kanzure> "... there is no source, the bytecode has multiple reentrent abstractions, is unstable and has a very low signal to noise ratio, the runtime is unbootstrappable, the execution is nondeterministic, it tries to randomly integrate and execute code from other computers... multiple reentrant and self-modifying abstractions. absolutely everything has subtle side effects."
11:42 < ujjwalt> any resource material i should go through to understand these properties
11:43 < ujjwalt> and what do you mean there is no source?
11:43 < justanotheruser> ujjwalt: biology is much more efficient at simulating life than a program
11:43 < ujjwalt> if it’s not too much pain can you explain your points in a little more depth?
11:43 < juri_> there are only binaries.
11:44 < kanzure> dna isn't exactly "source code"; the real "source code" is stuff like the set of constraints that make the whole thing work at all, plus the dna as well.
11:44 < kanzure> .. or something.
11:44 < ujjwalt> justanotheruser: It’s not simulating life. It is life?
11:44 < ujjwalt> DNA is like the bytecode of a VM right?
11:44 < justanotheruser> yes the most efficient simulation of something is that thing
11:45 < kanzure> if it's bytecode then it's terrible bytecode, because it's self-modifying and binds to random crap, and self-execution causes self-modification
11:45 < kanzure> ujjwalt: what is your background? biology? software?
11:45 < ujjwalt> software
11:46 < kanzure> ujjwalt: http://diyhpl.us/~bryan/papers2/bio/books/ http://diyhpl.us/~bryan/papers2/bio/ http://diyhpl.us/~bryan/papers2/neuro/ http://diyhpl.us/~bryan/papers2/longevity/
11:46 < kanzure> ujjwalt: http://diyhpl.us/~bryan/papers2/DNA/ http://diyhpl.us/~bryan/papers2/polymerase/
11:46 < ujjwalt> Why does everyone refer to the 4th edition of Molecular Biology of the Cell
11:46 < ujjwalt> why not the latest?
11:47 < kanzure> because books are evil
11:47 < kanzure> also there is "molecular biology of the gene" but i forget which one is which
11:47 < kanzure> the synthetic biology primer might be okay for starting out but whatever
11:48 < kanzure> if you want to be extremely productive then just focus on lab protocol manuals only
11:48 < ujjwalt> so engage me here
11:48 < kanzure> for everything else, wikipedia is usually sufficient, in tandem with the table of contents of campbell biology, molecular biology of the cell, or some other textbook
11:49 < kanzure> (or the index.. but the index is less entertaining i guess.)
11:49 < kanzure> https://en.wikipedia.org/wiki/Molecular_Biology_of_the_Cell_(textbook)
11:49 < ujjwalt> what you are seeing is that dna along with the chemical context just executes. It modifies itself and behaves arbitrarily
11:49 < ujjwalt> *saying
11:49 < kanzure> not arbitrarily
11:49 < ujjwalt> i mean
11:50 < ujjwalt> based on the chemical context but the situation fluctuates
11:50 < ujjwalt> because it keeps changing - both the bytecode and the VM
11:50 < kanzure> this article is surprisingly sparse: https://en.wikipedia.org/wiki/DNA
11:50 < kanzure> what's the "VM"?
11:50 < kanzure> reality?
11:51 < ujjwalt> the chemical context of the cell
11:51 < ujjwalt> different proteins and chemicals and their concentrations
11:51 < ujjwalt> Have you seen this - http://ds9a.nl/amazing-dna/
11:51 < kanzure> sure; but also, the dna molecule itself has physics of its own.
11:51 < kanzure> yes actually i have seen that, and yawn
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11:51 < ujjwalt> it helps a software guy like me but I’m aware its not all that accurate
11:51 < kanzure> this is a fairly old page by now
11:52 < ujjwalt> Yup
11:52 < ujjwalt> I’m new to synthetic biology so I’m trying to understand why exactly is it so hard to engineer biological systems
11:52 < kanzure> for molecular biology here's some animations that are a nice way to jump in, https://www.youtube.com/playlist?list=PLgO7JBj821uH_-G9H0lnYZkIrg0kqj1Ka
11:52 < ujjwalt> what do we need to do/invent/discover to engineer these systems
11:52 < kanzure> well, for example, dna synthesis is sorta complicated
11:53 < kanzure> http://diyhpl.us/wiki/dna/synthesis/notes/
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11:53 < ujjwalt> http://www.atdbio.com/content/17/Solid-phase-oligonucleotide-synthesis
11:53 < kanzure> also there are issues with genotype/phenotype prediction, so you often have to do bruteforcing or just sequence everything and find an existing implementation of what you want
11:53 < ujjwalt> this is pretty good too I guess
11:54 < kanzure> and https://en.wikipedia.org/wiki/Oligonucleotide_synthesis
11:54 < kanzure> didn't know about the atdbio article though...
11:54 < ujjwalt> There’s a pretty good course on dna synthesis on edX
11:55 < ujjwalt> https://courses.edx.org/courses/course-v1:KyotoUx+001x+2T2015/courseware
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11:55 < ujjwalt> yeah so you were saying
11:55 < ujjwalt> why it is hard to engineer these systems
11:55 < ujjwalt> I’m assuming we’ll never reach the point of electronics with natural systems
11:56 < ujjwalt> I see more promise in actual synthetic biology - non living molecular systems with bare minimum components to do one and only one thing
11:56 < ujjwalt> also I sometimes think what does it even mean to engineer a living system?
11:56 < ujjwalt> evolution solves problems in far more novel ways than I think we can come up with
11:56 < kanzure> "novelty" is just a matter of hiding your sources
11:57 < ujjwalt> directed evolution seems sort of the only way
11:58 < kanzure> you can directly engineer certain combinations of known components, but results aren't guaranteed in the same way that slapping together multiple transistors are guaranteed to work together http://diyhpl.us/wiki/dna/projects/
11:59 < ujjwalt> so we need better synthesis and sequencing obviously
11:59 < ujjwalt> what else?
11:59 < ujjwalt> accurate computer models of biochemistry should be possible given our knowledge of physiscs right?
11:59 < kanzure> mostly we need better synthesis more than we need better sequencing, at this point
12:00 < kanzure> faster design-test cycles are also very important
12:00 < ujjwalt> do you think if synthesis costs drop down to those of an ipad today we’ll mostly develop everything by the virtue of everyone being able to do amaetur experiments
12:01 < kanzure> "we'll mostly develop everything by virtue of".. ?
12:01 < kanzure> er, yes, if synthesis cheaper then it is much easier to synthesize more things. not sure what you're asking?
12:01 < ujjwalt> what I’m saying is
12:02 < ujjwalt> do you think that the lack of quantified models and research on understanding systems would be remedied if anyone with $500 can do biology at their place
12:03 < kanzure> i don't think it's a lack of quantified models or understanding
12:03 < ujjwalt> then?
12:04 < kanzure> cheap equipment is a remedy to expensive equipment
12:07 < ujjwalt> true
12:08 < ujjwalt> but we really do not understand biology well enough to reliably do synthetic biology.
12:08 < ujjwalt> the vision of future
12:08 < ujjwalt> thats being shown
12:08 < ujjwalt> is that of software or computer systems
12:08 < ujjwalt> is that even possible in such a dynamic system that is constantly changing
12:09 < kanzure> where is that being shown?
12:10 < ujjwalt> see when I learnt abut SynBio
12:10 < ujjwalt> the image that I got was
12:10 < ujjwalt> that soon we’ll be able to do with biology that we do with electronics
12:11 < ujjwalt> some people are even proclaiming today as 1975 in computers industry
12:11 < kanzure> people do that everywhere no matter what- diybio, synthetic biology, bitcoin, etc.
12:11 < ujjwalt> How successful are biobricks? Someone told me they’re great as an introduction and motivating students but not so much for serous work
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12:14 < ujjwalt> Sorry I’m asking quite arbitrary questions. Trying to make sense of where we actually are amongst all hullaballo being made about synthetic biology
12:15 < ujjwalt> Since I don’t have a baground in biology and have a lot to catch up I’m not quite getting what are the major roadblocks (besides sequencing and synthesis and cheap equipment) in terms of the science and what degree of engineering are we aiming to achieve
12:15 < kanzure> for many things it is more convenient to use gibson assembly than biobricks
12:15 < ujjwalt> is biology only being thought of as a manufacturing technology to produce materials and drugs? Sensors are other application
12:16 < kanzure> that is a strangely general question
12:17 < ujjwalt> hehe
12:17 < ujjwalt> excuse me for that
12:17 < ujjwalt> there’s mayhem in my head right now
12:18 < ujjwalt> What I’m basically trying to gauge is why synbio is so important? Is it actually going to deliver or is all this excitement based on popular media
12:19 < ujjwalt> because there’s a difference between what one reads on Wired and what scientist on the ground say
12:19 < kanzure> well that's your first mistake.. why should anyone read wired??
12:19 < ujjwalt> Hahaha
12:19 < ujjwalt> because I’m ignorant
12:20 < kanzure> yes only the propers get to read wikipedia......>?
12:20 < ujjwalt> LOL
12:20 < ujjwalt> Well one last thing. While we’re trying to engineer systems and they do work in special conditions - how much do we really understand in designing these systems
12:21 < ujjwalt> To what degree of reliability can we engineer biology today?
12:21 < ujjwalt> Just trying to gauge our understanding of the principles involved
12:42 < kanzure> hmm http://trammell.ventures/about.html
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12:57 < ujjwalt> kanzure: what about them?
12:58 < kanzure> well if i hadn't pissed him off i think he would have funded more projects that are on-topic to this channel
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13:33 < ujjwalt> lol
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15:31 < fenn> "you can directly engineer certain combinations of known components, but results aren't guaranteed" <- part of this is because claude shannon was a genius and biologists haven't caught up yet
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15:48 < kanzure> er, what would claude shannon do to fix biology?
16:04 < fenn> come up with a digital coding theorem for networks of genes and gene products
16:05 < fenn> so you could combine "biobricks" or whatever and it would actually work
16:05 < kanzure> it's weird that andy ellington hasn't published much of his anti-biobricks rants
16:06 < kanzure> .tw https://twitter.com/anselmlevskaya/status/268282467910316032
16:06 < yoleaux> Biobricks have always been an engineering cargo cult. Biology runs on DNA, not dogma. Build things that work. #synbio http://ellingtonlab.org/blog/2012/11/09/on-apologetics/ (@anselmlevskaya)
16:07 < fenn> dead link
16:07 < kanzure> http://www.ellingtonlab.com/andys-blog/2014/12/1/on-apologetics
16:12 < kanzure> hm he wrote something for beacon-center.org http://beacon-center.org/blog/2014/09/01/beacon-researchers-at-work-directed-and-real-evolution/
16:14 < fenn> hmm i remember some anti-biobrick rant on andy's blog that was better than this
16:15 < kanzure> i forgot how awesome this guy is. originally when i learned about him i was surprised that he was gangbanging with stu kauffman, which was one of the reasons i asked to work with him.
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16:17 < kanzure> i wonder if he has a bruteforcing-only argument that he could use against mike darwin
16:19 < kanzure> what's the actual opposite of bruteforcing?
16:20 < fenn> analysis
16:21 < kanzure> how is that not bruteforcing?
16:21 < fenn> you complete in o(1) instead of o(n)?
16:21 < kanzure> "magic happens here"
16:21 < fenn> sure, we've only moved the evolution up one level of abstraction
16:23 < fenn> mumble mumble eureqa symbolic regression
16:23 < kanzure> nah they turned that into some random company
16:23 < fenn> the idea is still good
16:24 < kanzure> postmark your hatemail to hod.lipson@cornell.edu
16:24 < fenn> dear hod, don't be a dick
16:24 < kanzure> "4 new PhD positions available - (ME or CS): Looking for creative candidates with research and/or project experience. PhD topics include  Robotics and Evolutionary Robotics, 3D Printing and digital manufacturing, Machine Learning and Deep Learning, Evolutionary Computation and Artificial Life. Please apply to Columbia. See application tips."
16:24 < kanzure> http://lipson.mae.cornell.edu/
16:25 < kanzure> oh "I am moving to Columbia University in NYC in July 1st, 2015"
16:26 < kanzure> http://me.columbia.edu/hod-lipson
16:27 < kanzure> "Soldercubes: a self-soldering self-reconfiguring modular robot system" http://link.springer.com/article/10.1007/s10514-015-9441-4
16:29 < fenn> when did "renting an article" become a thing?
16:30 < kanzure> blame readcube
16:31 < fenn> http://creativemachines.cornell.edu/soldercubes
16:32 < fenn> huh it looks just like the magnet cube thingy
16:32 < kanzure> disturbing that wayback machine didn't have this page. i thought they prioritized academic/.edu stuff.
16:32 < fenn> soldercubes is not what i expected at all
16:32 < fenn> i was thinking something like the harvard self assembling bee robot
16:34 < kanzure> .title https://www.youtube.com/watch?v=VxSs1kGZQqc
16:34 < yoleaux> Pop-up Fabrication of the Harvard Monolithic Bee (Mobee) - YouTube
16:34 < fenn> yeah that
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16:38 < fenn> the majority of the material is in the folding jig, which can be reused multiple times for better material efficiency
16:39 < fenn> i don't really buy any arguments about cost of materials not mattering because it's small
16:39 < fenn> the cheaper the whole system is, the more bees you get
16:43 < kanzure> "using DNA-protein conjugates to guide protein-protein assembly" http://pubs.acs.org/doi/abs/10.1021/bc500473s
16:44 < kanzure> "3d printing with nucleic acid adhesives" http://pubs.acs.org/doi/abs/10.1021/ab500026f  "By relying on specific DNA:DNA interactions as a “smart glue”, we have assembled microparticles into a colloidal gel that can hold its shape. This gel can be extruded with a 3D printer to generate centimeter size objects."
16:44 < kanzure> er... okay.
16:44 < kanzure> "This material can be assembled under biofriendly conditions and can host growing cells within its matrix. The DNA-based control over organization should provide a new means of engineering bioprinted tissues."
16:45 < kanzure> "Directed evolution of the substrate specificity of biotin ligase" (using in vitro compartmentalization) http://www.researchgate.net/profile/Rodney_Kincaid/publication/259491349_Directed_evolution_of_the_substrate_specificity_of_biotin_ligase/links/0c960539996df46ed1000000.pdf
16:46 < kanzure> 17-fold higher specificity in 6 rounds of selection
16:47 < kanzure> "mock selection to validate the selection strategy" neat idea
16:47 < kanzure> (page 4 figure 1)
16:48 < kanzure> aptamer/antibody-coated hollow gold nanospheres for binding to epidermal
16:48 < kanzure> growth factor receptors
16:48 < kanzure> blah stupid paste. http://pubs.acs.org/doi/abs/10.1021/nn406632u
16:51 < kanzure> "Continuous in vitro compartmentalization directed evolution of a ribozyme ligase" looks like a simplified lab/class exercise http://onlinelibrary.wiley.com/doi/10.1002/bmb.20742/abstract
16:51 < fenn> so that might be cool if they had grown centimeter sized crystals of DNA-bound nanoparticles instead of extruding a gel
16:53 < kanzure> "Engineered DNA ligases with improved activities in vitro" by fusing t4 dna ligase with various dna-binding proteins and dna repair proteins (7x increased activity of dna ligase) http://www.enzymes.org.nz/publications/PEDS-2013-Wilson.pdf
16:59 < kanzure> "Endowing cells with logic and memory" by using regulatory/genetic circuits http://www.rle.mit.edu/sbg/wp-content/uploads/2013/05/Endowing-cells-with-logic-and-memory.pdf
17:00 < kanzure> "In vitro selection of proteins via emulsion compartments" (review) ("up to 10^10 compartments per mL") http://www.sciencedirect.com/science/article/pii/S1046202312000643 "The key issue in designing and executing IVC selections is how to couple genotype and phenotype"
17:06 < kanzure> back to hod,
17:06 < kanzure> "Bitblox: Printable digital materials for electromechanical machines" http://creativemachines.cornell.edu/sites/default/files/IJRR14_MacCurdy.pdf
17:08 < kanzure> figure 12 shows a bitlbox inchworm robot with six linear actuators
17:08 < kanzure> and figure 11 shows an infrared remote control with 130 bitlbox units
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17:11 < kanzure> uses http://www.voxcad.com/
17:11 < kanzure> https://github.com/jonhiller/Voxelyze
17:17 < fenn> i'm not really a fan of using voxels unless absolutely necessary
17:18 < fenn> oh this is actually low-rez finite element analysis
17:23 < maaku> pretty much the only thing voxels are good for ;)
17:23 < fenn> MRI/CT stuff too
17:23 < maaku> or minecraft engineering
17:24 < fenn> nah minecraft sucks
17:24  * fenn hides
17:24 < maaku> never played it
17:24 < maaku> watched the mojang documentary though, which was cool
17:25 < fenn> it's basically a demo of really lame voxel physics and some tech tree stuff thrown in
17:25 < maaku> i'll have time to play games after death is defeated
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19:10 < kanzure> "Reverse-engineering non-linear analog circuits with evolutionary computation" http://link.springer.com/chapter/10.1007/978-3-319-08123-6_9
19:10 < kanzure> "Results show that an incremental algorithm outperforms naive approaches, and that it is possible to evolve robust nonlinear analog circuits with time-domain output behavior that closely matches that of black box circuits for any time-domain input."
19:11 < kanzure> electrowetting-based pick-and-place http://www.google.com/patents/US20150192923
19:13 < kanzure> "modularity evolves not because it conveys evolvability but as a byproduct from selection to reduce connection costs in a network" http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch007.pdf
19:16 < kanzure> "Ribosomal robots: evolved designs inspired by protein folding" http://creativemachines.cornell.edu/sites/default/files/Ribosomal%20Robots.pdf
19:16 < kanzure> i don't understand that last one. the figures are also wacky.
19:17 < kanzure> what does it mean to "encode a motor" into a "ribosomal robot tape"
19:17 < kanzure> looks like they mean "the motor is physically attached inside of the ribbon/tape"
19:22 < nmz787> howdy
19:22 < yoleaux> 17 Sep 2015 15:27Z <chris_99> nmz787: http://www.peachyprinter.com/#!peachy-printer-kit/c1uoo
19:24 < nmz787> abetusk: around?
19:27 < abetusk> hey nmz737
19:27 < abetusk> arg... nmz787
19:27 < abetusk> what's up?
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19:51 < nmz787> hey abetusk
19:52 < nmz787> was wondering if you had any ideas on how you might implement a web-based CAD in a different way, if you had to do it again, from scratch
19:52 < nmz787> at least for schematics
19:53 < nmz787> I am not sure how bleepsix is doing the drawing to screen, and grouping doesn't really seem to be in place, since when I dragged a component that they didn't stay connected
19:54 < abetusk> hm, the schematic part was actually pretty easy.  The pcb part was the real bear.
19:54 < nmz787> I was thinking about how to push the wire connections to openGL and thus the video card, etc
19:54 < abetusk> I opted to not do grouping because it's hard to know how to drag lines with what component
19:54 < abetusk> hm, yeah, if you had bigger schematics, then you could get some benefit from opengl I guess
19:55 < abetusk> A lot of the 2d drawing stuff has the potential to be hardware accelerated anyway
19:55 < nmz787> or even just get off to a good start, maybe there is some way to make browser handle more, so the JS does less
19:55 < abetusk> are you asking about high level "how do I want it to act" design, or lower level software design?
19:55 < nmz787> I had a hard time reading through the code :)
19:56 < abetusk> yeah, it became kind of a big project.  What do you want to do?
19:56 < nmz787> I guess at the software level
19:56 < nmz787> just thinking if there is a way to write less lines
19:57 < nmz787> well for the past week I created some schematics in excel, using a row for each pin to pin connection... so I really want some GUI for creating this stuff
19:57 < abetusk> so, it may not be well documented or even intuitive, but the code structure is not that bad.  The 'tools' are mostly isolated.  The 'controller' handles most of the dispatching.  The main 'schematic' does mostly data transformations
19:57 < abetusk> write less lines?  of code?
19:57 < nmz787> but it didn't look like I could just pull the template from meowcad and the JS and plop it in my flask project... couldn't really tell where things started and ended
19:57 < nmz787> yeah, of code
19:58 < abetusk> so, yeah...if I had to do it again, I would isolate the network communication more and allow for a more graceful way of storing locally.  I would also focus on a message dispatch system where different elements can subscribe to different message lines instead of this weird frankenstein system that became the gui
20:00 < nmz787> if I didn't want to use web, then I might choose something like floatcanvas with wxpython, or there like the elastic nodes example in QT    http://fado.dcc.fc.up.pt/      http://doc.qt.io/qt-4.8/qt-graphicsview-elasticnodes-example.html
20:01 < nmz787> buttt that is assuming that those libraries optimize what they're doing
20:01 < nmz787> and I really would prefer to go web, since I can start out as a desktop application (with a hidden local server), and then scale later to server based
20:02 < abetusk> So MeowCAD assumes network connectivity and transfers state change back to a central server.  The network portion of the schematic section (say) handles that communication.
20:02 < nmz787> and plus I kind of feel Chrome or Firefox is probably more highly optimized than wxpython or QT
20:02 < abetusk> You can cheat and run a local Docker image but you still need a server
20:02 < abetusk> ha, I wonder
20:03 < nmz787> I would think the browsers have more worldwide users... but maybe those users dont care as much about performance?
20:03 < nmz787> idk
20:03 < abetusk> yeah, I didn't relish the idea of programming in some weird windowing system that would break at the slightest whiff of a different desktop environment
20:03 < nmz787> mmm
20:03 < abetusk> my feeling was that for small to mid sized circuits, MeowCAD would do fine.  By the time it got to high level circuits, one could either do OpenGL optimizations or browsers would already be fast enough
20:05 < nmz787> hmm, yeah I didn't get that far with figuring out the code
20:05 < abetusk> I also only discovered web workers fairly late in the project so there are some places where "hard" computations will hang the browser until they finish.  That could (and should) have been put into a separate web worker
20:06 < nmz787> ah
20:06 < nmz787> cool
20:06 < abetusk> There are other schematic (open source) projects that you might want to check out
20:06 < abetusk> They're not as pretty (imo) and don't use KiCAD libraries, but I think they're functional
20:06 < nmz787> but not web based, right?
20:06 < abetusk> yes, web based
20:06 < nmz787> oh
20:07 < abetusk> http://logical.github.io/webtronix/schematic.html
20:07 < abetusk> https://github.com/logical/webtronix
20:08 < abetusk> I know you think "it should be simple" but there is a rabbit hole, so be careful
20:08 < nmz787> heh, that .io isn't working too well
20:08 < nmz787> my 4k monitor seems to freak a lot of webpages out though, so hard to tell where the fault lies
20:09 < abetusk> MeowCAD got kind of big but it also does a lot
20:09 < abetusk> like having boards available, letting you import KiCAD libraries, being able to view and use KiCAD libraries, letting you take snapshots, etc.
20:09 < nmz787> mmm
20:10 < nmz787> the download button on the site didn't seem to do anything for me
20:10 < nmz787> last night at least
20:10 < nmz787> not sure if i needed to be signed in (I wasn't)
20:10 < abetusk> If all you want to do is render stuff, take a look at the 'bleepsixRender.js' file along with the 'bleepsixSchematic.js'
20:10 < abetusk> ah, maybe a bug...
20:11 < abetusk> can you tell me which project it is?
20:11 < nmz787> ermm, not sure, I think I just added a resistor and capacitor and connected them together, then clicked downloa
20:11 < abetusk> alright, sorry about that
20:12 < nmz787> yeah this is just from clicking  'try it'
20:12 < abetusk> blech, yep
20:12 < nmz787> also, I am not sure if you drag a component, it seems to disconnect... but if you drag it back on top of the wire ends, does it reconnect?
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20:13 < abetusk> yes
20:13 < nmz787> and it is a bit weird that the wire icon tool resets back to the select pointer tool... but that is a feature request I guess ;)
20:13 < abetusk> or at least, it should
20:14 < abetusk> hm, yeah.  I worry about locking tools into a mode
20:14 < abetusk> I do get that a lot though so it's something that should be figured out.  You can use 'w' as a hot key
20:15 < nmz787> yeah was just checking out the help menu
20:15 < kanzure> https://en.wikipedia.org/wiki/In_vitro_compartmentalization
20:15 < nmz787> .wik in vitro compartmentalization
20:15 < yoleaux> "In vitro compartmentalization (IVC) is an emulsion based technology that generates cell-like compartments in vitro. These compartments are designed such that each contains no more than one gene. When the gene is transcribed and/or translated, its products (RNAs and/or proteins) become ‘trapped’ with the encoding gene inside the compartment." — https://en.wikipedia.org/wiki/In_vitro_compartmentalization
20:16 < nmz787> I don't even see wires in that webtronix
20:17 < kanzure> "meganucleases are DNA cleaving enzymes that specifically recognize long target sequences (approximately 20 base pairs)" from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416406/
20:17 < kanzure> "While stand-alone meganucleases are sufficiently active to introduce targeted genome modification, they can be fused to additional sequence-specific DNA binding domains in order to improve their performance in target cells."
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20:23 < fenn> nmz787: chrome is quite a pig when it comes to resource usage, even for simple text webpages
20:23 < fenn> firefox too
20:24 < fenn> too much "optimization" methinks
20:24 < nmz787> hmm
20:24 < abetusk> right... freaking .kicad_pcb
20:24 < nmz787> well, that may be OK since most everybody uses it
20:25 < nmz787> if it makes less work coding for me... then I may take it
20:25 < fenn> i only use it because i'm forced to by all the wacky shit html out there
20:25 < nmz787> since I have design-rules to think about coding too... anything GUI is just fanciness
20:25 < kanzure> if there are blood tests or other assays for cross-animal xenotransplantation compatibility, then we should be selecting small animal breeding for organ compatibility to pass thoes (and more) tests.
20:25 < nmz787> kanzure: that is a very good idea
20:26 < nmz787> are there animals which we can significantly modulate their refresh cycle (i.e. reproductive age)
20:26 < kanzure> did you also see the idea that goes like "select bacteria that helps human wound healing"
20:26 < nmz787> and such that we can still get them to grow big enough to be transplantable
20:26 < nmz787> no I didn't see that one
20:27 < nmz787> you might think that one is already covered
20:27 < fenn> nmz787: also webgl doesn't work on my computer (and will never work because nobody cares) so please have a fallback to software rendering
20:27 < nmz787> we just have to learn which to encourage or not kill
20:27 < kanzure> did you see "use psychometric testing and toxoplasma gondii in directed evolution / selection to get viable nootropics for mice based on toxo migration in specifi target brain regions"?
20:27 < CaptHindsight> so like a supersized hamster heart for human implant?
20:27 < kanzure> i'm p. sure we use pig organs for something
20:27 < nmz787> hahah, kanzure no I didn't... friggin pinky and the brain over here
20:27 < kanzure> https://en.wikipedia.org/wiki/Xenotransplantation#Potential_animal_organ_donors
20:28 < nmz787> yeah but if you could breed pigs in days or few weeks instead of months...
20:28 < fenn> heart valves was the first widespread use
20:28 < kanzure> nmz787: okay one last one then, did you see the "use selective breeding of animals to survive cryopreservation and cryoresuscitation (including cryoprotectant toxicity)"?
20:28 < nmz787> they only have to get large enough to test the compatibility... and grab some sperm/eggs I guess
20:29 < nmz787> hmm, I may have been around for that, or the beginnings of that talk
20:29 < kanzure> are heart valves all we're doing?
20:29 < kanzure> i think there was something about pig skin
20:29 < nmz787> I remember you posting frozen-dog-that-came-back stuff a while ago
20:30 < kanzure> "Chimpanzees were originally considered the best option since their organs are of similar size, and they have good blood type compatibility with humans, which makes them potential candidates for xenotransfusions. However, since chimpanzees are listed as an endangered species, other potential donors were sought. Baboons are more readily available, but impractical as potential donors because they are hilarious."
20:30 < kanzure> "Pigs are currently thought to be the best candidates for organ donation" what was that theory about early hominid cross-breeding with pigs, again?
20:32 < kanzure> wait what "Human organs have been transplanted into animals as a powerful research technique for studying human biology without harming human patients. This technique has also been proposed as an alternative source of human organs for future transplantation into human patients.[8] For example, researchers from the Ganogen Research Institute transplanted human fetal kidneys into rats which demonstrated life supporting function and growth.[9]"
20:32 < nmz787> aliens helped with some alien-love-booze
20:32 < kanzure> i guess that's one way to solve the problem
20:32 < kanzure> so breed mice that are more-compatible with human organs, store human organs in mice, keep mice alive or transfer organs when mice reach end-of-life to other mice
20:32 < kanzure> this seems like a highly ridiculous workaround
20:32 < nmz787> mmm
20:33 < nmz787> but a viable one
20:33 < fenn> tiny organs at least
20:33 < fenn> pretty sure this was in ghost in the shell
20:34 < fenn> pig farm with cloned human organs waiting around in case you need them
20:34 < fenn> they got into trouble when the pigs had human cyberbrains and were interfaced to the net
20:34 < kanzure> i hate it when that happens
20:34 < nmz787> $1 mil grant... sorry I can't apply: https://www-ssl.intel.com/content/www/us/en/wearables/americas-greatest-makers.html
20:35  * nmz787 ZOOLANDER: WHAT IS THIS, A TRANSPLANT LAB FOR ANTS!!!
20:35 < abetusk> nmz787, ok, I had to hack some things together but the download should be working.  I should be better about getting downloads to work under failure conditions and I should be better at creating .kicad_pcb files...
20:37 < nmz787> was it something that my design was doing (being crappy and not logical)?
20:37 < nmz787> oh, also the other day I showed this to someone, and they seemed to get stuck on the layout part
20:37 < nmz787> some cookie or something?
20:37 < nmz787> like even if they went back to the base URL
20:38 < nmz787> ah, yeah even now for me... I can't see the homepage, keep getting redirected to /portfolio
20:39 < kanzure> also, i think i have mentioned this before, but small animal organ survivability outside of the animal body should be selected for as well. things shouldn't just die on us because it's lacking blood for a few hours.
20:39 < fenn> fuck "makers"
20:40 < fenn> what a rip off
20:40 < fenn> where's my jetpack
20:40 < nmz787> abetusk: got a download! pretty cool!!
20:42 < abetusk> yeah, be wary of the .kicad_pcb file, it's probably got a lot of issues
20:43 < nmz787> hehe
20:43 < kanzure> why don't have i graph that shows me a comparison of creatures with largest brains, shortest lifecycle and most cognitive ability or suspected cognitive ability.
20:43 < nmz787> i've been known to manually hack kicad files
20:43 < kanzure> oh and most offspring
20:43 < kanzure> spider/octopus is probably all i'm going to get there
20:43 < abetusk> nmz787, this was a pattern I settled on....The idea is that you're now using an 'anonymous' account that persists.  You can clear history by going into the 'signup' (or is it 'register') page and hitting the appropriate button.
20:43  * nmz787 turns out it was the raccoon@
20:43 < nmz787> !
20:44 < abetusk> I wanted to funnel people into the 'register' page.  I think I should probably have the anonymous account be allowed to see the landing page though...
20:44 < abetusk> what I didn't want is to have someone spend a lot of time hacking around on a project, accidentally close the tab and lose all work.  This way work is saved.
20:44 < nmz787> abetusk: is the minus key supposed to do something? do I need the developer console open?
20:45 < fenn> two axis optimization (brain vs lifecycle) means you have to pick some arbitrary tradeoff constant
20:45 < nmz787> abetusk: ahh, I see, I guess that wouldn't be incompatible with letting them see the homepage again
20:45 < kanzure> (((one of the ideas was "select an existing animal with reasonable cognitive ability, then reduce brain size while keeping cognitive ability in tact, whether through selecting for hydrocephaly or whatever else, like physical intervention during neural tube growth, then figure out connectome or other data from the signifiantly smaller data set presented")))
20:46 < kanzure> yes i'm sure the tradeoff would be something like "well now you have giant brained creatures that do nothing but brainy things and burp out eggs" which is ok for most projects
20:46 < fenn> cuttlefish
20:46 < abetusk> Besides some special considerations, the anonymous account is an actual account.  Once you login to GitHub for example, you can't see the landing page anymore.  The expectations are weird since you haven't explicitely logged in (you've just been assigned an 'anonymous' account) but that's the basic reasoning
20:47 < fenn> https://www.xkcd.com/520/
20:47 < kanzure> (although after finding how smart snails seem to be, perhaps that's enough)
20:48 < nmz787> abetusk: is there a way to indicate ending a line without hitting escape or connecting it to a component?
20:48 < nmz787> like to add a netname?
20:48 < nmz787> oh, I need to add a label first I guess
20:48 < fenn> kanzure: no i mean you have to decide how much braininess is equivalent to how much fecundity, in order to optimize both of them at the same time
20:49 < fenn> it's okay if all their legs fall off and they have to eat from a tube
20:49 < kanzure> yes to the leg thing
20:50 < kanzure> tube feeding is inconvenient when you have a million hatchlings
20:50 < fenn> oh i see, you're trying to simplify the brain scanning problem
20:50 < kanzure> yes
20:50 < kanzure> i wasn't going to mention it, since i've said a similar thing before
20:50 < abetusk> nmz787, double click
20:50 < fenn> i just can't read and think at the same time apparently
20:51 < kanzure> a common infliction
20:51 < kanzure> yeah i mean i'm not very interested in learning that 80% of mouse brain mass is useless
20:51 < fenn> well mice are not very smart because they're inbred
20:52 < kanzure> i suspect a lot of the core cognitive abilities do not require that much brain matter, and smaller amounts of brain matter are easier to scan and trace
20:53 < fenn> yeah but a lot of "core cognitive abilities" are the other parts of brain that aren't neocortex
20:54 < fenn> maybe you'll get more out of looking at the way birds work and how they evolved homologous function in non-cortex parts of the brain
20:55 < fenn> "
20:55 < fenn> Homolog of Mammalian Neocortex Found in Bird Brain"
20:55 < fenn> this is news?
20:56 < kanzure> also unlear to me if larger brain would be easier to work with- e.g. get something size of whale brain. seems like more places for "interesting stuff" to hide and be hard to trace, though.
20:56 < kanzure> *unclear
20:56 < fenn> well it's certainly harder to scan
20:57 < kanzure> we should ship some whale brain to todd and friends
20:57 < nmz787> yeah I wonder, are there micrographs of whale brain?
20:58 < nmz787> are the cells just as dense?
20:58 < kanzure> internet is currently not very good at providing me arbitrary resolution scans of arbitrary brains
20:58 < nmz787> stupid old internet
20:58 < fenn> stupid new internet
20:59 < nmz787> .title https://www.youtube.com/watch?v=Q9A0Vufw3NQ
20:59 < yoleaux> Simpsons Internet Line - YouTube
21:00 < kanzure> i wouldn't mind a collection of formaldehyde-preserved mammalian brains for home decoration
21:00 < fenn> i'll see what i can do
21:02 < kanzure> "and this over here is my megaptera terrarium"
21:03 < kanzure> nmz787: http://diyhpl.us/~bryan/papers2/neuro/megaptera/Megaptera%20brain%20has%20a%20mass%20of%206800%20g,%20one-fifth%20of%20a%20percent%20of%20its%20body%20mass.pdf
21:03 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/megaptera/Structure%20of%20the%20cerebral%20cortex%20of%20the%20humpback%20whale,%20Megaptera%20novaeangliae%20(Cetacea,%20Mysticeti,%20Balaenopteridae).pdf
21:03 < nmz787> .title https://www.youtube.com/watch?t=6&v=mdDrQ9-5Ntc
21:03 < yoleaux> Chimp fights man - YouTube
21:07 < kanzure> "tumblr-style selective breeding and directed evolution: from a collection of 10 different species, randomly stitch animals together and pick the survivors over multiple generations"
21:08 < kanzure> er, where both members of a pair survived
21:10 < fenn> that's more or less how bacteria do it
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21:11 < kanzure> i wonder if that "implant human organs into pigs for incubation and survival" strategy would work for human brain matter. seems hard to judge compared to brain-in-a-jar which is also speculative. but at least the piggies could be selected for how well they keep other pig brains alive or other chimp brains alive.
21:11 < kanzure> (whereas it is harder to breed jars for better performance)
21:12 < fenn> brains aren't _that_ special
21:12 < fenn> at least i don't think they don't have to be in the skull cavity
21:13 < kanzure> in jars? need blood flow (easy) but also careful hormone balane across like 50-100 different molecules. ugh.
21:13 < kanzure> *balance
21:13 < fenn> in a pig abdomen
21:13 < fenn> in a jar in a pig abdomen :)
21:13 < fenn> aka cyberbrain
21:14 < kanzure> i would really prefer plain old jars but can't figure out how i would regulate blood contents sufficiently. seems like careful balancing act that would require a gazillion sensors and ability to filter stuff out of bloodstream.
21:15 < fenn> that flexible carbon nanotube electrode array will finally solve the electrical spinal interface problem
21:15 < kanzure> beause no microelectrode penetration?
21:15 < fenn> because mechanical impedance matching to neural tissue
21:16 < fenn> the glass/metal electrode arrays all resulted in tissue death in a couple months
21:17 < fenn> i don't remember if the carbon nanotube thingy had a dissolving needle for each electrode or not, i might have imagined that
21:17 < kanzure> yes well throw "evolved biocompatibility with our shitty microelectrodes" on to the list anyway
21:19 < kanzure> someone should bother to look around for exceptionally-slow brain aging people
21:20 < kanzure> (or anyone that has a non-cancerous inrease in brain mass after some period of aging-related brain mass decline; this too would be quite useful)
21:20 < fenn> all the supercentenarians had ok brain function
21:20 < kanzure> brains could potentially hang around in pig abdomens for quite a long time
21:21 < kanzure> brain function seems to be okay for lots of people even as mass declines. still freaks me out though.
21:21 < kanzure> 30%, come on
21:22 < fenn> meh just grow more
21:22 < kanzure> hm this number does not seem to be on wikipedia
21:23 < fenn> you wanna live forever, punk?
21:23 < nmz787> .title https://www.youtube.com/watch?v=9Mc4iaN-_RQ
21:23 < yoleaux> homer - shut up brain or ill stab you with a que tip - YouTube
21:23 < kanzure> well i wouldn't mind a few mind-numbing centuries more of this crap if that's what you're asking
21:23 < fenn> no i'm just ironically bringing up stupid identity issue crap
21:24 < fenn> nevermind
21:24 < kanzure> not impersonating heinlein? too bad.
21:25 < fenn> Come on, you sons of bitches, do you want to live forever?
21:25 < fenn> Battle cry at the Battle of Belleau Wood, World War I, June 1918
21:28 < fenn> "half a million" per starship trooper, well we're quite a ways past that already
21:29 < fenn> google says $850k per soldier-year
21:29 < kanzure> what was sirius xm's pig lung thing, again?
21:30 < kanzure> https://www.washingtonpost.com/lifestyle/magazine/martine-rothblatt-she-founded-siriusxm-a-religion-and-a-biotech-for-starters/2014/12/11/5a8a4866-71ab-11e4-ad12-3734c461eab6_story.html
21:30 < kanzure> "On a Virginia farm, she’s also raising genetically altered pigs, in the hope that someday their lungs (and other organs) will be modified for use in human transplant, creating a nearly inexhaustible supply of organ donors."
21:30 < kanzure> and then separately "In a lab on Spring Street, Rothblatt’s newest project appears lifted from science fiction: disembodied but breathing human lungs, hissing away in dome-shaped incubators, part of a clinical trial attempting to mend donated but not-quite-accepted-for-transplant lungs so that they can actually be placed in living human beings."
21:31 < kanzure> https://clinicaltrials.gov/ct2/show/NCT02234128
21:31 < kanzure> nice "This study is currently recruiting participants."
21:31 < fenn> well that shouldn't be hard
21:32 < fenn> i don't get the 18+ requirement
21:32 < fenn> kids are supposed to die because they can't sign a contract?
21:33 < kanzure> strange that the pigs are "genetically altered" instead of just bred.
21:33 < kanzure> what possible "genetic alterations" could they have bothered to picked. hm.
21:34 < fenn> well there's a whole bunch of options in the xenotransplantation article on wikipedia
21:34 < kanzure> like all terrible things in this world, i'm sure the details are available from the uspto
21:35 < kanzure> https://patents.google.com/?q=%22united+therapeutics%22&q=lung
21:35 < fenn> "1,3 galactosyl transferase gene knockouts; Increased expression of H-transferase (α 1,2 fucosyltransferase), an enzyme that competes with galactosyl transferase; Expression of human complement regulators (CD55, CD46, and CD59) to inhibit the complement cascade"
21:36 < kanzure> ... oh.
21:37 < fenn> "None of the major religions object to the use of genetically modified pig organs for life-saving transplantation."
21:38 < fenn> now there's a head scratcher
21:38 < fenn> oh, according to rothblatt
21:38 < fenn> right...
21:40 < kanzure> why pigs, again? why not human abdomen.
21:40 < kanzure> oh right, selection
21:40 < kanzure> lots of rough edges even if blood group compatibility with human
21:41 < fenn> sure it would probably be feasible to grow extra human organs in humans too
21:41 < kanzure> pig-human brain interation will be ugh
21:41 < kanzure> *interaction
21:42 < kanzure> extra human organs cause signaling problems (including w/ extra brain), although i suppose existence of pregnancy might suggest this is not completely problemati
21:42 < kanzure> *problematic
21:42 < fenn> i'm not too worried about that, it's not like you're adding an extra chromosome or an extra gonad
21:43 < fenn> pancreas may be problematic, or maybe not
21:43 < fenn> extra liver tissue would be a benefit i'd think
21:43 < kanzure> you're getting all the crazy neurohormone output from an extremely stressed detached brain... that's bound to cause problems in the human host.
21:43 < fenn> why would it be "extremely stressed"?
21:44 < kanzure> why wouldn't it be?
21:44 < fenn> um, because it's not doing anything?
21:45 < kanzure> brains don't normally do that
21:45 < fenn> is a human in a sensory deprivation tank "extremely stressed"?
21:45 < kanzure> after 100 hours, sure. absolutely.
21:46 < kanzure> it's not just neural input/output stimulation though, it's everything else that gets dumped into the blood supply as a messaging system for the brain to manage itself and its host.
21:47 < kanzure> plus severed neural tissue during extraction, like spinal cord
21:48 < kanzure> anyway, pig hosts can be selected that help manage and reduce guest brain stress
21:49 < CaptHindsight> maybe India, grow organs back already sold along with an extra, I'm sure you'd get volunteers
21:50 < kanzure> that's the place to go for surrogate pregnancy, yeah
21:58 < fenn> i'm not finding any information about extended duration sessions in a sensory deprivation/float/isolation tank
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22:19 < nmz787> abetusk: just found this, it is helpful https://github.com/abetusk/bleepsix/wiki/0_Home
22:22 < nmz787> abetusk: looking at your pykicad repo, have you used python sexpdata?
22:23 < nmz787> abetusk: also not sure if this is interesting or not https://github.com/nmz787/kicad-bom-tool
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22:46 < fenn> juri_: is there any interest in the open source car community in building the now-defunct aptera? do you kno what happened to all their cad models development work and test data?
23:18 < fenn> "Aptera USA has most of the original company’s prototypes, equipment, patents and designs, so it wouldn’t be starting from scratch." -> dead
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--- Log closed Wed Sep 23 00:00:36 2015