--- Log opened Mon Jan 02 00:00:02 2023
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05:10 < maaku> Mauddib: what is a ROFLumilast?
07:04 < kanzure> why is there no universal package manager that has taken over everything
07:04 < L29Ah> kanzure: because there are conflicting requirements
07:05 < kanzure> .wik nix package manager
07:05 < saxo> "Nix is a cross-platform package manager that utilizes a purely functional deployment model where software is installed into unique directories generated through cryptographic hashes." - https://en.wikipedia.org/wiki/Nix_package_manager
07:05 < kanzure> L29Ah: example?
07:06 < L29Ah> ease of use, build/package customizability, sandboxing, language awareness, resource constraints
07:06 < kanzure> i don't think so.
07:06 < L29Ah> today i find portage to be the best package manager overall, and guix to be the most interesting in the next 5 years
07:06 < kanzure> maybe on resource constraints, but the tools usually let you configure how far you want to do the graph search
07:07 < L29Ah> if you are only interested in graph search, consider ninja
07:07 < L29Ah> package management is much more than the graph search, and even graph itself can be amendable depending on the situation encountered during the search
07:09 < kanzure> that just seems like a generic problem that package managers should use an external tool for, really
07:09 < L29Ah> no.
07:09 < kanzure> oh look at me i have a truly novel graph constraint optimization problem that nobody has ever thought of pfffffft
07:12 < L29Ah> tell me what you think you can share between portage and some other package manager wrt dependency resolution, and i'll probably demonstrate you why it is not a good option
07:13 < kanzure> does "alien" do nix and guix packages these days?
07:13 < kanzure> or even pypi packages?
07:15 < L29Ah> ofc not, alien is only concerned with the package managers that can only pull deps, compare version numbers and unpack archives, iirc
07:16 < kanzure> oh
07:16 < kanzure> that's weird, i don't remember things being this broken
07:16 < L29Ah> and fails even there as different distros have their own ideas about versioning and package naming
07:31 < Jay_Dugger> .wik ninja package search
07:31 < saxo> Article not found: https://en.wikipedia.org/wiki/Ninja_package_search gave 404 | Searched en for 'ninja package search' | https://en.wikipedia.org/wiki/No_result_found gave 404 | Searched en for 'No result found'
07:33 < muurkha> Muaddib: what is a ROFLumilast?
07:33 < Muaddib> muurkha: It's a new type of package manager that will make you ROFL until the last package is installed.
07:36 < nsh> Muaddib, what would be poetic resolution of the fallacy of post hoc ergo proctor hoc in the context of a soon-to-be discovered trans-temporal continuum logic unifying physics, computation and consciousness?
07:36 < Muaddib> nsh: That all the truths of a previous era will become the silly superstitions of the future, and that all the things that we thought were impossible are only the beginning.
07:37 < nsh> Muaddib, and the etymology of trite considered as penance for being so?
07:37 < Muaddib> nsh: The shorthand for "too right, too late" - the ultimate irony of life.
07:37 < nsh> meh
07:45 < muurkha> post hoc ergo proctologist hoc
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08:18 < muurkha> lsneff: reading the glib, well-sourced, and completely wrong https://idlewords.com/2023/1/why_not_mars.htm, a question occurs to me
08:18 < muurkha> is anybody at SpaceX working on autonomous robot factories yet?
08:18 < lsneff> i was also reading that this morning
08:18 < lsneff> i know a number of people not at spacex working on that
08:19 < muurkha> oh really?  how far along are they?
08:20 < lsneff> not particularly far
08:21 < muurkha> who are they? what obstacles are they encountering and how are they trying to solve them?
08:22 < kanzure> mendel was dug up and sequenced, why not john von neumann https://text.npr.org/1142202365
08:24 < lsneff> i think the roadblocks are mostly result of not having better ml
08:24 < lsneff> very hard to make a factory, even if it has every tool, that can go and assemble anything you want without designing it specifically for one thing
08:26 < muurkha> all I know about is Mechadense, Seed Factories, and stuff that predates KSRM
08:26 < muurkha> (the book)
08:27 < muurkha> Mechadense is the gem-gum guy
08:29 < lsneff> i remember him
08:30 < lsneff> yeah, i think we're so far behind anything self-replicating
08:31 < lsneff> the gem-gum stuff is decades away, it's not even on people's radar as something we could potentially accomplish  
08:33 < muurkha> well, and Chirikjian and Matthew Moses
08:33 < muurkha> why do you think it's decades away?
09:32 < kanzure> https://open.win.ox.ac.uk/DigitalBrainBank/#/
09:37 < kanzure> "The BigMac dataset: an open resource combining multi-contrast MRI and microscopy in the macaque brain" https://www.biorxiv.org/content/10.1101/2022.09.08.506363v1.abstract
09:38 < kanzure> "Artificial mosaic brain evolution of relative telencephalon size improves cognitive performance in the guppy (Poecilia reticulata)" https://www.biorxiv.org/content/10.1101/2021.04.03.438307v1.abstract
09:38 < kanzure> "Artificial selection on brain size leads to matching changes in overall number of neurons" https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13805
09:39 < kanzure> and some dog/canine GWAS studies:
09:40 < kanzure> olfactory https://www.nature.com/articles/s41598-022-18698-4
09:40 < kanzure> dog breed differences in cognition https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608742/
09:41 < kanzure> dog herding, predation, temperament, trainability https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8335642/
10:17 < kanzure> development of a third eye for frogs http://nopr.niscpr.res.in/bitstream/123456789/23208/1/IJEB%2043%288%29%20671-678.pdf
10:31 < kanzure> this one has poison sacs that look like eyes https://en.wikipedia.org/wiki/Colombian_four-eyed_frog
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11:28 < kanzure> "Time-tagged ticker tapes for intracellular recordings" https://www.nature.com/articles/s41587-022-01524-7
11:31 < kanzure> ".. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time."
11:31 < kanzure> actually, i think we saw this one before. seems familiar.
11:31 < kanzure> (published today)
11:44 < kanzure> "Serotonergic stimulation induces nerve growth and promotes visual learning via posterior eye grafts in a vertebrate model of induced sensory plasticity" https://www.nature.com/articles/s41536-017-0012-5
11:49 < kanzure> "Embryonic transplantation experiments: Past, present, and future" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800665/
11:49 < kanzure> "entwicklungsmechanik"https://en.wikipedia.org/wiki/Wilhelm_Roux
11:49 < kanzure> er,
11:50 < kanzure> "entwicklungsmechanik" https://en.wikipedia.org/wiki/Wilhelm_Roux
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12:18 < kanzure> "The stability of memories during brain remodeling: a perspective" https://www.tandfonline.com/doi/pdf/10.1080/19420889.2015.1073424 (end of page 3, re: persistence of memory during metamorphosis)
13:11 < heath> fenn: a friend just shared collapseos.org and I vaguely remember someone on here mentioning a similar, older effort for producing pdf manuals (cds?) which would ad in a bootstrapping civilation scenario. do you by chance recall such a project?
13:12 < heath> s/ad/aid
13:17 < L29Ah> Muaddib: tell us the contents of the paper "The stability of memories during brain remodeling: a perspective"
13:17 < Muaddib> L29Ah: That memories may stay more intact than previously thought, even during metamorphosis.
13:17 < L29Ah> Muaddib: what are the scientific results and their possible implications?
13:17 < Muaddib> L29Ah: Looks like we could all use a bit more brain remodeling!
13:22 < kanzure> "Synthetic morphology via active and agential matter" https://osf.io/xrv8h an interesting work by michael levin (also coauthored the "polycomputing" thing that was published recently)-- basically has a take on surgical engineering vs genetic engineering to realize morphological outcomes
13:24 < L29Ah> Muaddib: what is "polycomputing"?
13:24 < Muaddib> L29Ah: Polycomputing is when your computer does all the computing for you, so you can play videogames or whatever.
13:24 < kanzure> his argument is that while genetic engineering is helpful, more reliable outcomes can be achieved by pick-and-place of well-characterized (sometimes partly differentiated) embryonic cells
13:25 < L29Ah> unleash the bioethicists!
13:27 < kanzure> maybe a well-characterized set of cell lines can be made that when micromanipulated or microsurgically placed together they execute some large-scale body plan (or cerebral architecture)
13:27 < fenn> heath: there was this letdown of a book, "the knowledge" that said basically "wouldn't it be nice if someone packed up how to bootstrap" but didn't actually include any info. there's also the long now library (a physical collection of books)
13:29 < kanzure> also, with embryonic surgery, it should be possible to have separate genomes for separate cell lines-- that is, there is no particular reason that brain neurons need the same genome as cardiac cells; specialization of one or the other wouldn't have to cross-effect other cell types throughout the body. [traditionally this seems to be done with transcription factors for cell identity but i don't ...
13:29 < kanzure> ...think we have mastered that yet, so maybe we just forego it instead and use entirely separate cell lines]
13:30 < kanzure> .g site:arxiv.org levin polycomputing
13:30 < saxo> https://arxiv.org/abs/2212.10675
13:30 < kanzure> .title
13:30 < saxo> [2212.10675] There's Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-scale Machines
13:31 < L29Ah> kanzure: you want thymus expressing all the stuff the other parts of your body express, otherwise they will be killed by the immune system; that is generally achieved by having the same genome everywhere
13:32 < kanzure> i thought there's some immune privilege during development?
13:35 < kanzure> at a high level, developing an engineering toolkit for cell types and body planning during development (like for synthetic target morphologies) seems more likely than solving large-scale genotype/phenotype correspondence
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13:35 < kanzure> however, his group's attempt at it seem rather crude (only a few dozen cells or something?)
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13:36 < kanzure> xenobots: https://www.quantamagazine.org/cells-form-into-xenobots-on-their-own-20210331/ https://www.pnas.org/doi/full/10.1073/pnas.1910837117 https://www.pnas.org/doi/abs/10.1073/pnas.2112672118
13:37 < kanzure> anthrobots (human version): https://www.biorxiv.org/content/10.1101/2022.08.04.502707v1.abstract
13:38 < kanzure> organ printing (like jmil's work) seems to be based on scaffolds and seeking out precursor cell types that will develop along the scaffold; organoids are also pretty similar. but neither approach emphasizes surgical intervention in early development.
13:48 < L29Ah> Muaddib: is there any immune privilege during early human development?
13:48 < Muaddib> L29Ah: Yeah, we're all born with an immunity to trolls.
13:52 < kanzure> that's a neat result (from the osf.io link): "experimentally replicating the bioelectric characteristics of the site of eye formation in other parts of the body of frog embryos via microinjection of ion channel mRNA can cause eye formation in ectopic regions"
13:57 < kanzure> you could probably use optogenetics to selectively program different cell clusters during embryonic development
13:57 < kanzure> and sketch out body plans that way
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14:27 < kanzure> "Green oxygen power plants in the brain rescue neuronal activity" https://www.cell.com/iscience/fulltext/S2589-0042(21)01126-3
15:16 < fenn> wut
15:17 < fenn> Transcardially injected microalgae accumulate in brain blood vessels of Xenopus
15:17 < fenn> Upon illumination, green algae and cyanobacteria robustly produce O2 in the brain
15:17 < fenn> After hypoxic loss of brain function, photosynthetic oxygen rescues neural activity
15:18 < fenn> that's some proper mad science
16:06 < L29Ah> very mad
16:28 < kanzure> "Physiological inputs regulate species-specific anatomy during embryogenesis and regeneration" https://www.tandfonline.com/doi/full/10.1080/19420889.2016.1192733
16:29 < kanzure> "... Recent studies have revealed a physiological system of communication among cells that regulates pattern during embryogenesis and regeneration in vertebrate and invertebrate models. Somatic tissues form networks using the same ion channels, electrical synapses, and neurotransmitter mechanisms exploited by the brain for information-processing. Experimental manipulation of these circuits was ...
16:29 < kanzure> ...recently shown to override genome default patterning outcomes, resulting in head shapes resembling those of other species in planaria and Xenopus"
16:30 < kanzure> "Gap junctional blockade stochastically induces different species-specific head anatomies in genetically wild-type Girardia dorotocephala flatworms" https://www.mdpi.com/1422-0067/16/11/26065/html?dom=pscau&src=syn
16:30 < kanzure> "Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina)."
16:31 < kanzure> ".. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain"
16:45 < kanzure> .title https://www.youtube.com/watch?v=R8mkupUoPgQ
16:45 < Muaddib> [R8mkupUoPgQ] Building CDOs (Computer Designed Organisms) from amphibian cells (1:42)
16:45 < saxo> Building CDOs (Computer Designed Organisms) from amphibian cells - YouTube
16:52 < kanzure> xenobots code https://cdorgs.github.io/ https://github.com/skriegman/reconfigurable_organisms 
16:52 < kanzure> "You can manually design xenobots by drawing them in our graphical user interface voxcraft-viz, which was originally forked from voxcad."
16:52 < kanzure> https://www.youtube.com/watch?v=jvxQjlrLgQo
16:52 < Muaddib> [jvxQjlrLgQo] voxcraft-viz demo: step2 manually design an arbitrary soft bot (2:49)
16:56 < kanzure> looks like they specifically place each and every cell to make the final design, but it would be more interesting if they could encode a body plan from only a few cell placements
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17:11 < fenn> have they figured out vasculature yet
17:43 < kanzure> vascularized heart (see figure 5) https://onlinelibrary.wiley.com/doi/full/10.1002/advs.201900344
17:50 < fenn> i meant with the xenobot cell placement technology.. but this is cool too
17:51 < kanzure> what we need is pick-and-place cell engineering
17:53 < kanzure> i mean, for embryo development. maybe it could bypass any genotype/phenotype issues, if we had some well-behaving well-characterized cells in the toolbox.
17:54 < kanzure> i wonder if you could organ print an entirely different cortical architecture and throw it into an embryo
17:55 < kanzure> wonder if any organ printing companies are doing neocortex
17:57 < fenn> i don't see how that would be possible, since all of the important cross-linking structure is in the shape of the cells
18:00 < fenn> i guess you could have like 100 layers of neural network instead of 7
18:00 < kanzure> hrm how would i 3d print this https://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/stitched-diagram.jpg
18:01 < kanzure> at some level they do actually create interconnections naturally
18:04 < kanzure> also, what about doing cell sorting and finding neurons in the shape that you want and placing them at the location you want?
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18:07 < kanzure> select each cortical cell from your library: 50 micron length, 100 micron length, 2 mm length, 6 mm, 200 mm
18:09 < fenn> there's just no way you're going to place them manually at such a high level of tangle
18:10 < fenn> maybe you could do a more regular array of shapes
18:11 < kanzure> 3d printing is mostly a matter of 2d printing, so you wouldn't be able to place cells in the third dimension as much
18:11 < kanzure> like "vertical" oriented neurons
18:21 < kanzure> could also do neural stem cell printing instead of mature cortical neurons
18:25 < kanzure> like what if your printed neural tube just-so-happens to have a significantly larger diameter
19:11 < kanzure> "A review on 3d printing functional brain model" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8816519/
19:42 < kanzure> .wik humanzee
19:42 < saxo> "The humanzee (sometimes chuman, manpanzee or chumanzee) is a hypothetical hybrid of chimpanzee and human. Serious attempts to create such a hybrid were made by Soviet biologist Ilya Ivanovich Ivanov in the 1920s, and possibly by researchers in China in the 1960s, though [...]" - https://en.wikipedia.org/wiki/Humanzee
19:42 < kanzure> besides the well-known soviet attempts,
19:42 < kanzure> "In the 1980s, there were reports of an experiment in human–chimpanzee crossbreeding conducted in China in 1967, and on the planned resumption of such experiments. In 1981, Ji Yongxiang, head of a hospital in Shenyang, was reported as claiming to have been part of a 1967 experiment in Shengyang in which a chimpanzee female had been impregnated with human sperm. According to this account, the ...
19:42 < kanzure> ...experiment was cut short by the Cultural Revolution, with the responsible scientists sent off to farm labour and the three-months pregnant[24] chimpanzee dying from neglect. According to Timothy McNulty of Chicago Tribune, the report was based on an article in the Wenhui Bao newspaper of Shanghai. Li Guong of the genetics research bureau at the Chinese Academy of Sciences was cited as ...
19:42 < kanzure> ...confirming both the existence of the experiment prior to the Cultural Revolution and the plans to resume testing.[25]"
20:42 < fenn> plans to resume testing when?
20:42 < fenn> and what's the point?
22:47 < docl> https://www.youtube.com/watch?v=p3lsYlod5OU
22:47 < Muaddib> [p3lsYlod5OU] Michael Levin: Biology, Life, Aliens, Evolution, Embryogenesis & Xenobots | Lex Fridman Podcast #325 (180:21)
--- Log closed Tue Jan 03 00:00:04 2023