--- Log opened Sat Dec 23 00:00:51 2017
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05:36 < jrayhawk> there are some factorio mods that add an order of magnitude more detail to tech progression and resource management/processing
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05:37 <@kanzure> there's always a way to take code
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07:17 < JayDugger> fenn, did you see the http://thespaceshow.com/show/19-dec-2017/broadcast-3038-jay-wittner-josh-powers
07:17 < JayDugger> podcast interviewing the Integrated Space Plan
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09:08 <@kanzure> https://bitcoinmagazine.com/articles/forkgen-anyone-can-now-create-their-own-bitcoin-fork-even-us/
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10:33 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=8fcf632c Bryan Bishop: transcript: block propagation >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-11-27-advances-in-block-propagation/
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11:15 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=
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11:48 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f848a2b3 Bryan Bishop: fix up transcript, add links >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-11-27-advances-in-block-propagation/
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11:53 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=51de0092 Bryan Bishop: add tweeter link >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-11-27-advances-in-block-propagation/
12:44 < CaptHindsight> kanzure: what's the base pair to bit ratio in the DNA for data storage you had mentioned? 100:1 or higher?
12:53 <@kanzure> depends on your technique .... but i'm looking at something that might do 1 bit per 100 bp.
12:53 <@kanzure> possible to do much better, again it all depends on technique
12:54 < CaptHindsight> thanks
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13:31 < abetusk> https://bioinformatics.stackexchange.com/questions/1/whats-the-most-efficient-format-to-store-dna-sequence
13:32 <@kanzure> sort of strange not to see charts comparing the efficiencies heh
13:33 < abetusk> It's not clear what the theoretical lower bound is for humans but I think it's in the range of 1 bit per 500-1k bp
13:35 <@kanzure> CaptHindsight was asking about something else actually (encoding data into DNA molecules)
13:36 <@kanzure> and i would disagree with your assessment of 1 bit per 1k bp for storage of DNA data on a computer! with VCF you can exclude entire chromosomes if the chromosomes happen to be identical.
13:38 < abetusk> ah, sorry, didn't read too far ahead.  In terms of your VCF statement, while theoretically true in practice that's rare.  The data storage requirements for human dna is an empirical question on how much variation there is in the population.
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13:53 < MrHindsight> abetusk: was just asking about his bp : bit
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14:21 < CaptHindsight> https://phys.org/news/2017-12-dna-bricks-enable-self-assembly-d.html
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14:58 <@kanzure> .title
14:58 < yoleaux> kanzure: Sorry, that doesn't appear to be an HTML page.
15:02 < Hooloovo0> <!DOCTYPE html>
15:02 < Hooloovo0> pls
15:03 <@fenn> don't be racist
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16:53 <@kanzure> what happened to halcyon's high speed electron microscopes? did they happen?
16:56 <@kanzure> dna nanoscopy + a billion nanopores instead of electron microscopes?
17:00 <@kanzure> so can electron beams be faster than a billion nanopores with dna nanoscopy?
17:02 <@kanzure> yeah nanopores are going to be higher throughput... because it's a bulk chemistry reaction, not raster scanning with an electron beam.
17:02 <@kanzure> (or multiple electron beams even)
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17:26 <@kanzure> i remember looking at the math for this and i was quickly looking at numbers like 10^20 and 10^23 or something, which wasn't very encouraging....
17:27 <@kanzure> "The team also calculated the planet's equivalent of computing power: the speed of DNA transcription. Given the average rate of genetic transcription for different organismal groups, they found that the biosphere processes more than 10^24 subunits of DNA per second."
17:27 <@kanzure> 22:04 < kanzure> so 40% of 10^27 cells are getting killed by viruses in the ocean every day
17:28 <@kanzure> http://gnusha.org/logs/2017-09-25.log
17:28 <@kanzure> .tw https://twitter.com/kanzure/status/912360801444524038
17:28 < yoleaux> @wyssinstitute @AdamMarblestone i wonder if this could be used for connectome sequencing. Synapses are large gaps, might need connecting objects? (@kanzure, in reply to tw:912303082356269056)
17:28 <@kanzure> .tw https://twitter.com/kanzure/status/912362153004453888
17:28 < yoleaux> @wyssinstitute @AdamMarblestone Also sounds like this has the potential to detect receptors embedded in neuronal membranes.Gets put into giant graph of barcoded objects. (@kanzure, in reply to tw:912360801444524038)
17:29 <@kanzure> 10:21 < kanzure> how many barcodes would you need to label every item of interest in the brain? you need at least the number of neurons, synapses, and receptors.
17:29 <@kanzure> 10:26 < kanzure> so say 100 trillion synapses, and 1 million receptors per synapse (which is probably a low estimate?), is 1e20 objects, so at minimum you'd need 34 bp barcodes? let's say 36 bp to be safe. so that would require 4^36 unique dna barcode molecules. about 1e21 custom dna molecules.
17:31 <@kanzure> if the entire biosphere is processing 10^24 bp/sec and for brain uploading we need like 10^22 dna molecules.. ehh.   i guess the biosphere was never optimized for dna processing throughput, it might be feasible to outcompete the entire performance of the biosphere on dna processing metric.
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17:57 <@kanzure> there's like 10^20something *features* in the brain that we want to detect, map and store
17:58 <@kanzure> and then you hvae to calculate with the total surface area of the brain-- including synapses, neuron membranes, etc.
17:58 <@kanzure> this site seems to say typical surface area of a typical neuron is 2000 mm^2 http://bionumbers.hms.harvard.edu/bionumber.aspx?id=110856&ver=0
17:59 <@kanzure> so about 200 km^2 for an entire human brain
17:59 <@kanzure> assuming 100 billion neurons
18:04 <@kanzure> and then you need good coverage over the entire surface area... and then you need to store the data somehow.   you can discard most of the data (since you don't need the full shape of every single neuron), and you might even be able to discard a lot of the data as you go since once you're done with one 3d chunk of brain matter you don't need to keep the exact neuronal surface forever ...
18:05 <@kanzure> ...especially if you have already seen the totality of the neuron.
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18:38 < winsoff> kanzure, what's the legality of dna manipulation in the US?
18:40 <@kanzure> you can do whatever you want, but certain research projects are frowned upon, and you can't sell products because a lot of gene therapy is regulated by the fda
18:42 < winsoff> Ah, okay. Also, I have wanted to try DIY tissue culture for plants--is there any crossover in equipment? I've been wondering how to make a "clean box" or a laminar flow hood at home.
18:45 <@kanzure> yeah it's all the same equipment
18:47 < winsoff> Are there any confirmed-good guides out there that you can recommend? I'm supremely novice.
18:47 < winsoff> Also, what is your typical typing speed when freehand?
18:48 < winsoff> Additionally, on this page: http://diyhpl.us/wiki/genetic-modifications/ I see a lot of individual statements, though I wonder: Are there any studies that verify that these are the only things these genes do, or is it just relational?
18:51 <@kanzure> there's some stuff here http://diyhpl.us/wiki/diybio/faq
18:52 <@kanzure> my typing speed is maybe 160 wpm sometimes 200 wpm http://www.seanwrona.com/typeracer/profile.php?username=kanzure
18:55 < winsoff> Nice. Do you read with a voice in your head?
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19:12 <@kanzure> i can speak in my head if that's what you mean
19:12 < winsoff> Right, but do you, typically, when reading? What about when typing?
19:13 <@kanzure> usually it's a voice outide of my head when typing http://diyhpl.us/wiki/transcripts
19:14 < winsoff> lol
19:14 < winsoff> Good point.
19:14 <@kanzure> biological co-processors startup thing http://koniku.com/
19:16 < winsoff> Are neurons really that effective? Couldn't we make better systems?
19:17 <@kanzure> well we haven't made anything better than a human brain yet... so.
19:17 < winsoff> Also, why the obsession with bitcoin?
19:17 <@kanzure> it's funding my expensive hobbies http://diyhpl.us/wiki/hplusroadmap
19:17 < winsoff> What happens on crash?
19:18 <@kanzure> you mean like a segmentation fault?
19:18 < winsoff> Sorry; when bitcoin crashes, that is.
19:18 <@kanzure> it goes up, it goes down, just like any other asset ever... that' not a property unique to bitcoin.
19:19 <@kanzure> meanwhile: "(There are exotic single-nanopore proposals by which you could sequence ~10 million bases/second/nanopore, but those are potentially more like multibillion dollar projects with physical unknowns...)"
19:21 < winsoff> Right, but bitcoin's volatility is unique, comparatively, right? Also, are all current sequencing methods done on non-living, extracted tissue?
19:29 <@kanzure> "The pattern of heavy atoms in organometallic aptamers could enable huge EM-based multiuplxing for receptor ID. ed was into this concept."
19:30 <@kanzure> winsoff: thanfully there are ways to handle volatility, such as options, and thankfully i work for the only regulated bitcoin options exchange
19:30 < winsoff> kanzure, did you have a hand in choosing the name?
19:31 <@kanzure> hm?
19:31 < winsoff> The name of LedgerX (I'm assuming that's the bitcoin options exchange)
19:32 <@kanzure> you are quite inquisitive for someone that merely wanted to challenge me to a typing race :-)
19:33 < winsoff> Biological stuff is always interesting, and I had no idea you existed until recently. Public personalities are always interesting.
19:55 <@kanzure> nmz787: i think focused ion beam milling of neurons + electron microscopy imaging of tissue slices might turn out to be higher performance than my dna geometry imaging brain uploading technique
19:55 <@kanzure> well, wait, can you really ablate specifically only 1 nm from the surface of a neuron?
20:26 <@kanzure> alright well maybe we really need just a fleet of like a few million electron microscopes
20:27 <@kanzure> halcyon molecular was calculating about one electron microscope for a year to do an entire human brain
20:29 < winsoff> What's the eventual point of the digitization of the entire brain?
20:31 <@kanzure> biology is unreliable and not appropriate for our long-term plans
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20:32 < winsoff> Ah, okay; I thought so. So in that case, why do we need to digitize the brain, when it's mostly for dealing with systems unnecessary in cyberspace?
20:33 <@kanzure> some people are really attached to their brain stuff (like memories)
20:34 <@kanzure> .title https://news.ycombinator.com/item?id=15997196
20:34 < yoleaux> Papercraft with Blender | Hacker News
20:36 < winsoff> kanzure, surely, but we can keep memories and drop the corpus callosum, for example. the duality of the brain's structure is not necessary, either, right?
20:37 <@kanzure> rough order of magnitude of the problem is still the same even if you drop the corpus callosum and auditory cortex and other boring stuff
20:37 < winsoff> Have you noticed that the typical yuppies from ycombinator/hackernews often have no idea of the industries they think tech can revolutionize?
20:37 < winsoff> Interesting, though.
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20:39 <@kanzure> "A DNA nanoscope via auto-cycling proximity recording" https://www.nature.com/articles/s41467-017-00542-3
20:40 <@kanzure> "Programmable autonomous synthesis of single-stranded DNA" https://yin.hms.harvard.edu/publications/2017.per.pdf
20:41 <@kanzure> "Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT" https://www.nature.com/articles/s41467-017-02028-8
20:42 <@kanzure> .wik epitope mapping
20:42 < yoleaux> "Epitope mapping is the process of experimentally identifying the binding sites, or 'epitopes', of antibodies on their target antigens. Identification and characterization of the binding sites of antibodies can aid in the discovery and development of new therapeutics, vaccines, and diagnostics." — https://en.wikipedia.org/wiki/Epitope_mapping
20:58 <@kanzure> i wonder if halcyon molecular soured all the investor on electron microcopy
20:58 <@kanzure> *microscopy
21:18 <@kanzure> i bet we could do directed evolution on dna nanopore sequencing (e.g. evolved proteins for higher performance and fidelity)
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23:01 < superkuh> It's impressive that scribd manages to be worse every year.
23:32 <@fenn> you don't need to synthesize custom dna oligos just for making random barcode labels
23:32 <@fenn> the immune system does it all the time when constructing antibodies
23:32 <@fenn> https://en.wikipedia.org/wiki/V(D)J_recombination
--- Log closed Sun Dec 24 00:00:52 2017