--- Log opened Wed Jun 24 00:00:50 2015
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03:50 < eleitl> What's the state of nanoengineer, kanzure?
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03:55 < kanzure> still dying of bitrot
03:56 < kanzure> i think i saved all of the old software to run it in some chroot
03:56 < eleitl> Ok. Maybe someone can resurrect it eventually.
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04:10 < kanzure> .title http://www.futuremedicine.com/doi/10.2217/nnm.15.52
04:10 < yoleaux> An Error Occurred Setting Your User Cookie
04:11 < kanzure> (magnetoelectric nanoparticles for brain stimulation and imaging)
04:13 < kanzure> hahaha brainport has finally been fda approved... what a joke, took forever http://www.medicalnewstoday.com/articles/295709.php
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04:15 < kanzure> archels: nest git repo is available now https://github.com/nest/nest-simulator
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06:46 < kanzure> bloop
06:47 < namespace> Pong.
06:47 < namespace> What's up?
06:55 < kanzure> jealous about "replacing the entire planet's genomic content" ambitions
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07:15 < kanzure> "To put this in perspective, 38% of meat products available for sale in the UK test PCR positive for T. gondii tissue cysts, some of which are probably viable (Aspinall et al. 2002)."
07:16 < kanzure> "Up to half of the world's human population is estimated to carry a Toxoplasma infection.[3] The most recent U.S. data from 2014 indicated the rate as 22.5% nationwide and 29.2% in the northeast U.S.[4] One study claimed a seroprevalence of 75% in El Salvador.[5] Official assessment in Great Britain places the number of infections at about 350,000 a year.[6]"
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07:19 < kanzure> i wonder what percent of these are brain dwelling
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07:20 < kanzure> hmm this claims that it preferentially forms cysts in the brain, http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003283
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08:27 < eleitl> Brain symbiontes are a dead end.
08:28 < kanzure> why's that
08:29 < eleitl> Because they're not going to give you an easy route you expect, and will tie up you for years. Plus, pathogen research is expensive.
08:29 < eleitl> Certainly not DIY, unless you want to deal with fed raids.
08:30 < eleitl> Why not cryopreservation instead? Much easier.
08:30 < eleitl> Your selective breeding thing would probably produce results. Not dramatic results, but measurable ones.
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08:33 < kanzure> with the exception of raids, i think the same statements could be said for cryonics :-)
08:33 < kanzure> (although raids are sitll likely; just dramatically less likely)
08:33 < eleitl> Not really. You can work with fresh cadaver tissue.
08:34 < kanzure> i'm a little surprised that nobody has gone looking for evidence of microbes in other animal brain tissue--- surely there are more than just pathogens
08:34 < eleitl> And of course you can get licensed for animal research, it's just complicated and expensive.
08:34 < eleitl> I would expect they're almost certainly 100% pathogens
08:35 < eleitl> There is certainly no evidence to the contrary.
08:35 < kanzure> swithching the topic slightly, but i don't see any obvious ways of designing chemical nootropics
08:35 < eleitl> I agree. The potential is limited.
08:35 < kanzure> too many receptors to consider, too many ligands, binding sites, side-effects...
08:35 < eleitl> Real enhancement will require invasive nanoware.
08:36 < eleitl> We won't have any in any meaningful time, obviously.
08:36 < eudoxia> what's nanoware going to do that chemicals can't though
08:36 < kanzure> hm.
08:36 < eleitl> Critters don't have nearly as much control.
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08:36 < kanzure> eudoxia: a good example of nanoware is stuff like the unfolding mesh net that expands into brain capillaries
08:36 < eleitl> You can go in and build scaffolding with support, alternative processing in-situ.
08:36 < kanzure> although that's not very nano
08:36 < eudoxia> oh, i thought you were talking about MNT robutts
08:37 < eleitl> You can do great I/O if you've got ~um sized active electrodes.
08:37 < eleitl> A few 100 million or a billion probes, bidirectional ones.
08:37 < kanzure> eleitl: i would esitmate that transcranial ultrasound simulation of the brain is far easier than both chemical and microbial nootropics (although it's not clear whether stimulating specific regions of brain matter would ever have an enhancing effect on any mental performance whatsoever)
08:37 < eleitl> Bugs are out of control and stupid. Bacteria can't even do the shapes you want.
08:38 < kanzure> bacteria can do shapes you want- although you have to be careful during experimental design
08:38 < kanzure> http://diyhpl.us/~bryan/papers2/bio/The%20selective%20value%20of%20bacterial%20shape.pdf
08:38 < eleitl> Make a bacteria do me a Purkinje.
08:38 < kanzure> replace a purkinje?
08:39 < eleitl> Do an arbitrary defined shape of complexity of a Purkinje.
08:39 < eleitl> Just holding the shape.
08:39 < eleitl> No other function, just go in, and hold the shape.
08:39 < kanzure> selecting for shape is quite trivial i think...
08:40 < eleitl> Except you would have to reinvent the machinery of a specialized animal cell for that.
08:40 < kanzure> microfluidic platform; put single cells in each bubble (water-in-oil-in-water); pass the bubbles by a camera; toss the rodents that are less close to the shape you want. breed the remainders, either through horizontal gene transfer or through other mechanisms.
08:40 < eleitl> Neurons are not stupid, and they have lots of gadgets onboard.
08:40 < kanzure> but you wanted shape- for some reason
08:41 < kanzure> microbial nootropics are unlikely to interface electrically as part of an action spike train, instead they are more likely to direct axon growth or something
08:41 < eleitl> If you need a complicated function you will need a complicated shape.
08:41 < eleitl> They need to know where they are. How can you teach them chemical labelling in the CNS?
08:41 < eleitl> And evade the immune system?
08:41 < eleitl> None of that is easy.
08:41 < kanzure> they don't need to know- you can just select the ones that die in the wrong spots
08:42 < kanzure> evading the immune system: start with a strain that does.
08:42 < eleitl> Then, you should try a pilot, and see how far you'll get in 5 years.
08:42 < kanzure> yes it's on the list....
08:42 < eleitl> (please do not do that, you'll be disappointed)
08:42 < kanzure> cryonics is higher priority
08:43 < eleitl> It's about the only thing that barely works.
08:43 < kanzure> oh also: the reason why i said microbial notroopics and not retroviral nootropics is because i think selection would be easier with larger genomes. viruses don't have as many options, and are less easy to force into symbiosis.
08:44 < eleitl> You can probably do lots of good dog experiments in Asia.
08:47 < kanzure> also.... wound healing (for certain kinds of wounds) could benefit from using selection as well; oyu could cultivate bacteria and apply to skin cuts and pick the bacteria that tend to not impact the timeline until wound healing. then pick the ones that decrease the amount of time until healed.
08:47 < kanzure> this method is really underutilized in biotech
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09:00 < delinquentme> HOOOOOOOKAY
09:08 < eleitl> I think you will need human subjects. I'm sure some channel regulars would volunteer.
09:14 < JayDugger> How big a wound?
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09:18 < kanzure> whatever size is necessar to remove your brain
09:18 < eleitl> Just a tiny pinpick.
09:19 < delinquentme> so you're pulling it out through my nose egyptian style ?
09:19 < eleitl> The flesh-eating amobae make sure no hook is required.
09:19 < eleitl> It will just run out of your nose and ears.
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10:39 < FourFire> kanzure, ++ "another selection project i want to try eventually is infecting mice with brain-dwelling bacteria, then select populations of bacteria that correlate with mice that have better smartness test scores (and breed/mutate those bacteria)
10:39 < FourFire> "
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13:07 < ryankarason> i often think about my stomach brain and how the gut flora and ecosystem of other bacteria affect its thoughts
13:08 < ryankarason> to what decree, i am very curious
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14:42 < kanzure> expressing some neural growth factors in the gut is less likely to effect the brain than expressing that sort of protein directly in the brain
14:42 < kanzure> i wonder if there's a patch clamp study of this
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15:07 < fenn> there are polysaccharides that influence brain BDNF, for example in lion's mane (supposedly)
15:08 < fenn> also, the gut has a higher total mass of neurotransmitters than the brain and as such can raise or lower them by sucking up all the precursors for its own use
15:09 < fenn> something like that
15:09 < fenn> .wik brain gut axis
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15:10 < fenn> https://en.wikipedia.org/wiki/Gut%E2%80%93brain_axis
15:13 < fenn> well that was a pretty vague article
15:15 < kanzure> i would be really upset if blood neuro-relevant precursor depletion is the main mechanism for modulating levels or for the brain to control its own levels (e.g. i was hoping for local messaging)
15:16 < fenn> what can i say, biology is a pile of shoddy hacks
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15:17 < fenn> sugar cravings -> eat sugar -> insulin -> nonspecific amino acid transport -> tryptophan crosses the blood-brain barrier
15:31 < kanzure> well, i'm sure the same microbe design strategy can be used for gut microbes, it's just slightly less cool to talk about
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15:32 < kanzure> and also it seems slightly less likely that you can get very specific brain region targeting
15:32 < kanzure> with microbes literally in the brain you can just slice the brain up and count the microbes in the region of interest
15:32 < kanzure> with gut microbiota signaling all you can do is some sort of antibody staining
15:32 < kanzure> i mean antibody staining in the brain region of interest
15:33 < kanzure> also: i am v. disappoint about my inability to find scientific documentation regarding variations between adult human brain anatomy, such as normal structural variation
15:34 < kanzure> oh right.. how are you going to do antibody staining when you don't even know what your microbial critters have released into the bloodstream from the gut? what are you going to be looking for...
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18:17 < kanzure> otherwise i think we would have already done that sort of gut-biome-brain-influence stainin
18:17 < kanzure> staining
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19:01 < kanzure> "Stable small quantum dots for synaptic receptor tracking on live neurons" http://people.physics.illinois.edu/Selvin/PRS/Angew%20%20Chem%20%20Int%20%20Ed%20%20Engl%20%202014%20Cai.pdf
19:03 < kanzure> "Specific retrograde transduction of spinal motor neurons using lentiviral vectors targeted to presynaptic NMJ receptors" http://www.nature.com/mt/journal/v22/n7/abs/mt201449a.html
19:03 < kanzure> "To understand how receptors are involved in neuronal trafficking and to be able to utilize them for specific targeting via the peripheral route would be of great benefit. Here, we describe the generation of novel lentiviral vectors with tropism to motor neurons that were made by coexpressing onto the lentiviral surface a fusogenic glycoprotein (mutated sindbis G) and an antibody against a cell-surface receptor (Thy1.1, p75NTR, or ...
19:03 < kanzure> ... coxsackievirus and adenovirus receptor) on the presynaptic terminal of the neuromuscular junction. These vectors exhibit binding specificity and efficient transduction of receptor positive cell lines and primary motor neurons in vitro. Targeting of each of these receptors conferred to these vectors the capability of being transported retrogradely from the axonal tip, leading to transduction of motor neurons in vitro in compartmented ...
19:03 < kanzure> ... microfluidic cultures. In vivo delivery of coxsackievirus and adenovirus receptor-targeted vectors in leg muscles of mice resulted in predicted patterns of motor neuron labeling in lumbar spinal cord. This opens up the clinical potential of these vectors for minimally invasive administration of central nervous system-targeted therapeutics in motor neuron diseases."
19:04 < kanzure> welp....
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19:14 < kanzure> "Insulin can induce the expression of a memory-related synaptic protein through facilitating AMPA receptor endocytosis in rat cortical neurons" http://www.researchgate.net/profile/Tsan-Ju_Chen/publication/261408690_Insulin_can_induce_the_expression_of_a_memory-related_synaptic_protein_through_facilitating_AMPA_receptor_endocytosis_in_rat_cortical_neurons/links/54e80e800cf25ba91c7ad389.pdf
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--- Log closed Thu Jun 25 00:00:05 2015