--- Log opened Sun Oct 11 00:00:53 2015
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03:43 < archels_> "biologically (not too im-)plausible models"
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05:17 < kanzure> bloop
05:22 < kanzure> https://mitpress.mit.edu/index.php?q=books/biological-emergences
05:24 < kanzure> "In Biological Emergences, Robert Reid argues that natural selection is not the cause of evolution. He writes that the causes of variations, which he refers to as natural experiments, are independent of natural selection. Reid proposes an alternative theory to explain how emergent novelties are generated and under what conditions they can overcome the resistance of natural selection. He suggests that what causes innovative variation ...
05:24 < kanzure> ... causes evolution, and that these phenomena are environmental as well as organismal. After an extended critique of selectionism, Reid constructs an emergence theory of evolution, first examining the evidence in three causal arenas of emergent evolution: symbiosis/association, evolutionary physiology/behavior, and developmental evolution. Without selectionism, Reid argues, evolutionary innovation can more easily be integrated into a ...
05:24 < kanzure> ... general thesis. Finally, Reid proposes a biological synthesis of rapid emergent evolutionary phases and the prolonged, dynamically stable, non-evolutionary phases imposed by natural selection."
05:29 < kanzure> oh weird, wikipedia cites natural selection as a "cause" of genetic change? i guess so: "Natural selection is the only known cause of adaptation but not the only known cause of evolution. Other, nonadaptive causes of microevolution include mutation and genetic drift.[19]"
05:30 < kanzure> i think wikipedia needs to review aristotle's 27 causes
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05:35 < kanzure> or salthe stuff http://www.nbi.dk/~natphil/salthe/
05:37 < kanzure> http://www.nbi.dk/~natphil/salthe/Aristotelian_Causes.pdf
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06:38 < JayDugger> Morning, all.
07:00 < kanzure> "such as the geologically-recent-but-not-to-me domestication of foxes, which I submit as contrary evidence to your claims of how unproductive the ordeal is"
07:00 < kanzure> "The inescapable first priority is the continuation of life. Opportunities only come to the living. Behavioural change precedes genetic fixation."
07:02 < kanzure> not sure that is true, the behavioral differences were already presenting themselves as a result of genetics, and then they were prioritized and elaborated
07:02 < kanzure> oh right wasn't there some crazy-stupid "genetic potential" concept?
07:13 < kanzure> how are there no good papers about "population genetics" and domestication? what's wrong with this planet >:(
07:20 < kanzure> page 8 suggests that there has been selection for adult humans with continued production of lactase for milk digestion ability http://www.researchgate.net/profile/Greger_Larson/publication/235647788_A_population_genetics_view_of_animal_domestication/links/0deec51d53c90caec1000000.pdf
07:20 < kanzure> seems reasonable.
07:26 < kanzure> "Group responses to specially skilled individuals in a macaca fascicularis group" http://www.loper-os.org/pub/codemonkey.pdf
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07:34 < kanzure> "Evaluating the roles of directed breeding and gene flow in animal domestication" http://www.pnas.org/content/111/17/6153.short
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07:37 < kanzure> some criticism http://pure.abdn.ac.uk:8080/portal/files/48950971/Response_to_M_P_PURE.pdf
07:38 < kanzure> "Despite these reservations, the dichotomous framework in which small bones are considered domestic and large ones wild boar is frequently employed." gah
07:42 < kanzure> "Second, there may simply be few domestication loci with major effects in animals. Early animal domestication may have happened by shifting the allele frequencies at many loci, each with small individual effects, thereby altering the phenotype. This scenario would be consistent with the observation that many domestic animals (e.g., pigs) can readily establish feral populations that in many aspects mimic the phenotype of their wild ...
07:42 < kanzure> ... ancestors (55)."
07:42 < kanzure> from http://anthropology.si.edu/archaeobio/cm/Larson%20et%20al%20PNAS%202014.pdf
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07:45 < kanzure> er, this paper (page 5) claims that most domestication was probably selection over existing allele frequencies, and not de novo mutation
07:46 < kanzure> .wik selective sweep
07:46 < yoleaux> "A selective sweep is the reduction or elimination of variation among the nucleotides in neighboring DNA of a mutation as the result of recent and strong positive natural selection." — https://en.wikipedia.org/wiki/Selective_sweep
07:52 < kanzure> "Some 250,000 angiosperm species; less than 500 species domesticated" from a slide deck here http://www.plantsciences.ucdavis.edu/gepts/Gepts%20AIBS-NABT%20Chicago%202004.pdf
07:54 < kanzure> there is no "genetic potential" article on wikipedia
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10:55 < kanzure> why did the space weather page disappear anyway?
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11:50 < sution> I don't know. Why is this channel all just you?
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11:59 < maaku> why are we not cryo-preserving endangered species?
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12:14 < archels_> someone in Russia is probably doing that already
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12:19 < kanzure> sution: because everyone else is boring
12:20 < kanzure> archels_: i don't know if "russia is (probably) on top of things" is a good strategy :-)
12:21 < streety> would there be any advantage to cryo-preserving endangered species over just sperm and eggs?
12:22 < archels_> from the point of the individual animal, yes
12:22 < kanzure> yes, most eggs and embryos require very specific environments for growth, many of these details we don't currently know
12:23 < archels_> they might get to have their brains uploaded
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12:23 < kanzure> you could select for eggs and embryos that grow more readily cross-species, but that will take time and effort
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12:23 < kanzure> and you still need to have at least one working womb mechanism
12:25 < drethelin> https://www.youtube.com/watch?v=LyDliT0GZpE
12:25 < kanzure> .title
12:25 < yoleaux> Russell Barkley explains ADHD / forklarer ADHD - YouTube
12:25 < kanzure> yes he usually says okay things about adhd
12:25 < kanzure> this was the one i saw once https://www.youtube.com/watch?v=SCAGc-rkIfo
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12:30 < kanzure> https://www.reddit.com/r/Futurology/comments/3ocsbi/ama_my_name_is_liz_parrish_ceo_of_bioviva_the/
12:32 < kanzure> gerontology research group mailing list has exploded with questions about "what is a reddit" and "how do i use reddit"
12:32 < kanzure> i guess this is predictable since none of them seem to understand technology
12:33 < kanzure> that's the poeple we have looking into anti-aging, peeps :-/
12:33 < drethelin> wait so
12:33 < drethelin> did she become CEO of this company to reverse her own aging?
12:33 < kanzure> finding a patient that is well-informed is difficult, and perhaps she found a legal loophole for using herself as ceo as patient zero
12:34 < kanzure> usually "patient zeros" for this type of work requires someone who can sign off on informed consent and has medical background and law background, so that you can be protected from them coming back in the future and suing about something gone terribly wrong. i forget where i first saw this strategy though....
12:34 < drethelin> well legally speaking as long as the procedures and chemicals aren't illegal to acquire it's perfectly legal to just chomp them yourself right
12:34 < drethelin> I don't think it's illegal to test things on yourself
12:34 < kanzure> let me introduce you to the fda :-)
12:35 < kanzure> i mean, i agree with you that what you put into your body is your own business, but....
12:35 < kanzure> http://diyhpl.us/wiki/fda/
12:36 < drethelin> all of those are because of distribtion and sales to others though
12:36 < drethelin> don't get me wrong the FDA is awful
12:38 < kanzure> hmm maybe i am thinking of patent law, can't find any evidence about this with the fda
12:38 < archels> We've got a journal club coming up on Nov 13 with Randal Koene and colleagues on whole brain emulation. We're looking for 3-4 folks to join us in the room as panelists to ask questions. Please email me back if you're interested, thanks!
12:38 < kanzure> bioviva probably didn't pioneer this trick but essentially instead of buying a drug, the ceo bought shares in a company that is going to give her the drug, which is essentially selling the drug to the ceo, heh
12:38 < archels> (via OpenWorm)
12:39 < archels> https://plus.google.com/u/0/events/cv9l18020h2cc0doj62h29errn0
12:39 < kanzure> archels: "WTF WHY DO YOU KEEP USING VIDEO, DIE" would be an appropriate question
12:41 < kanzure> but more realistically:
12:41 < kanzure> ask about existing open-source brain emulation software frameworks, or plans for such, or good architecture strategies for such
12:42 < archels> kanzure: this Barkley guy is pretty full of himself
12:42 < kanzure> also ask them whether they use modeldb or the eventual fate of modeldb, how many physiologically characterized neurons they expect to see on the interwebs, and who maintains or tests those models long-term
12:43 < kanzure> archels: yes that's true, he is the prototypical "psychiatrist" person. i'm pretty sure he is a clone of the dude from what about bob.
12:43 < drethelin> all the smartest people are full of themselves
12:43 < maaku> streety: in theory you could just sequence the dna and call it done. but when actually setting out to revive a species it would be nice to have a fully developed specimen to calibrate against
12:43 < archels> haha I know that movie
12:43 < kanzure> archels: right? looks exactly like him. talks the same too.
12:44 < kanzure> maaku: indeed, plus we don't presently know how to bootstrap cells from scratch given just a genome. biological reproduction is a necessary component so far. venter hasn't quite cracked this one yet.
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12:45 < streety> you don't need to cryo-preserve for that though. Fixed specimens would likely work just as well
12:46 < drethelin> Kanzure: I think the  closest we've come to that is we can completely replace the genome of some simple cells
12:46 < maaku> streety: maybe. but it's lot a lot of effort to cryopreserve an adam and an eve for each, plus 100+ cell samples from other specimens
12:47 < kanzure> although, it would be interesting to try to take a breeding approach to the mycoplasma laboratorium problem... instead of just stripping everything out of the genome, you (over a number of rounds of iteration and selection) progressively strip things out of the chasis, such that the genome has to self-bootstrap a greater number of its own components, until you can bootstrap cells from in vitro protein reactions in a single pot.
12:47 < maaku> or even just the female would probably do
12:47 < maaku> *it's not a lot of effort
12:47 < kanzure> (what would a genome look like if it had to constantly refer to how to bootstrap the cell membrane from nothing? polymerase might attach somewhere random at first. i guess you could say a few primers are okay to include....)
12:47 < kanzure> streety: fixed specimens?
12:48 < kanzure> drethelin: yes we can replace the genome, that's true
12:48 < maaku> kanzure: I assume he means plastination
12:48 < maaku> which would also be better than nothing...
12:48 < kanzure> huh?
12:48 < kanzure> .wik plastination
12:48 < yoleaux> "Plastination is a technique or process used in anatomy to preserve bodies or body parts, first developed by Gunther von Hagens in 1977. The water and fat are replaced by certain plastics, yielding specimens that can be touched, do not smell or decay, and even retain most properties of the original sample." — https://en.wikipedia.org/wiki/Plastination
12:49 < kanzure> huh? how would that help
12:49 < maaku> anatomical comparison? idk. I'm not arguing for it
12:50 < kanzure> heh lousy steelman :-) but ok
12:50 < maaku> much better to cryopreserve a viable female
12:51 < kanzure> eggs and sperm are much easier to preserve; once you get an egg and embryo that can develop in $arbitrary_mammalian_womb then you have much better chances of resuscitation later. but which is harder: getting an embryo that can develop more easily in alternative wombs, or getting cryonics to work? :-)
12:52 < kanzure> and no you can't handwave about your glorious MNT future-self rescuing the cryopreserved specimens
12:53 < streety> yes, that's the issue.
12:53 < kanzure> (i mean, i agree molecular nanotechnology will help with cryonics resuscitations, sure.)
12:57 < maaku> kanzure: I'm equally interested in the memories stored in an adult specimen, at least for social species
12:58 < kanzure> ah right you mentioned this the other day
12:58 < maaku> preserving genetics doesn't preserve culture
12:58 < kanzure> you want cinamax/technocolor playback of ancient t-rex memory?
12:58 < maaku> that would be nice
12:59 < maaku> it would solve A LOT of disputes in paleontology
12:59 < maaku> of course memories don't work that way, but you know that
12:59 < drethelin> this makes me want to play an assassin's creed game that lets you play as a bunch of animals
13:00 < kanzure> epigenetic basis of memory is still being figured out, but dna from >1 million years ago is already nucleated to hell and back :-(
13:00 < maaku> hahaha that would be awesome
13:00 < kanzure> maybe siberia though
13:01 < maaku> I'll be clear that I hold no hope for >1mya samples being recoverable ... but today's technology is primitive
13:01 < kanzure> well if you had your nanofog of molecular nanotechnology, you could go digging in siberia to find deep frozen dna molecules
13:02 < maaku> if I could destructively disassemble a soft-tissue fossil and get the exact structure and location of every molecule, computer science can do more than chemistry in geneme recovery
13:02 < maaku> see for example the shredded stasi files
13:04 < maaku> sadly Ötzi was already defrosted numerous times before he was found, but imagine if another ice man discovery were made, and he was kept frozen until such technology existed
13:05 < maaku> if any of his linguistic memories were recoverable, that alone would solve a lot of questions about pre-history
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13:05 < fenn> better find them quick then, before the permafrost thaws
13:06 < maaku> but no one thinks about neural-archaeology
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13:07 < drethelin> well consider how few people must be both experts in neurology AND paleontology
13:07 < kanzure> actually there's neural paleontologists
13:08 < kanzure> .wik paleoneurology
13:08 < yoleaux> "Paleoneurology is the study of brain evolution by analysis of brain endocasts to determine endocranial traits and volumes. Considered a subdivision of neuroscience, paleoneurology combines techniques from other fields of study including paleontology and archaeology. It reveals specific insight concerning human evolution." — https://en.wikipedia.org/wiki/Paleoneurology
13:08 < kanzure> mostly for brain size reasons
13:08 < maaku> yeah but that's more about analyzing skull shapes
13:09 < drethelin> how many paleoneurologists are there
13:09 < kanzure> well i see at least ten different names in the citations at the bottom of that article
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13:37 < pasky> oh, assassin's creed on hplusroadmap?
13:59 < kanzure> i haven't played. or watched.
14:08 < kanzure> page 33 has timeline of discovery of neurotransmitters http://diyhpl.us/~bryan/papers2/brain-emulation-roadmap-report.pdf
14:22 < archels> "We think it is possible to build safe cargo drone routes connected by cheap droneports across much of the planet."
14:23 < kanzure> what, with 10 minute batteries the whole way?
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14:25 < archels> shrug, just load them up with petrol
14:25 < archels> er, kerosine
14:26 < kanzure> wasn't the idea to use blimps for that? or did the physics never work out in favor of that.
14:27 < kanzure> "industrial-scale capture of carbon dioxide from the atmosphere" http://carbonengineering.com/our-technology/
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14:32 < kanzure> linuxcnc controlling a working puma 560 robot arm https://www.youtube.com/watch?v=9cQpkbdhSRw
14:34 < chris_99> Do you still have a robot arm kanzure, a while ago i read that biopunk book heh, and i thought it mentioned you having one iirc
14:35 < kanzure> someone else has the arm at the moment
14:37 < chris_99> what kind of arm is it
14:37 < chris_99> a pneumatic one?
14:38 < kanzure> https://en.wikipedia.org/wiki/Programmable_Universal_Machine_for_Assembly
14:38 < chris_99> cool
14:44 < kanzure> looks like victor scheinman's site got hacked? http://web.archive.org/web/20130718071255/http://vicarm.com/
14:44 < kanzure> hm maybe not
14:45 < kanzure> something about a kitchen sink? https://bugzilla.mozilla.org/show_bug.cgi?id=122411
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14:51 < kanzure> "Selection of animals for visible "desirable" traits may make them unfit in other, unseen, ways. The consequences for the captive and domesticated animals were reduction in size, piebald color, shorter faces with smaller and fewer teeth, diminished horns, weak muscle ridges, and less genetic variability. Poor joint definition, late fusion of the limb bone epiphyses with the diaphyses, hair changes, greater fat accumulation, smaller ...
14:51 < kanzure> ... brains, simplified behavior patterns, extended immaturity, and more pathology are a few of the defects of domestic animals. All of these changes have been documented in direct observations of the rat in the 19th century, by archaeological evidence, and confirmed by animal breeders in the 20th century.[22] A 2014 commentary published in Genetics proposed that many of these features may arise due to mild neural crest deficits that also ...
14:51 < kanzure> ... cause tameness; hence, selectively breeding tame animals also selects for these negative traits.[23]"
14:51 < kanzure> from https://en.wikipedia.org/wiki/Domestication#Negative_aspects
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14:53 < kanzure> "Researchers at the Max Planck institute in Germany are attempting to find a genetic basis for the processes of taming and domestication. They have obtained two strains of grey rats which were bred by Dmitry Konstantinovich Belyaev at the Institute of Cytology and Genetics in Novosibirsk, Russia, research which was later continued by Irina Plyusnina. One strain had been selected for aggressiveness while the other had been selected for ...
14:53 < kanzure> ... tameness, mimicking the process by which neolithic farmers are thought to have first domesticated animals."
14:53 < kanzure> cool someone actually bothered to do the opposite
14:53 < kanzure> i want me some evil rats
14:54 < kanzure> .title http://biorxiv.org/content/early/2014/04/17/004234
14:54 < yoleaux> Genetic Influences on Brain Gene Expression in Rats Selected for Tameness and Aggression | bioRxiv
14:54 < maaku> kanzure: aerodynamics never worked in favor of blimps
14:55 < kanzure> "Inter-individual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior towards humans for more than 64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified ...
14:55 < kanzure> ... four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of ...
14:55 < kanzure> ... correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40 and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals."
14:58 < kanzure> these rats would be good candidates for brain scanning and comparative neuroscience
14:59 < kanzure> also, it's interesting that there was no explicit mutagenesis involved throughout these 64 generations
15:01 < kanzure> and they froze all the brains in liquid nitrogen. great.
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16:18 < kanzure> .g babyslayer
16:18 < yoleaux> http://www.youtube.com/watch?v=Kr_rEr5kdBs
16:19 < kanzure> .title
16:19 < yoleaux> The origin of bodybuilding.com's "Babyslayer" - YouTube
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16:24 < kanzure> jrayhawk: ^
16:27 < mgin> love bb.com lol
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16:34 < mgin> just watched that whole video
16:34 < mgin> cool dude
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16:39 < jrayhawk> https://www.youtube.com/watch?v=VVhvy6T8dIA good lord
16:42 < jrayhawk> .title
16:42 < yoleaux> George "babyslayer" Leeman 875x4 deadlift - YouTube
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16:43 < kanzure> basement dwelling goon is going to need to work on his origin story some more to top that
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16:46 < mgin> beast
16:47 < kanzure> like you might have to go for something like "everyone i ever knew had leukemia"
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19:30 < kanzure> 26-50% of fetal brain tumors are teratomas
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20:15 < kanzure> his disappointment in others could be fixed by injecting them with inflammatories
20:15 < kanzure> guilt-ridden inflammatories, i guess
20:16 < kanzure> i bet chronic stress injections would be less villified than steroids, too
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20:34 < kanzure> "Small volume of mouse cortex is already successfully scanned at 3x3x20nm voxel resolution, with smallest synaptic details being visible http://www.cell.com/abstract/S0092-8674(15)00824-7 " apparently that was the atlum microscope
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20:34 < kanzure> from https://news.ycombinator.com/item?id=10370468
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20:45 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=23666fe7 Bryan Bishop: rewrite transhumanism section >> 
20:45 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=2d53b298 Bryan Bishop: move declaration -> transhumanism >> http://diyhpl.us/diyhpluswiki/transhumanism/
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20:46 < kanzure> remote: From /srv/git/diyhpluswiki
20:46 < kanzure> remote:    8290e98..2d53b29  master     -> origin/master
20:46 < kanzure> remote: error: Your local changes to the following files would be overwritten by merge:
20:46 < kanzure> remote: 	declaration.mdwn
20:46 < kanzure> wut?
20:47 < kanzure> rebuildrepo fixed things. dunno.
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21:10 < kanzure> ugh the author of this description of moravec transfer was eliezer :-/ http://everything2.com/title/Moravec+Transfer
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22:36 < fenn> guy went to all that trouble to build a robot arm controller and then he draws crude cartoons in 2d as a demo...
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22:36 < fenn> at least stack some blocks or something
22:37 < fenn> my issue with the cartoon is you can't really tell if it's inaccurate, it will look the same either way
22:38 < fenn> the problem with controlling robot arms with linuxcnc is the trajectory planner works with cartesian axis acceleration limits but physical reality constrains the joint torques
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22:39 < fenn> there will be more torque to accelerate at 1mm/s^2 if the arm is fully extended vs if it is in its sweet spot
22:40 < fenn> so you have to either severely constrain the workspace to only the sweet spot, or derate all of the motions for the worst case scenario
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22:41 < fenn> there is some hacking on a git branch to at least get the code into shape where this might be fixed, but nobody wants to merge it into main line because it will involve changing a bunch of parameter names and annoying end users
22:42 < fenn> i have yet to see a hobbyist robot doing anything even remotely useful
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22:48 < fenn> kanzure do you still have that robot arm?
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--- Log closed Mon Oct 12 00:00:54 2015