--- Log opened Thu Mar 24 00:00:08 2016
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04:54 < mcleodx> Is anyone there??
04:56 < archels> yes, hello
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04:57 < mcleodx> Hi Archels, this is the first time I've used IRC, just checking I'd connected properly
04:58 < archels> everything seems to be working
04:58 < archels> what client are you using?
04:58 < mcleodx> Good News, Freenode
04:58 < archels> no, that's the IRC network that you are connected to
04:58 < mcleodx> Oh the client, Limechat
04:58 < mcleodx> IOS
04:58 < archels> alright, I don't know it
04:59 < archels> logs for this channel are in the topic by the way—if you were to use a shell account to connect you would always get backlogs of past conversation
04:59 < mcleodx> No worries seems good.
05:00 < archels> kanzure: what did you mean by this? < kanzure> it doesn't make sense to directly work with your main processes
05:01 < mcleodx> @archels I'd actually been directed here from a guy in a slack.com group for Transhumanism chat
05:03 < mcleodx> I was looking for a group that are a bit more pragmatic in their approach to h+
05:03 < mcleodx> There's a lot of chat that happens there which is very random/trivial
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06:32 < kanzure> http://techcrunch.com/2016/03/23/y-combinator-winter-2016/
06:32 < kanzure> "low-cost android devices for industrial equipment"
06:34 < kanzure> opentrons..
06:34 < kanzure> "histowiz - send tissue by mail and then view microscopy results online"
06:36 < kanzure> i don't understand why "loop genomics" has a deal with twist biosciences
06:36 < kanzure> osvehicle..
06:37 < kanzure> "iron ox - robotic greenhouses"
06:42 < kanzure> "lygos - yeast making industrial chemicals" wasn't there another ycombinator startup doing this...
06:49 < kanzure> alright well that was a waste of time
06:49 < kanzure> "mov is Turing-complete" http://www.cl.cam.ac.uk/~sd601/papers/mov.pdf
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08:54 < kanzure> archels: i mean that if you were a working software emulation of human brain matter, there's no reason to have a "single threaded" persona that is interacting with virtual environments. "location" isn't an entirely relevant concept (although caching and load times and processing times are relevant concepts).
08:56 < archels> you're always going to be interacting with *some* simulated environment
08:56 < archels> I don't think it's such a clear-cut case
08:57 < archels> if I'm Bob's mindclone from 2 minutes ago, having solved some problem and having committed my results, maybe I wouldn't like to be terminated
08:58 < kanzure> right, so about that.... "mindclones" are going to be computationally infeasible due to resource requirements at first. i mean, we are still taking multiple days to run simulations of a few microseconds of neural firing.
08:58 < kanzure> all of this is going to be extremely resource constrained
08:59 < kanzure> i also suspect there will be lots of competition for computing resources, probably going to the highest payers
09:00 < kanzure> oops i shouldn't say "computationally infeasible" i should say "economically infeasible"
09:02 < kanzure> even with continued reductions in computing prices, i think that there is almost always going to be high demand to run certain more economically profitable algorithms.
09:02 < kanzure> i'm not entirely convinced that people are going to spin up entire auditory cortex simulations to appreciate millions of hours of robo-mozart or whatever.
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09:34 < maaku> kanzure: while you speak the truth, it is a hard sell. what do we appreciate in mozart in the first place? other than abstract respect, the enjoyment itself is a result of our inefficient, bizarre sensory apparatus
09:36 < maaku> we'll have to emulate those sense to appreciate historical human works of art, or to engage in the still-living subculture of retro art
09:36 < maaku> but i'm sure that most people and artists wlil have moved on to using and appreciating less wasteful senses
09:37 < maaku> people will see that as losing humanity though, hence the hard sell
09:39 < maaku> kanzure: also I 100% support and encourage the MIT media lab harassment plan
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09:45 < kanzure> maaku: they invited me under the pretense of bitcoin stuff but they seem OK with me using the opportunity to let fenn harass neil gershenfeld and ed boyden and the other nutjobs there
09:45 < nmz787_i> is there a artificial general intelligence thing on the internet that I could ask something like: what is a unique descriptive word for each of the following wordlists [ohm, farad, volt] [kilo, mega, pico, nano]
09:45 < kanzure> uh... wordnet? but it's not agi.
09:45 < nmz787_i> (I called the former scientific units, the latter SI units... but I'm not sure that's right)
09:47 < nmz787_i> how does wordnet work?
09:47 < nmz787_i> I searched kilo and it gave some uninteresting result
09:48 < nmz787_i> oh, wrong search page
09:48 < kanzure> wordnet works by converting thousands of hours of grad student life force into finely grinded pellets of language knowledge for general consumption
09:48 < maaku> nmz787_i: google had something similar http://googlesystem.blogspot.com/2011/08/google-sets-will-be-shut-down.html
09:48 < maaku> that's not an agi problem
09:51 < archels> kanzure: I'm really glad to hear you say that, everyone seems to think that resources (and in particular, computation) will just come for free
09:51 < kanzure> perhaps if emulation algorithm stuff turns out to be costless to implement....... but i see no evidence to believe tihs.
09:51 < kanzure> *to run
09:52 < maaku> kanzure: it would be much less costly with quantum computaiton
09:53 < archels> apparently if you're running on a reversible computer, you cost almost no power to run
09:53 < maaku> archels: as long as you're not doing anything interesting
09:55 < archels> aren't reversible computers Turing complete though?
09:55 < maaku> opentrons demoed at YC yesterday http://opentrons.com/
09:56 < archels> https://www.weizmann.ac.il/complex/tlusty/courses/InfoInBio/Papers/Bennett1973.pdf
09:56 < archels> "The biosynthesis of messenger RNA is discussed as a physical example of reversible computation."
09:57 < maaku> archels: memory isn't infintie. if you're doing anything adaptive or responsive to different environments then you need to be doing memory erasure, which is not reversible
09:57 < archels> it might tradeoff storage complexity for reversibility though
09:57 < archels> .title http://opentrons.com/
09:58 < archels> right
09:58 < yoleaux> archels: Sorry, that command (.title) crashed.
09:58 < maaku> it's a $3k liquid handler
09:58 < maaku> great for doing your own micro-transcriptic
09:58 < kanzure> yep they have been around for a while now... delinquentme did his own version a few years ago.
09:59 < kanzure> and before that, jcline did some silly reverse engineering work to get some tecan equipment to work
09:59 < kanzure> actually you guys might have used jcline's work if it hadn't been perl (it was perl)
10:04 < maaku> also loop genomics : http://www.loopgenomics.com/
10:04 < maaku> and boom, albeit a little OT : http://boom.aero/
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10:05 < maaku> it's insane how big the YC batches have become
10:08 < nmz787_i> ..title https://nar.oxfordjournals.org/content/36/17/e107.full
10:08 < nmz787_i> .title https://nar.oxfordjournals.org/content/36/17/e107.full
10:08 < yoleaux> De novo DNA synthesis using single molecule PCR
10:08 < nmz787_i> .title
10:08 < yoleaux> De novo DNA synthesis using single molecule PCR
10:08 < nmz787_i> sorry
10:10 < nmz787_i> kanzure: have you heard of that? I can't quote tell much from the abstract other than something about recursion
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10:59 < kanzure> nmz787_i: there's no way that "cloning and sequencing" is the bottleneck of dna synthesis :)
11:00 < kanzure> anyway, having an alternative to yeast-based cloning is nice
11:00 < kanzure> "Divide and Conquer (D&C), the quintessential recursive problem solving technique, is used in silico to divide the target DNA sequence to be constructed into fragments short enough to be synthesized by conventional oligo synthesis, albeit with errors (15); these oligos are synthesized and are recursively combined in vitro, forming target DNA molecules with roughly the same error rate as the source oligos; error-free parts of these ...
11:01 < kanzure> ... molecules identified by cloning and sequencing are extracted and used as new, typically longer and more accurate inputs to another iteration of the recursive synthesis procedure"
11:01 < kanzure> so... they are just using traditional oligonucleotide synthesis. yawn.
11:01 < kanzure> i'm not convinced that biologists know what a bottleneck is supposed to be :)
11:13 < nmz787_i> ah, hmm, thanks... when the abstract didn't sound interesting, and scanning briefly didn't yield anything seemingly interesting... I had my doubts there was anything interesting there
11:13 < nmz787_i> (especially because I am thinking about coding stuff at the moment)
11:14 < kanzure> nmz787_i: here, have some coding music https://www.youtube.com/watch?v=ddtkszic4II&t=4m30s
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14:23 < maaku> .title http://www.nature.com/news/minimal-cell-raises-stakes-in-race-to-harness-synthetic-life-1.19633
14:23 < yoleaux> ‘Minimal’ cell raises stakes in race to harness synthetic life : Nature News & Comment
14:24 < maaku> someone leak that genome plz
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14:30 < kanzure> "Design and synthesis of a minimal bacterial genome" http://science.sciencemag.org/content/sci/351/6280/aad6253.full.pdf (2016)
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14:59 < nmz787_i> hmm, so the small cells are about 200nm diameter... so 100nm radius... plugging that into volume of sphere, I get 4.19 million cubic nanometers
14:59 < nmz787_i> so 473 genes, that's 8858 nm^3 per gene
14:59 < nmz787_i> which isn't really that useful
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15:00 < kanzure> easy to select for cells with larger cell membrane volume
15:01 < nmz787_i> i guess you could start peel a nanometer or two from the cell diameter, if you assume the membrane is 1nm thick
15:01 < kanzure> and it is plausible that minor amounts of mutation over 473 genes can cause larger cell bodies to be constructed
15:01 < kanzure> oh you wanted smaller?
15:02 < nmz787_i> well just thinking about how many molecules would be inside
15:02 < nmz787_i> how many would be non-water
15:02 < nmz787_i> what would the crowding be like... but I guess we'd need to know relative expression numbers or something
15:02 < nmz787_i> or an image of a dessicated cell.. to at least know the water factor
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17:04 < kanzure> http://www.viruscomix.com/page588.html
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17:22 < archels> grm, neuromorpho has so many entries now that their site freezes my browser
17:23 < kanzure> it's well known that browsers are the cause of the fermi paradox / fermi silence, any sufficiently stupid civilization to invent web browsers all suffer the same fate
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17:50 < fenn> i'm surprised nobody's doing semiballistic passenger glide-rockets
17:51 < fenn> i guess rocketry knowhow isn't widespread enough
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18:16 < fenn> i applied to the MIT media lab for grad school in 2011 but they only accept 10 applicants out of 300 so i didn't get in
18:16 < fenn> how is a "residency" different?
18:17 < fenn> they probably only want you because so few people understand bitcoin at all
18:18 < fenn> i don't see how bitcoin fits in really
18:18 < kanzure> mit digital currency initiative is joi ito
18:18 < kanzure> and media lab is joi ito
18:19 < kanzure> therefore, secret backdoor
18:19 < kanzure> tell me, how quickly can you say "merkle tree"?
18:19 < kanzure> and can you say it in a pretentious german accent or anything special
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18:22 < kanzure> the near-term MIT media lab trip is not their residency thingy, it's something slightly lighter- like a one or two week forced comingling
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18:26 < kanzure> lots of potential victims:
18:26 < kanzure> http://www.media.mit.edu/people/visiting
18:26 < kanzure> http://www.media.mit.edu/people/faculty
18:26 < kanzure> http://www.media.mit.edu/people/staff
18:27 < kanzure> http://www.media.mit.edu/people/students
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18:39 < kanzure> .tw https://twitter.com/AdamMarblestone/status/712875209762676736
18:39 < yoleaux> Looking for a research scientist candidate to barcode the connectome at MIT: http://www.media.mit.edu/about/opportunities/research-scientist-neuronal-barcoding-connectomics cc @eboyden3 (@AdamMarblestone)
18:41 < kanzure> "Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications" http://www.nature.com/articles/srep22691
18:41 < kanzure> "Assembly and operation of the autopatcher for automated intracellular neural recording in vivo" http://www.nature.com/nprot/journal/v11/n4/full/nprot.2016.007.html
18:42 < kanzure> "Whole-cell patch clamping in vivo is an important neuroscience technique that uniquely provides access to both suprathreshold spiking and subthreshold synaptic events of single neurons in the brain. This article describes how to set up and use the autopatcher, which is a robot for automatically obtaining high-yield and high-quality whole-cell patch clamp recordings in vivo. By following this protocol, a functional experimental rig for ...
18:42 < kanzure> ... automated whole-cell patch clamping can be set up in 1 week. High-quality surgical preparation of mice takes ~1 h, and each autopatching experiment can be carried out over periods lasting several hours. Autopatching should enable in vivo intracellular investigations to be accessible by a substantial number of neuroscience laboratories, and it enables labs that are already doing in vivo patch clamping to scale up their efforts by ...
18:42 < kanzure> ... reducing training time for new lab members and increasing experimental durations by handling mentally intensive tasks automatically."
18:42 < kanzure> "Functional and topological diversity of LOV domain photoreceptors" http://www.pnas.org/content/113/11/E1442.abstract
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18:52 < kanzure> "A Whole-Cell Computational Model Predicts Phenotype from Genotype" http://www.cell.com/abstract/S0092-8674(12)00776-3
18:53 < kanzure> "Reconstruction of Natural Scenes from Ensemble Responses in the Lateral Geniculate Nucleus" http://www.jneurosci.org/content/19/18/8036.long (yes i know this is cliche by now)
18:53 < kanzure> also, i support the trend of microscopy techniques getting their own marketing sites http://expansionmicroscopy.org/
18:53 < kanzure> http://expansionmicroscopy.org/Materials_ListV1.3.xlsx
18:54 < kanzure> http://expansionmicroscopy.org/ExM_Cultured_Cell_ProtocolV1.4.docx
18:54 < kanzure> http://expansionmicroscopy.org/ExM_Slice_ProtocolV1.4.docx
18:54 < kanzure> http://expansionmicroscopy.org/DNA-Antibody_Conjugation_ProtocolV1.2.docx
18:56 < kanzure> "... Arigos Biomedical, a firm working on high-pressure vitrification. New firms abound: Tissue Testing Technologies is working on ways of warming organs uniformly; Sylvatica Biotech is perfecting recipes for cryoprotectants; X-therma is attempting to mimic cryoprotective proteins."
18:56 < kanzure> from http://www.economist.com/news/science-and-technology/21690025-after-decades-piecemeal-progress-science-cryogenically-storing-human
18:57 < kanzure> fruit fly brain image scans for connectomics algorithm development reasons https://github.com/BigNeuron/Data/releases/tag/data_v1.0_first2000
18:57 < kanzure> which is data from this paper apparently? "Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution" (2011? but why was this data posted last month?) http://www.cell.com/current-biology/abstract/S0960-9822(10)01522-8
18:58 < kanzure> above data set is from http://alleninstitute.org/bigneuron/about/
18:58 < kanzure> that is a cool thing.
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19:11 < kanzure> "Real time selective sequencing using nanopore technology" (2016) http://biorxiv.org/content/biorxiv/early/2016/02/03/038760.full.pdf
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19:13 < kanzure> "Coordinated activation of distinct Ca2+ sources and metabotropic glutamate receptors encodes Hebbian synaptic plasticity" http://www.nature.com/ncomms/2016/160113/ncomms10289/full/ncomms10289.html
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19:16 < kanzure> "Nanoscale Architecture of the Axon Initial Segment Reveals an Organized and Robust Scaffold" http://www.cell.com/cell-reports/abstract/S2211-1247(15)01382-0
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19:19 < kanzure> "Generating Sentences from a Continuous Space" http://arxiv.org/abs/1511.06349
19:19 < kanzure> "The standard unsupervised recurrent neural network language model (RNNLM) generates sentences one word at a time and does not work from an explicit global distributed sentence representation. In this work, we present an RNN-based variational autoencoder language model that incorporates distributed latent representations of entire sentences. This factorization allows it to explicitly model holistic properties of sentences such as style, ...
19:19 < kanzure> ... topic, and high-level syntactic features. Samples from the prior over these sentence representations remarkably produce diverse and well-formed sentences through simple deterministic decoding. By examining paths through this latent space, we are able to generate coherent novel sentences that interpolate between known sentences. We present techniques for solving the difficult learning problem presented by this model, demonstrate ...
19:19 < kanzure> ... strong performance in the imputation of missing tokens, and explore many interesting properties of the latent sentence space."
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19:28 < kanzure> (music) https://www.youtube.com/watch?v=QmEvB2BVnYc&t=45s
19:32 < fenn> "Expansion Microscopy (ExM) is a sample preparation tool for biological samples that allows investigators to identify small structures by expanding them using a polymer system.[1] The premise is to introduce a polymer network into cellular or tissue samples, and then physically expand that polymer network using chemical reactions to increase the size of the biological structures."
19:33 < fenn> like those tiny gel dinosaurs
19:34 < kanzure> in a video somewhere on youtube, ed boyden was mentioning the idea might have originated from diapers? or he was just making an analogy.
19:34 < kanzure> but seeing as how he is a recent father i'm pretty sure his inspiration was diapers
19:35 < fenn> diapers contain sodium polymethacrylate granules to absorb the pee
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19:50 < kanzure> http://questionablecontent.net/view.php?comic=3183
19:50 < kanzure> http://questionablecontent.net/view.php?comic=3184
19:58 < kanzure> "While we're talking about the Google Cloud Vision API I'll take the opportunity to plug the Chrome extension I wrote that adds a right-click menu item to detect text, labels and faces in images in your browser: https://chrome.google.com/webstore/detail/cloud-vision/nblmokgbialjjgfhfofbgfcghhbkejac " https://cloud.google.com/vision/ https://news.ycombinator.com/item?id=11354454
20:03 < fenn> "In nature, the optimum is almost always in the middle somewhere. Distrust assertions that the optimum is at an extreme point."  i wonder how well this holds up in practice
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20:21 < fenn> echo bind ^F whereis main >> ~/.nanorc
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23:07 < fenn> fourfire i think the trick is disguising your helmet as a hat
23:08 < fenn> you could put an oversized baseball cap on the top part and then cover the bottom with shaggy hair, then it will just look like you have a huge fluffy mullet
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23:46 < maaku> I think a bad ass motorcycle helmet would be more fashionable than a fluffy mullet
--- Log closed Fri Mar 25 00:00:09 2016