--- Log opened Mon Jun 05 00:00:13 2017
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01:59 < kanzure> rk[ghost]: no, i am not in their area. i think juul would know more about their printer project.
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02:04 < juul> rk[ghost]: not sure how that project is going. patrik d or maria are the ones to ask
02:06 < rk[ghost]> kanzure: aye
02:07 < rk[ghost]> juul: right-o..
02:09 < rk[ghost]> when i was in the area, i was quite interested in the project- but the distance to bike there wasn't convenient (as i was near Milapitas/San Jose north)
02:10 < rk[ghost]> however, the past year of living about in northern california / southern oregon in the mountains made me realize that nature is wiser than i'll ever be.. so i have currently taken full hiatus of biohackery.
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05:09 < kanzure> well that's a lame reason
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06:36 < kanzure> "Tractography-based connectomes are dominated by false-positive connections" http://biorxiv.org/content/early/2016/11/21/084137 https://twitter.com/stefan_fraessle/status/870920205496705024
06:36 < kanzure> "Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain dataset with ground truth white matter tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 re...
06:37 < kanzure> ...search groups. While most state-of-the-art algorithms reconstructed 90% of ground truth bundles to at least some extent, on average they produced four times more invalid than valid bundles. About half of the invalid bundles occurred systematically in the majority of submissions. Our results demonstrate fundamental ambiguities inherent to tract reconstruction methods based on diffusion orientat...
06:37 < kanzure> ...ion information, with critical consequences for the approach of diffusion tractography in particular and human connectivity studies in general."
06:41 < kanzure> http://spectrum.ieee.org/biomedical/imaging/ai-designers-find-inspiration-in-rat-brains
06:41 < kanzure> also has an image of a FISSEQ machine http://spectrum.ieee.org/image/MjkwMjI1NQ.jpeg
06:42 < kanzure> "In Church's estimation, the Microns goal of reverse engineering the brain may not be achievable. The brain is so complex, he says, that even if researchers succeed in building these machines, they may not fully understand the brain's mysteries--and that's okay. "I think understanding is a bit of a fetish among scientists," Church says. "It may be much easier to engineer the brain...
06:42 < kanzure> ... than to understand it.""
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06:52 < kanzure> so he wants to engineer some prefrontal cortex organoids to do task-specific things?
06:53 < kanzure> berger did neural tissue petri dish + electrode array + flight simulators using mouse neural tissue, maybe it's enough to say that human neural tissue might perform better "because humans are s-m-r-t"
06:53 < superkuh> I feel like they probably won't do much prefrontally-like without the thalamocortical loops.
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06:54 < kanzure> i really doubt they are going to make useful isolated regions of brain tissue-- genetically we do not have a way to say "give me just a visual cortex" AFAIK.
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06:57 < kanzure> best i can come up with is: make a million randomly mutated cortical organoids, electrodes on each one, test them all against some task, see which ones can be trained to do handwriting recognition or arithmetic.
07:00 < kanzure> superkuh: does this diagram show those thalamocortical connections? http://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/stitched-diagram.png
07:00 < kanzure> from http://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/Cognitive%20consilience:%20Primate%20non-primary%20neuroanatomical%20circuits%20underlying%20cognition%20-%202011.pdf
07:01 < kanzure> ("Ts" i think)
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09:32 < nmz787_i> rk[ghost]: where in SO OR? I am in NO OR
09:32 < nmz787_i> rk[ghost]: nature is the ultimate biohacker... maybe you're just still in-training
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09:50 < nmz787_i> talked to a guy on my street who used to work on calculations and paperwork for building cleanrooms... he said I probably don't need a clean room if I can somehow keep things clean between transferring from one clean place to another... which begs the question of where I'd be deprocessing ICs, or spin-coating photoresist
09:51 < nmz787_i> sooo, I guess I still need to plan for some positive pressure (the guy said 20 air changes per hour, so just do the math on whatever blower fan I get can pump/push)... and also probably a fume hood, though I'm not sure how that would work with a positive-pressure room... I'd need to ensure more fresh air is being forced in than sucked out
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10:29 < kanzure> an okayish bitcoin walkthrough http://www.samlewis.me/2017/06/a-peek-under-bitcoins-hood/
10:43 < kanzure> http://pyvideo.org/pycon-us-2017/optimizations-which-made-python-36-faster-than-python-35.html
11:04 < kanzure> http://aleph.se/andart2/space/the-aestivation-hypothesis-popular-outline-and-faq/
11:05 < kanzure> "Isn't there more to life than information processing?" "No."
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14:08 < rk[ghost]> nmz787_i: josephine county. (near cave junction)
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14:29 < nmz787_i> rk[ghost]: nice! I drove up past 8 dollar Mountain (BLM land I think) a good ways last year
14:29 < rk[ghost]> :O
14:29 < nmz787_i> rk[ghost]:  I still need to visit the caves down there
14:29 < rk[ghost]> nice. i knew a man that lived on valley next to $8
14:30 < rk[ghost]> there is a lake in the mountain
14:30 < rk[ghost]> and he had it tapped.
14:30 < rk[ghost]> the water was a-amazing
14:30 < rk[ghost]> also, i lived on Onion Mountain for 5 days a few months ago
14:30 < rk[ghost]> currently traveled north to northern WA (Seattle)
14:31 < rk[ghost]> onion mountain is about couple miles north of $8, btw
14:32 < rk[ghost]> whilst i am alive in this realm.. i will always be "in-training" ;P
14:32 < rk[ghost]> anyhoot though, i realized i would rather just farm and see what nature does than try to tell nature what to do
14:46 < adlai> uh, sorry for 'politics', but isn't the easiest way to "engineer some prefrontal cortex organoids" called "brainwashing"? or, i mean, "parenting"
14:47 < adlai> the aim should, if i may split normatives, be understanding consciousness's physical substrate to the point where it can be abstracted; not merely building better goo
14:49 < nmz787_i> adlai: can't morally test things like kanzure wants
14:52 < rk[ghost]> i am curious, if ya'll were able to generate such organoids, how would you even know if you did it right.. would there be a way to extract the information gained by it without also developing its actuators for it to express such information?
14:53 < adlai> rk[ghost]: if you're trying to develop an organoid to babysit centrifuges... let it babysit a [simulated] centrifuge
14:53 < adlai> nmz787_i: can't linguistically parse things like nmz787_i sayd
14:54 < adlai> the point is that there's H+ and h-minus, and i don't see automation as particularly plusful. if it's cheaper than automation-by-biomass, sure, have a cookie, go eat it somewhere else.
14:59 < nmz787_i> rk[ghost]: yes there's have to be a way to extract a pass/fail, otherwise it would be a pretty bad test!
14:59 < kanzure> rk[ghost]: there have been projects where neural tissue cultures were forced to play flight simulator games
14:59 < rk[ghost]> ah, interesting.
15:00 < adlai> my pass/fail is "does it move the game's minimax/schelling point to another row/column, or merely adjust the scalars within"
15:01 < adlai> "insufficient data for meaningful answer" being a natural default should the p/f resolution not prove to terminate
15:02 < adlai> kanzure: flying? really? iirc, you can make a walking bugbot with about as many "neurons" as servos, and 'flying' isn't much more complicated...
15:02  * adlai doth troll too much, should sleep
15:02 < nmz787_i> http://neural.bme.ufl.edu/page12/page1/assets/NeuroFlght2.pdf
15:03 < nmz787_i> googled: flight simulator neuron culture
15:04 < nmz787_i> this too, just a robot on a floor though: https://pdfs.semanticscholar.org/c3c5/8bcf3d014b104a44f0b7640f2ce30471774c.pdf
15:04 < nmz787_i> .wik multi-electrode array
15:04 < yoleaux> "Multielectrode arrays (MEAs) or microelectrode arrays are devices that contain multiple plates or shanks through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry." -- https://en.wikipedia.org/wiki/Multi-electrode_array
15:05 < kanzure> adlai: flight simulator hookup was not complex, no. so in that sense yeah it's entirely disappointing.
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15:40 < rk[ghost]> anyone one of you with equiptment want to take on replicating the DNA "teleportation" experiment (https://en.wikipedia.org/wiki/DNA_teleportation) as to put the naysayers to rest?
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16:18 < nmz787_i> adlai: well kanzure asked for a million mutations of a brain section... pretty hard to get that approved as an experiment on i.e. children, and quite awful to think about really.
16:23 < nmz787_i> rk[ghost]: there's definitely a lot to learn from nature, but at the same time, nature's been doing it's thing regardless of us for a long time... developing new tools that don't exist hasn't been done (unless all history of it has somehow been obliterated)... so in some ways not trying to tell nature what to do is boring and seems pointless
16:26 < nmz787_i> adlai: as for person-power... maybe 2 people would be more effective with raising a child as far as engineering their frontal cortex, than if they were trying to reverse-engineer and then re-engineer things from the ground up... but <insert speach about collaboration and building on the shoulders of giants>
16:26 < nmz787_i> also, I am sure plenty of brain scientists also have kids
16:40 < rk[ghost]> aye nature is just so robust; machines that feed, repair, and propogate themselves... !
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17:43 < kanzure> https://medium.com/@GaetanBurgio/should-we-be-worried-about-crispr-cas9-off-target-effects-57dafaf0bd53
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18:52 < kanzure> yashgaroth: sup
18:53 < yashgaroth> kinda want to buy this http://www.ebay.com/itm/Applikon-Fermentor-Bioreactor-Vessel-2L-with-Mixing-Motor-Heating-Blanket-Stand-/282510532473
18:55 < yashgaroth> what else...turns out the TIMP2 study was done by people associated with alkahest, which kinda muddies its credibility
18:56 < yashgaroth> oh and acceleron people claim that producing a follistatin-Fc fusion doesn't work well since the two follistatin domains fuck each other up somehow during expression
18:57 < yashgaroth> could've been a factor when I was doing it in e.coli; also they have some new molecule ACE-2494 that they claim doesn't have the vascular effects of actriib-Fc fusion proteins, but I can't tell what the hell protein it is
18:58 < yashgaroth> probably just a mutated actriib that doesn't have the off-target effects, but they haven't published the sequence yet; should be in phase 1 soon so we'll see
19:09 < yashgaroth> ahh fuck I bought it
19:13 < kanzure> it's a mixing motor?
19:13 < yashgaroth> bioreactor
19:14 < yashgaroth> usually one outfitted like that is 3-10x as expensive
19:19 < yashgaroth> if you can get it before someone else does, that is; needs a few parts, but nothing hard to source
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19:21 < kanzure> paint bucket and blowing carbon dioxide into the thing doesn't work?
19:22 < yashgaroth> oxygen for e.coli, though you can get away with air if they're lower temperature; co2 is for mammalian where keeping it sterile is a pain so no paint bucket
19:22 < yashgaroth> getting a bucket together and working well would cost more than this thing, at least in labor
19:24 < kanzure> uh what was i using co2 for.. i was pumping it into a bucket once.
19:24 < kanzure> algae?
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19:25 < yashgaroth> probably algae with co2 yeah
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23:29 < heath> https://patents.google.com/patent/US7745594B2/en
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--- Log closed Tue Jun 06 00:00:14 2017