| --- Log opened Thu Dec 31 00:00:51 2015 | ||
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| archels | Everything you do, you do by standing on the shoulders of giants. Or a big pile of dwarves, it works either way. | 03:16 |
|---|---|---|
| archels | (via Joscha Bach) | 03:16 |
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| archels | .g International Journal of Synthetic Emotions | 03:21 |
| yoleaux | http://www.igi-global.com/journal/international-journal-synthetic-emotions-ijse/1144 | 03:21 |
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| maaku | that's an interesting journal | 04:06 |
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| chris_99 | http://observer.com/2015/06/artificially-intelligent-computer-outperforms-humans-on-iq-test/ | 05:57 |
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| kanzure | "Monopropellant powered linear pneumatic actuators" http://www.vanderbilt.edu/dces/PDF/papers/conference/ICRA02_monoprop%20powered%20actuators.pdf (2002) | 06:38 |
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| kanzure | .title http://smackerelofopinion.blogspot.com/2015/12/incorporating-and-accesses-binary-data.html | 07:08 |
| yoleaux | A Smackerel of Opinion: Incorporating and accessing binary data into a C program | 07:08 |
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| kanzure | apparently we did not have any video of living 12-feet-long giant squid? http://www.nytimes.com/2015/12/30/science/giant-squid-video-japan.html | 07:12 |
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| xentrac | no, only sperm whales brought them to us | 07:23 |
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| kanzure | they brought them to us? | 07:39 |
| maaku | little gifts on the doorstep, like the cat bringing in a dead mouse | 07:40 |
| maaku | no seriously they hunt giant squid, and sometimes the carcases wash up on shore | 07:40 |
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| kanzure | if they start purring that's when you know | 07:42 |
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| xentrac | well, they didn't know it was to us that they were bringing them | 07:42 |
| xentrac | that part was a surprise! | 07:42 |
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| kanzure | "Solving verbal comprehension questions in IQ tests by knowledge-powered word embedding" http://arxiv.org/pdf/1505.07909.pdf (using word2vec stuff) | 08:06 |
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| TMA | kanzure: if former czechoslovakia is any indication, the plans were not public in their entirety. sure there was Law of the Czech National Council about State Plan for Development of the National Economy of the Czech Socialist Republic for the years 1986 - 1990 (Law about the Five-year Plan)" but it is just a summary with blanket powers to the government | 09:12 |
| TMA | kanzure: http://www.zakonyprolidi.cz/cs/1986-87 this is the text | 09:12 |
| TMA | kanzure: the first five year plan law in czechoslovakia: http://www.zakonyprolidi.cz/cs/1948-241 | 09:14 |
| TMA | google translation is surprisingly usable for these | 09:17 |
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| TMA | kanzure: the equivalent soviet laws were even translated into the czech language http://www.worldcat.org/title/zakon-o-petiletem-planu-obnovy-a-rozvoje-narodniho-hospodarstvi-sssr-na-leta-1946-50/oclc/85438006 | 09:21 |
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| TMA | 86 pages - it too is not detailed | 09:23 |
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| kanzure | http://neurolex.org/wiki/Main_Page | 09:36 |
| kanzure | https://github.com/SciCrunch/NIF-Ontology/blob/master/BiomaterialEntities/NIF-Neuron-BrainRegion-Bridge.owl | 09:36 |
| kanzure | https://confluence.crbs.ucsd.edu/display/NIF/Download+NIF+Ontologies | 09:36 |
| kanzure | ontology apocalypse so soon? | 09:37 |
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| kanzure | "We present the hypothesis that cognition is fundamentally controlled via the TL1 thalamocor tical projection system. We hypothesize all thalamocortical layer 1 projections have a similar functional role in cognitive control through the activation of cortical modules to drive cortico- thalamocortical information processing and working memory. While the VAmc/VM nuclei might be considered ’centralized control’, the matrix layer 1 ... | 09:41 |
| kanzure | ... projections from other distributed thala mic locations might be considered ’local feedback control’." | 09:42 |
| kanzure | "By analogy, if alpha motor neurons activate individual muscles and TL1 projections activate individual cortical modules, then the TL1 projecting neurons might be considered ’alpha motor neurons of thought’. If a cortical region like Brodmann’s area 8 or 9 targets this region with cortico-thalamocortical C6t projections then that region might be considered ’primary thought cortex’. Human lesion studies to these areas resulting ... | 09:42 |
| kanzure | ... in the elimination of voluntary cogni- tive processes are consistent with this hypothesis (e.g. patient M.F.)(Penfield & Rasmussen, 1968). Multiple experiments could be created to test this hypothesis in the primate, all be- ginning with first locating the exact thalamic region capable of exciting diffuse surface wave potentials described by Hanbery and Jasper(Hanbery & Jasper, 1953)." | 09:42 |
| kanzure | "Similar to the basal ganglia the cerebellum receives excitatory input and outputs a GABAergic inhibitory projections. Although the Dcn introduce one additional nuclei between the cerebellum and the thalamus, we emphasize that the cerebellum and the basal ganglia operate on the principle of disinhibition. Disinhibition appears to be the general principle of control input to the thalamus. Direct disinhibition of the intralaminar thalamus ... | 09:43 |
| kanzure | ... by the basal ganglia and disinhibition of excitatory input to the ventral thalamus by the cerebellum. A release from inhibition may form a fast precise method of temporal triggering, through rebound spikes, without the concern for ongoing excitation. Notably, the cerebellum does not project to the intralaminar thalamus, therefore the cerebellum may have two control triggering functions: 1) aiding in the selection of motor and ... | 09:43 |
| kanzure | ... cognitive perception representations through Ts layer 3b ventral thalamocortical projections and 2) coordinating the activation of cortical modules through TL1 projections." | 09:43 |
| kanzure | disappointed that he would bring up "perceptions" there. | 09:44 |
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| kanzure | i have backed up his interactive visualization thingy http://www.frontiersin.org/files/cognitiveconsilience/index.html at http://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/ | 09:46 |
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| kanzure | "Many specialists for suppressing cortical excitation" http://journal.frontiersin.org/article/10.3389/neuro.01.026.2008/full | 09:53 |
| kanzure | "Computational models of basal-ganglia pathway functions: focus on functional neuroanatomy" http://journal.frontiersin.org/article/10.3389/fnsys.2013.00122/full | 09:54 |
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| kanzure | "The field of neuroanatomy is still in its infancy, the modern form beginning just over 100 years ago. Although modern technology has introduced novel experimental methods, huge gaps exist in our neuroanatomical knowledge for unexplained reasons. The last comprehensive Golgi staining assessment of a complete brain was published in 1899–1904 (Cajal, 2002). The last comprehensive histological Nissl staining study of a human brain was ... | 10:00 |
| kanzure | ... published in 1929 (von Economo, 1929). While these works were seminal and have lasted the test of time, the study by von Economo involves roughly 100 photographs of the human brain. Why not advance our understanding by redoing Cajal’s seminal work or redoing von Economo’s complete brain histology with twenty-first century capabilities?" | 10:00 |
| kanzure | wat? you mean nobody bothered to do a review with anything more than 100 photographs? | 10:00 |
| xentrac | that does seem quite strange. what do you suppose happens to the brains that people "donate to science"? | 10:08 |
| xentrac | maybe they get dissected in medical schools to train medical students? | 10:08 |
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| kanzure | xentrac: and many get preserved in formaldehyde... i'm sure they get measured in various ways, but i'm also confident that it's unlikely that every person who sits down to measure some property of a formaldehyde-preserved brain is going to think "hmm i should document all of the major pathways". | 10:12 |
| kanzure | or, more a more interesting fialure mode is whatever fenn was thinking- "there's no way any of this is going to be valuable without high-resolution connectomics-related scanning results". | 10:15 |
| kanzure | *failure mode | 10:15 |
| kanzure | hmm maybe i should go convince this guy to document the differences between human and other mammals. many of these circuits are preserved across species but not all. | 10:16 |
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| xentrac | you can probably get pig, cow, and dog brains several orders of magnitude cheaper than human brains | 10:29 |
| xentrac | especially if you speak Spanish on the cow brains | 10:29 |
| xentrac | do you know how to do Golgi and Nissl stains? | 10:29 |
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| kanzure | golgi staining is performed in high school and undergrad classes afaik | 10:34 |
| xentrac | I don't imagine that either of them are that difficult in an absolute sense. i was just trying to gauge how practical it would be for you to go a few blocks to your local Mexican grocery store, bring home a cow brain, slice it up, and start in on the photomicrographs with Golgi stains | 10:37 |
| xentrac | like, whether that would represent an hour, ten hours, a hundred hours, or a thousand hours for you to do | 10:39 |
| xentrac | if that was a thing that you thought would be valuable | 10:39 |
| kanzure | my microscope is not that good :-) | 10:39 |
| xentrac | basically because if you think it would be valuable it would be a shame if you didn't do it just because you didn't realize you had a ready supply of freshly killed brains | 10:40 |
| kanzure | wait, i have no idea if my microscope is better than the one von economo had. | 10:40 |
| xentrac | yeah, that's what I was thinking ;) | 10:40 |
| kanzure | well, i definitely can't slice at 50 nm thickness with the tools i have at the moment. | 10:40 |
| kanzure | or whatever it is that 3scan is doing | 10:40 |
| xentrac | what is 3scan doing? | 10:42 |
| kanzure | 50nm thickness slicing of brains, for scanning | 10:42 |
| kanzure | http://3scan.com/ | 10:42 |
| xentrac | ah, as a service to hospital pathology departments | 10:43 |
| xentrac | and not just brains; any tissue | 10:43 |
| kanzure | "Our technology really shines in applications requiring high throughput of large volume samples. The new KESM can process up to 3,600 slices per hour of any tissue sample (e.g. a whole mouse brain) at submicron resolution (a voxel size of 0.6 um x 0.7 um x 1.0 um). This vastly outweighs the depth offered by confocal or 2-photon microscopy and outperforms the resolution capabilities of other tools such as micro-CT. To handle ... | 10:43 |
| kanzure | ... high-resolution outputs of up to a terabyte per cm3, 3Scan offers data processing software to model 3D tissue reconstructions, provide interactive image views, and apply quantitative analytics." | 10:44 |
| xentrac | but not yet | 10:44 |
| xentrac | sounds promising. you could wait and hope that they do what you need done with no effort on your part | 10:44 |
| kanzure | what precisely do i need done? :-) | 10:44 |
| xentrac | mapping out the brain connectome at the level of individual synapses, I think | 10:45 |
| kanzure | also: i wonder how you would esitmate to what extent there is specific cytoskeleton structure in the thalamus responsible for regulation, versus feedback-based temporary signal looping stuff, for internal cognitive resource provisioning or control. | 10:45 |
| kanzure | *estimate | 10:45 |
| xentrac | or, more modestly, mapping out dead brains at a higher level of detail than has been done so far | 10:46 |
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| xentrac | I don't know what microtome technology was like in 1929 | 10:46 |
| xentrac | but even if you only improved the resolution in two of the three dimensions, it might be interesting | 10:47 |
| kanzure | i suppose that looking at the actual neurons would answer the question, if they are highly uniform then it would make sense that it's either a feed-forward or other cybernetic system not dependent on specific cytoskeletoarchitecture, whereas if the neurons are highly varied and have specific interconnections, then cytoskeletoarchitecture would presumably be playing a much higher role. | 10:47 |
| kanzure | (in particular i mean the thalamocortical projections that the paper talks about for "cognitive control") | 10:47 |
| xentrac | yes, although you probably want to do that in lots of different parts of the brain | 10:48 |
| kanzure | also: in particular, cytoskeletoarchitecture stuff means "genetic regulatory network stuff plays a much higher role in determining the shape and structure and function of this particular region". | 10:48 |
| kanzure | in case that is not clear)[H( | 10:48 |
| xentrac | I mean we know the visual cortex is columnar, right? | 10:48 |
| kanzure | i was only intending to speculate on this particular area | 10:48 |
| kanzure | page 16 "ventral thalamus" http://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/Cognitive%20consilience:%20Primate%20non-primary%20neuroanatomical%20circuits%20underlying%20cognition%20-%202011.pdf | 10:49 |
| kanzure | "thalamocortical layer 1 (L1) projections" and such. | 10:50 |
| xentrac | hmm, I'm not sure that's necessarily true about the genetic regulatory network. you could have irregular structures that develop over time through a process of trial and error during your lifetime | 10:50 |
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| kanzure | structure development (like from plasticity) is maintained through genetic regulatory stuffs, like even AMPA receptor synpase weighting is maintained through some upregulation of some sort of transcription factor or something | 10:50 |
| kanzure | well okay, i see your point, AMPA receptor maintenance is not the same thing as a region-specific genetic regulatory network | 10:51 |
| xentrac | you mean §4.6.3? | 10:51 |
| kanzure | also 4.6.2 | 10:51 |
| kanzure | and 4.6.4 | 10:51 |
| xentrac | so I see | 10:52 |
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| kanzure | so regarding AMPA-style synaptic weighting, versus genetic regulatory planning stuff, yes i do doubt that you would be able to visually distinguish between the two on first inspection | 10:53 |
| kanzure | also... regarding long-range projections to other systems or regions or feedback diffusers or w/e, it would be unfortunate to discover that some work purely by action potential signal coding, while others work by neurohormone stuff or neurotransmitter-specific alternatives. it would muddle investigations. | 10:56 |
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| kanzure | transgenic knockout something could probably resolve the question though | 10:58 |
| xentrac | that some what work purely by action-potential signal coding? | 10:59 |
| xentrac | some whatevers? I am sure that there do exist Things that work in all three of those ways | 11:00 |
| kanzure | projections (signal coding vs other methods) | 11:00 |
| kanzure | "transgenic knockout something" as in probably a mouse | 11:00 |
| kanzure | ooh, if there were any particular regions of the brain that had a specific genetic regulatory network controlled structure (other than through conventional known synaptic plasticity), i feel like that result would be widely known at this point | 11:02 |
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| kanzure | "Patterning centers, regulatory genes and extrinsic mechanisms controlling arealization of the neocortex" http://web.mit.edu/~tkonkle/www/BrainEvolution/Meeting3/OLeary%202002%20CurrOpinNeuroBio.pdf (2002) | 11:08 |
| kanzure | unfortunately this seems to be large-scale anatomy | 11:09 |
| kanzure | "Neuronal subtype specification in the cerebral cortex" http://hscrb.harvard.edu/sites/default/files/Macklis_Molyneaux_Nature%20Reviews%20Neuroscience_2007-06.pdf | 11:11 |
| kanzure | not quite what i wanted either.. | 11:11 |
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| kanzure | "Early motor activity drives spindle bursts in the developing somatosensory cortex" gah | 11:12 |
| kanzure | "Mutation of the BiP/GRP78 gene causes axon outgrowth and fasciculation defects in the thalamocortical connections of the mammalian forebrain" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515720/ | 11:14 |
| kanzure | "Novel β-catenin target genes identified in thalamic neurons encode modulators of neuronal excitability" | 11:15 |
| kanzure | "Developmental synaptic plasticity at the thalamocortical input to barrel cortex: Mechanisms and roles" http://www.sciencedirect.com/science/article/pii/S1044743107000024 | 11:17 |
| kanzure | "The thalamocortical (TC) input to layer IV provides the major pathway for ascending sensory information to the mammalian sensory cortex. During development there is a dramatic refinement of this input that underlies the maturation of the topographical map in layer IV. Over the last 10 years our understanding of the mechanisms of the developmental and experience-driven changes in synaptic function at TC synapses has been greatly ... | 11:17 |
| kanzure | ... advanced. Here we describe these studies that point to a key role for NMDA receptor-dependent synaptic plasticity, a role for kainate receptors and for a rapid maturation in GABAergic inhibition. The expression mechanisms of some of the forms of neonatal synaptic plasticity are novel and, in combination with other mechanisms, produce a layer IV circuit that exhibits functional properties necessary for mature sensory processing." | 11:17 |
| kanzure | "Developmental programming of early brain and behaviour development and mental health: a conceptual framework" https://pure.uvt.nl/portal/files/1360743/van_den_BerghDMCN2011.pdf | 11:20 |
| kanzure | bottom of page 3 "Both intrinsic activity and sensory-driven neural activity influence the development of brain circuits and mature connectivity" | 11:21 |
| kanzure | so apparently a bunch of it is self-stimulation | 11:21 |
| kanzure | i think "intrinsic activity" is too much of a cop-out | 11:22 |
| kanzure | hard to tell whether that means we've actually checked if single-axon-specificity is enforced. | 11:25 |
| kanzure | (for that particular microscopic chunk of brain matter) | 11:25 |
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| heath | https://github.com/Automattic/wp-calypso/issues/650 | 13:54 |
| heath | paul fernhout on react's patents file | 13:55 |
| kanzure | .title | 14:11 |
| yoleaux | Replace React with Mithril for licensing reasons · Issue #650 · Automattic/wp-calypso · GitHub | 14:11 |
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| kanzure | vicarion: hi. | 15:26 |
| vicarion | kanzure: greetings | 15:30 |
| kanzure | what brings oyu here | 15:30 |
| kanzure | *you | 15:30 |
| vicarion | a new year resolution, i think | 15:32 |
| vicarion | what exciting things are going on here? | 15:33 |
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| kanzure | .title http://www.ncbi.nlm.nih.gov/pubmed/26716448 | 15:55 |
| yoleaux | DNA Assembly in 3D Printed Fluidics. - PubMed - NCBI | 15:55 |
| kanzure | "We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a ... | 15:56 |
| kanzure | ... manufacturing paradigm for designing and fabricating hardware for synthetic biology." | 15:56 |
| kanzure | "DNA Assembly in 3D Printed Fluidics" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143636 | 15:56 |
| Diablo-D3 | kanzure: YES | 15:56 |
| kanzure | "Many designs were created and tested for each of the three fluidic devices (Fig 2) used in the DNA assembly experiments. Five (A-E) of 13 iterations of the Form 1+ 3D Micromixer (Fig 2B) can be seen above. Several design changes can be seen A-E: The design of the 3D micromixer was changed from a recti-linear channels with square cross-sections (A-B) similar to previous 3d micromixer designs [19,36,37], to a design using a circular ... | 15:57 |
| kanzure | ... cross-section and smooth curves (C-E). A mount held the initial designs (A-B); later versions (C-E) stood freely on a base. All 13 iterations are in S4 Fig | 15:57 |
| kanzure | doi:10.1371/journal.pone.0143636.g004" | 15:57 |
| kanzure | Diablo-D3: what? | 15:57 |
| Diablo-D3 | as in YESSSSSSSSSS | 15:57 |
| kanzure | ugh calm the hell down, it's just golden gate assembly dude | 15:58 |
| kanzure | use your excitement and do something productive like read this stuff, http://diyhpl.us/~bryan/papers2/microfluidics/ | 15:58 |
| Diablo-D3 | what is golden gate assembly? | 15:58 |
| kanzure | "The design files for all of the devices presented in this work can be found in ‘Metafluidics’ (www.metafluidics.com), an open repository of design files for microfluidics." | 15:58 |
| Diablo-D3 | all I see is "assembling DNA and not fucking it up" | 15:58 |
| kanzure | haha their site redirects to http://metafluidics.staging.wpengine.com/ | 15:59 |
| kanzure | how sad | 15:59 |
| kanzure | Diablo-D3: yea golden gate assembly would only be interesting in microfluidic designs if it was a highly parallilized system for 100-10000000 reactions or something. this is just a simple demonstration of conventional microfluidics for mixing. it's not going to iteratively assemble a genome. | 16:00 |
| Diablo-D3 | damnit. | 16:00 |
| kanzure | i'm confused whether if i show you large-scale dna assembly projects if you are actually going to read them, or if you are just excited about being excited | 16:01 |
| kanzure | like gibson assembly | 16:01 |
| Diablo-D3 | I might read them, depends on how dense the language is | 16:01 |
| kanzure | http://diyhpl.us/~bryan/papers2/DNA/Large-scale%20de%20novo%20DNA%20synthesis:%20technologies%20and%20applications%20-%20Church%20-%202014.pdf | 16:06 |
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| kanzure | spreadsheet thingy for fermi estimation modeling https://github.com/getguesstimate/guesstimate-app https://news.ycombinator.com/item?id=10816563 | 17:18 |
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| kanzure | weird, in the logs there's no commentary from fenn about the cognitiveconsilience stuff http://gnusha.org/logs/2014-12-01.log i wonder what i was remembering yesterday when i ascribed some opinions to him | 20:16 |
| kanzure | 17:21 < kanzure> i mean why are you quicker to prescribe number of neurons to unique human abilities rather than neural circuits | 20:20 |
| kanzure | 17:22 < fenn> i have no idea what a neural circuit is actually | 20:20 |
| kanzure | 17:22 < fenn> is that a thing? | 20:20 |
| kanzure | 17:22 < kanzure> there are these loops in the brain between "regions" and "clusters" | 20:20 |
| kanzure | 17:22 < kanzure> visually distinguished by long-range projection neurons | 20:20 |
| kanzure | 17:23 < fenn> are "regions" connected by long range projections also? | 20:20 |
| kanzure | 17:24 < kanzure> see page 3 figure 3 http://diyhpl.us/~bryan/papers2/neuro/randall-oreilly/Towards%20an%20executive%20without%20a%20homunculus:%20computational%20models%20of%20the%20prefrontal%20cortex%20basal%20ganglia%20system.pdf | 20:20 |
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| kanzure | page 7 figure 4 http://diyhpl.us/~bryan/papers2/neuro/The%20evolution%20of%20distributed%20association%20networks%20in%20the%20human%20brain.pdf | 20:23 |
| kanzure | okay i see. fenn was done looking by the time i found the cognitive consilience paper thingy. | 20:28 |
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| kanzure | page 18 section 2.2 discusses local microcircuit differences in various brain regions http://diyhpl.us/~bryan/papers2/neuro/Designing%20scalable%20biological%20interfaces%20-%20Marblestone.pdf | 20:36 |
| kanzure | freeman dyson is still around? | 20:46 |
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| kanzure | "A direct search for life in Europa's ocean would today be prohibitively expensive. Impacts on Europa give us an easier way to look for evidence of life there. Every time a major impact occurs on Europa, a vast quantity of water is splashed from the ocean into the space around Jupiter. Some of the water evaporates, and some condenses into snow. Creatures living in the water far enough from the impact have a chance of being splashed ... | 20:51 |
| kanzure | ... intact into space and quickly freeze-dried. Therefore, an easy way to look for evidence of life in Europa's ocean is to look for freeze-dried fish in the ring of space debris orbiting Jupiter." | 20:51 |
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| kanzure | TMA: thanks for the link about the first five year plan ( http://www.zakonyprolidi.cz/cs/1948-241 ). a lot of this is highly prescriptive, i don't see any intentional attempts at reasoning in here. were they drawing numbers from a hat? | 20:56 |
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| kanzure | gentoognuhurd: hi.. oh. | 22:00 |
| gentoognuhurd | kanzure: hi | 22:01 |
| gentoognuhurd | why the oh | 22:02 |
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| fenn | should i read this "consilience" paper? it looks really boring | 23:20 |
| fenn | i'm particularly unimpressed with the "interactive visualization" google maps hack | 23:21 |
| fenn | it's basically a poster with footnotes | 23:21 |
| --- Log closed Fri Jan 01 00:00:52 2016 | ||
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