--- Log opened Tue Jan 03 00:00:04 2023
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05:15 < kanzure> yesterday: "Time-tagged ticker tapes for intracellular recordings" https://www.nature.com/articles/s41587-022-01524-7 https://twitter.com/NatureBiotech/status/1609952652044935173
05:15 < kanzure> today: "Recording of cellular physiological histories along optically readable self-assembling protein chains" https://www.nature.com/articles/s41587-022-01586-7 https://twitter.com/NatureBiotech/status/1609950240517373953
05:16 < kanzure> or, yesterday too i guess.
05:16 < kanzure> pretty cool way to do debugging inside of cells
05:36 < kanzure> wasn't there a similar thing from zador lab or kording lab. i don't see that cited.
05:37 < kanzure> "We thank F. Wang, M. Bear, A. Keating, G. Church, K. Tyo and K. Kording for useful discussions" well ok
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05:39 < kanzure> oh, that was the other one.
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07:16 < kanzure> nmz787: do you have a good image that demonstrates good wire routing management in asic/cpu design? not seeing the kind of image i expect here: https://course.ece.cmu.edu/~ee760/760docs/lec15.pdf
07:20 < kanzure> also trying to find a reference for patterned neuronal cultures... it was something about painting a flat surface and then the neurons would grow in the described shape.
07:31 < kanzure> https://diyhpl.us/~bryan/papers2/neuro/Reliable%20neuronal%20logic%20devices%20from%20patterned%20hippocampal%20cultures.pdf
07:52 < kanzure> .wik hybrot
07:52 < saxo> "A hybrot (short for 'hybrid robot') is a cybernetic organism in the form of a robot controlled by a computer consisting of both electronic and biological elements." - https://en.wikipedia.org/wiki/Hybrot
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07:58 < kanzure> who comes up with these names
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08:33 < nsh> a person walking with a stick is a cybernetic organism. a shod horse is a cybernetic organism. a man at a tiller is the canonical cybernetic organism. useful is understanding that the principles of control theory are supervenient over the arbitrary ontological boundaries we use to separate phenomena into concepts for ratiocination
08:33 < nsh> this is symbolically captured by the concept/icon/totem of the yoke
08:33 < nsh> or tantra
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14:07 < kanzure> mlaga97: greetings
14:07 < kanzure> stipa: are you related to sipa
14:20 < muurkha> I like "a person walking with a stick is a cybernetic organism. a shod horse is a cybernetic organism. a man at a tiller is the canonical cybernetic organism."
14:23 < docl> if you make a synthetic organ with some computational and some biological parts it's a cyborgan, right?
14:23 < kanzure> Muaddib: what do you think?
14:23 < Muaddib> kanzure: A cyborg walks into a bar...the bartender says "Hey, we don't serve your kind here!"
14:29 < muurkha> Muaddib: is that supposed to be a joke?
14:29 < Muaddib> muurkha: Why yes, yes it is! The bartender thought he had the upper hand, but he probably didn't expect the cyborg to respond with, "That's ok, I don't serve your kind either!"
14:29 < muurkha> Muaddib: serve your kind how?
14:29 < Muaddib> muurkha: With a nice robotic handshake!
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15:12 < nmz787> kanzure: that PDF covers most of the key points from the 5 mins I just spent skimming it
15:12 < kanzure> yeah but i want the pretty picture to show someone
15:13 < nmz787> they had like one
15:13 < kanzure> of a neat wiring job
15:13 < nmz787> at a die level, you really won't see much in terms of individual wires, it's too dense
15:15 < nmz787> die level is block-level routing, you're just connecting already routed IP blocks (or FUBs, functional unit blocks)
15:15 < nmz787> this may be better for you??? https://ieeexplore.ieee.org/abstract/document/6658541/similar#similar
15:19 < nmz787> other terms that may be helpful for searches "APR - automated place and route"
15:22 < nmz787> kanzure: maybe stuff like this? http://www.qmtpro.com/~nes/chipimages/visual2c02/
15:22 < nmz787> from the "visual" column here https://siliconpr0n.org/archive/doku.php?id=digitized
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15:58 < stipa> kanzure: no
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17:38 < Jay_Dugger> Hello, everyone.
17:38 < muurkha> no
17:53 < lsneff> hey jay
18:03 < kanzure> nmz787: actually that looks overly disorganized. maybe i'm thinking of a PCB.
18:18 < fenn> https://t.eremex.com/img/photos/25_big.jpg 
18:18 < fenn> (topoR autorouter)
18:19 < fenn> ugly but complicated https://www.eremex.com/images/434667.jpg
18:23 < kanzure> context: i was trying to explain to someone that brain wiring is much more dense and three-dimensional and you have to keep good wire management for microchips
18:24 < kanzure> 434667.jpg is probably multi-layer, ya?
18:24 < fenn> 2 layer
18:24 < fenn> a tidy one https://everipedia-storage.s3-accelerate.amazonaws.com/ProfilePics/1848224__04988.jpeg
18:25 < fenn> sorry i just like this stuff
18:25 < kanzure> that's much better but now a schematic instead of a photo
18:25 < fenn> i think this is multi layer
18:25 < fenn> https://www.eremex.com/images/383394.jpg
18:26 < fenn> the more 3d it is the less interesting it looks because it approaches straight line routing
18:26 < fenn> in a brain everything gets scrunched together
18:27 < kanzure> 25_big.jpg is pretty close, i'm convinced now that i was thinking of PCB diagrams.
18:29 < kanzure> microfluidic chips have a similar requirement
18:30 < fenn> you've seen diffusion tensor images of the brain right https://images.medicaldaily.com/sites/medicaldaily.com/files/2013/08/04/0/74/7436.png
18:31 < kanzure> https://i0.wp.com/www.kadvacorp.com/wp-content/uploads/2017/10/Anyone-Who-Works-In-IT-Satisfied-9.jpg?resize=577%2C1024&ssl=1
18:31 < fenn> wire wrap board https://motherboard-images.vice.com/content-images/contentimage/no-id/143587327969837.jpg
18:31 < fenn> yeah there are whole subreddits devoted to pleasing ethernet cables
18:33 < fenn> "structured cabling"
18:34 < kanzure> .wik structured cabling
18:34 < saxo> "In telecommunications, structured cabling is building or campus cabling infrastructure that consists of a number of standardized smaller elements (hence structured) called subsystems." - https://en.wikipedia.org/wiki/Structured_cabling
18:34 < fenn> https://heritagecomm.us/wp-content/uploads/2019/08/Cabling-before-after.jpg
18:35 < kanzure> and how much downtime between?
18:36 < fenn> i'm always amazed at how messy the wiring is in physics labs
18:37 < L29Ah> i'm always amazed at how some people manage to create non-messy wiring
18:38 < L29Ah> seems like a very hard work to me
18:39 < L29Ah> my current 3d printer wiring is a suspended disaster for instance, but i have no clue on improving it
18:40 < kanzure> "Could a neuroscientist understand a microprocessor?" https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005268
18:41 < kanzure> from kording lab
18:43 < kanzure> also, before i forget,
18:44 < kanzure> cortical/brain printing could be achieved in a three-dimensional hydrogel or other kind of viscuous medium, with neurite growth proteins embedded in the paths where you want the neurons to grow
18:44 < kanzure> you could also deposit neural stem cells at different locations in 3d space as you construct the full gel, without having to route each axon or dendrite in strange directions
18:44 < kanzure> limitation will be print resolution of depositing the protein trace lines
18:45 < kanzure> and, backing up a sec, i think tissue printing of neural tubes (or neural tube precursors) is more likely to work-- but won't be able to support the large variety of architectures that could be directly printed by a gel-based printed voxel matrix thing
18:49 < fenn> i think the phrase "neural tube" is taken already by a larger scale structure
18:49 < kanzure> yeah
18:49 < kanzure> it's the precursor to your brain
18:49 < kanzure> .wik neural tube
18:49 < saxo> "In the developing chordate (including vertebrates), the neural tube is the embryonic precursor to the central nervous system, which is made up of the brain and spinal cord." - https://en.wikipedia.org/wiki/Neural_tube
18:51 < fenn> the protein idea won't work because the cells won't know which trail of growth breadcrumbs are meant for them specifically, vs being meant for another cell nearby
18:51 < kanzure> good point. it's high density :\.
18:52 < fenn> you could lead the growing tip around with a 2-photon spot of light like leading a cat with a laser pointer
18:53 < kanzure> one neuron at a time?
18:53 < fenn> must be closed loop control, and fully interconnected layers cant be very thick
18:53 < fenn> could do many in parallel as long as the growing tips don't get too close
18:54 < kanzure> do the thin brain hydrocephaly people have long-range projections or not? or was the scientific consensus that it's all made up?
18:56 < fenn> well they're real people and they function more or less normally, but i think their heads are bigger overall, so the total active brain tissue volume is the same? volume is not very intuitive
18:56 < kanzure> do their long-range projections travel a greater distance across the surface of the skull?
18:56 < fenn> i looked a little bit but it's not easy to get detailed data about individuals
18:57 < fenn> what's the longest myelinated brain neuron anyway? more than 1 cm?
18:58 < muurkha> in my childhood I somehow got the idea that axons in the brain could be 100mm long or more, but I really don't know
18:58 < kanzure> chatgpt: "The longest neurons in the human brain are the axons of the pyramidal cells in the motor cortex, which can be over one meter in length. These axons, also known as corticospinal fibers, extend from the motor cortex in the brain down to the spinal cord, where they transmit signals to control the movement of muscles in the body. The axons of these neurons are surrounded by a layer of ...
18:58 < kanzure> ...myelin, which helps to insulate and protect them, and enables them to transmit signals more efficiently."
18:59 < muurkha> apparently it didn't totally make that up: https://en.wikipedia.org/wiki/Pyramidal_tracts
19:00 < kanzure> feels like corticospinal stuff should be excluded
19:00 < fenn> i'm wondering if it's a point to point network or multi-hop
19:01 < muurkha> not sure about the "over one meter" part
19:01 < fenn> have you accepted chatGPT as your lord and saviour?
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19:01  * fenn hands muurkha a contract to sign, in blood
19:01 < muurkha> shouldn't I sign it in weights and biases?
19:03 < kanzure> "... the corpus callosum is a distinct tract for only about 15 to 35 mm, but its fibers range in length up to about 300 mm"
19:04 < kanzure> from:
19:04 < kanzure> "An estimation of the absolute number of axons indicates that human cortical areas are sparsely connected" https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001575
19:04 < kanzure> "Here, we estimate the absolute number of axons linking cortical areas from a whole-cortex diffusion MRI (dMRI) connectome, calibrated using the histologically measured callosal fiber density. Median connectivity is estimated as approximately 6,200 axons between cortical areas within hemisphere and approximately 1,300 axons interhemispherically, with axons connecting functionally related areas ...
19:04 < kanzure> ...surprisingly sparse. For example, we estimate that <5% of the axons in the trunk of the arcuate and superior longitudinal fasciculi connect Wernicke’s and Broca’s areas. These results suggest that detailed information is transmitted between cortical areas either via linkage of the dense local connections or via rare, extraordinarily privileged long-range connections."
19:04 < kanzure> hey that's good news.
19:05 < fenn> that's way less than i expected
19:07 < fenn> you could actually do surgery and intecept all of them
19:07 < kanzure> "It has long been recognized that as the number of cortical neurons increases, maintaining the same probability of connectivity between neurons would require that axon number increase approximately with the square of neuron number, and this would require too much volume, impose an unsustainable metabolic load [6], and actually decrease computational power due to conduction delays [7]. The ...
19:07 < kanzure> ...consequent imperative to minimize long-distance corticocortical fibers has been posited to be reflected in exponential decline in cortical connectivity with distance [8] and to be partially compensated for with a small-world graph architecture [9], granting special properties to rare long-distance fibers in a log-normal neural physiology and anatomy [10]. However, this organizing principle is ...
19:07 < kanzure> ...rarely explicitly addressed in terms of individual axon counts..."
19:11 < kanzure> "The corpus callosum was used to calibrate the estimate because of its unique properties: It has a well-defined cross-sectional area, more than approximately 99% of interhemispheric corticocortical axons are routed through it [3,36], and essentially no fibers leave or enter the tract between the 2 hemispheres."
19:19 < kanzure> an intro to that article: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001612
19:25 < kanzure> i wonder if inter-regional connectivity is the dominant factor for hoo-mons, or the local connectivity and recurrent processing
19:25 < kanzure> my guess would be that most mammalian brains have similar connectivity
19:25 < kanzure> across regions i mean.
19:26 < fenn> my understanding is that autism is more biased toward local connectivity than the average human
19:27 < fenn> i'm not sure if that also applies to the long range neurons
19:27 < fenn> like it could just be inter-minicolumn connectivity
19:28 < fenn> are there model animals for autism?
19:28 < kanzure> well.. yes.. but i don't think we actually know if it's really "like autism"-- all you can do is observe the behavior of mice.
19:28 < kanzure> or compare anatomy
19:29 < muurkha> the etiology of autism is pretty varied
--- Log closed Wed Jan 04 00:00:05 2023