--- Log opened Mon May 09 00:00:09 2016
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06:46 < kanzure> hm.
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06:55 < Aurelius_Work2> hm?
06:57 < kanzure> hrm.
07:08 < Aurelius_Work2> Kanzure is Siegward of Catarina
07:08 < kanzure> probably
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07:26 < kanzure> http://i.imgur.com/zGWas8v.png
07:35 < kanzure> https://www.reddit.com/r/worldnews/comments/4ih686/cbs_report_russian_gold_medalists_used_steroids/
07:35 < kanzure> some long interview about steroid use in sports or something, not sure about quality https://www.youtube.com/watch?v=azzhD2QJ8B0
07:36 < kanzure> well, http://www.youtube.com/watch?v=azzhD2QJ8B0&t=8m09s at least skip the intro stuff
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10:02 < kanzure> "Scripts are written is RiSC-16  ... and are running in a shared memory space" well there's your problem right there... i don't think this is a realistic "bitcoin" CFT.
10:02 < kanzure> *CTF
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10:07 < maaku> why RiSC 16?
10:07 < kanzure> maaku: "because otherwise it woudn't be exciting" i think is the answer. i'm asking the guy in #hackchain at the moment.
10:09 < maaku> if there was a gcc or llvm backend it'd be interesting, i guess
10:09 < kanzure> it did mention something about a debugger
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15:06 < CaptHindsight> anyone ever make a DNA synthesizer or sequencer? It's been about a year since I was asked about making an inkjet oligo printer
15:08 < kanzure> nope, haven't executed on that, are you still willing?
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15:24 < CaptHindsight> I wonder if there would be enough interest for a full kit with inkjet, gibson assembly and crispr on indegogo or similar
15:25 < CaptHindsight> make 100+ kits
15:25 < kanzure> yep probably. but also, i would be willing to fund it anyway regardless of that level of interest.
15:26 < CaptHindsight> as long as the check clears
15:26 < kanzure> also, there's significant design problems that have not yet been resolved regarding how to go from "a flat surface with 100 million dots" to "alright now do automated pipetting to do gibson assembly a few thousand times".
15:26 < kanzure> well, gibson assembly *a few million times
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15:28 < CaptHindsight> nah, at most you're making a gene or just a subsection
15:28 < kanzure> the straightforward way is micropipetting but i have heard significant resistance to this idea from e.g. fenn, regarding calibration and accuracy of a micro tip or something. it sounds like a plausible problem so that's why i was thinking about alternative ways to do the assembly reactions after synthesizing all the oligos.... like depth-based flooding.
15:29 < kanzure> if you are only making a single gene then you don't need to use inkjets. you could do traditional pipetting like delinquentme's thing, or the opentrons equipment.
15:33 < CaptHindsight> the inkjet just automates it
15:33 < kanzure> opentrons is also automated, without using an inkjet
15:33 < kanzure> http://opentrons.com/
15:33 < CaptHindsight> sure
15:34 < CaptHindsight> but it's not available a few $K
15:35 < CaptHindsight> heh, opentrons
15:35 < CaptHindsight> nevermind, we're not on the same page
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15:36 < kanzure> i think using an inkjet makes sense for high-volume highly-parallel gene synthesis
15:36 < kanzure> which we should do
15:39 < fenn> the problem is it takes too much time to move a pipette tip around 100,000 times
15:39 < kanzure> oh what. was that the problem?
15:42 < kanzure> not sure if that is even solvable. you need to have separated isolated areas for different fragments and then you need to bring them together for dna assembly. depth-level flooding might save a few operations but only if the dna in that region/group happened to have no errors that would significantly break the yield.
15:43 < fenn> well it's only a couple days of pipetting time, not impossible
15:43 < kanzure> *happened to have no errors significantly breaking the yield
15:43 < kanzure> what numbers did you assume?
15:43 < fenn> 100k * 1 second
15:44 < kanzure> these are 25 micron diameter circles or something on a flat surface. travel time needs to be considered, and possibly a wash step and wash time :(.
15:44 < kanzure> s/flat surface/surface
15:45 < kanzure> and wash steps might also require wash travel time to nearest designated wash area if any
15:45 < fenn> i was assuming each microwell would contain 10 inkjet dots or so
15:46 < kanzure> yeah i think even a few weeks is probably okay
15:46 < kanzure> especially if there is inline verification during the operations, to confirm that you are not compeletely wasting your time
15:48 < kanzure> i think the other remaining requirements are things like bringing some heat to different regions of the surface to meet the requirements of gibson assembly (or whatever assembly reactions) and then dna sequencing things
15:49 < kanzure> can we do multiple centimeter travel at ~10 micron steps in ~1 second?
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17:44 < kanzure> .title https://www.youtube.com/watch?v=PhGfgREoBj4
17:44 < yoleaux> James Webb Space Telescope Mirror Rollover Timelapse - YouTube
17:47 < kanzure> "The back of the telescope looks like it's all blurred out."
17:47 < kanzure> :( "There is proprietary hardware and we have to respect the intellectual property of our industry partners"
17:52 < kanzure> .title https://www.reddit.com/r/IAmA/comments/4i5euw/im_dr_josiah_zayner_former_scientist_at_nasa/
17:52 < yoleaux> Too Many Requests
17:53 < kanzure> http://www.gizmag.com/home-crispr-gene-editing-kit/40362/ and other diybio things. (he's from the diybio mailing list)
17:53 < kanzure> cc jrayhawk
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20:19 < kanzure> john clark argues, "We don't yet know what the brain's master learning algorithm is but we can put upper limits on how complex that algorithm can be, and we know for a fact it can't be all that complex. In the entire human genome there are only 3 billion base pairs. There are 4 bases so each base can represent 2bits, there are 8 bits per byte so that comes out to  750 meg. Just 750 meg!  And all that 750 meg certainly can be used just ...
20:19 < kanzure> ... for the master learning software algorithm, you've got to leave room for instructions on how to build a human body as well as the brain hardware.  So the instructions MUST contain wiring instructions such as "wire a neuron up this way and then repeat that procedure exactly the same way 917 billion times". And the 750 meg isn't even efficiently coded, there is a ridiculous amount of redundancy in the human genome. So there is no way, ...
20:19 < kanzure> ... absolutely no way, the algorithm can be very complex, and if Evolution could find it then it's just a matter of time before we do too."
20:19 < kanzure> i am pretty sure he is wrong
20:19 < kanzure> it's only 750 megs but that's when you have nucleic acids and amino acids and whatever other shit flying through your body interacting with dna and proteins
20:20 < kanzure> and, additionally, a learning algorithm is probably insufficient for whatever his goal is...
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20:20 < kanzure> any other major errors?
20:20 < kanzure> ah right, the thing about neuron wiring as sufficinet for whatever his goal is. we don't actually know if wiring is sufficient.
20:38 < maaku> 750MB of pure program text is fucking huge.
20:38 < kanzure> have you worked at google
20:39 < maaku> Program text, meaning compressed machine code, no data
20:40 < maaku> E.g. off you sum the stripped executable sizes of the default install of Debian, I'd be surprised if it is larger
20:40 < 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."
20:41 < maaku> "It might only be as complex as the largest, multi generational collaborative software project humanity has ever done"
20:42 < kanzure> "bitcoin but a billion times worse"
20:42 < maaku> Yup
20:42 < maaku> That said I think there is structural evidence that the One Algorithm is rather simple indeed
20:45 < kanzure> we really need lots more comparative neuroanatomy data. as soon as connectomics people start doing better work, we should ramp up the number of different mammalian brains that have high-resolution scan data available online.
20:52 < maaku> Sure but at least regarding the neocortex, at birth (or just prior) it seems to be a nearly uniform grid
20:53 < maaku> So the range of possible algorithms are quite constrained
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21:09 < kanzure> perhaps for connectivity
21:09 < kanzure> maaku: http://diyhpl.us/~bryan/papers2/neuro/Generation%20of%20dense%20statistical%20connectomes%20from%20sparse%20morphological%20data%20-%20Egger%20-%202014.pdf
21:09 < kanzure> maaku: http://diyhpl.us/~bryan/papers2/neuro/An%20algorithm%20to%20predict%20the%20connectome%20of%20neural%20microcircuits%20-%20Markram%20-%202015.pdf
21:13 < maaku> Connectome information about the noncortical part of the brain is most critical to my work
21:13 < maaku> I'll read those links. Thanks.
21:14 < maaku> Also kanzure remind me sometime when I'm not putting kids to sleep to run an open source Google Now idea past you
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--- Log closed Tue May 10 00:00:10 2016