--- Log opened Tue Mar 09 00:00:51 2021
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05:12 < docl> .title https://kk.org/thetechnium/scenius-or-comm/
05:12 < saxo> The Technium: Scenius, or Communal Genius
05:13 < docl> .wik Aptamer
05:13 < saxo> "Aptamers (from the Latin aptus – fit, and Greek meros – part) are oligonucleotide or peptide molecules that bind to a specific target molecule." - https://en.wikipedia.org/wiki/Aptamer
05:21 < fenn> aptamers are wacky because they are both the effector and the information storage molecule, so you can directly select for the most effective sequence
05:22 < fenn> the sequence which binds most strongly will be the one that's bound to your target. so pull the target out and the best sequences will be attached. then replicate and mutate them and try again, lather, rinse, repeat
06:16 < docl> replicate as in dna replication? sounds like the term includes peptides, so those you'd need to synthesize (via rna perhaps).
06:29 < L29Ah> .t https://pubmed.ncbi.nlm.nih.gov/14654093/
06:30 < saxo> The effects of IDRA 21, a positive modulator of the AMPA receptor, on delayed matching performance by young and aged rhesus monkeys - PubMed
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07:41 < kanzure> docl: lsneff: has mr. spiroligomer done aptamer stuff with spiroligomers?
07:41 < kanzure> or is bulk random synthesis not a thing
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08:06 < docl> kanzure: google doesn't think so, nor google scholar :/
09:43 < lsneff> kanzure: no idea, haven’t talked to him in a while
09:43 < lsneff> decided against working for his lab this summer
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12:02 < kanzure> https://scholar.archive.org/
12:22 < lsneff> Nowhere near as complete as scihub unfortunately
12:22 < lsneff> though it may have more older works
12:26 < lsneff> prediction: a gpt-3 size transformer trained on a database of all papers in a specific field would be useful for searching through the conglomeration of all research in that field
13:16 < lsneff> .t https://arxiv.org/abs/2006.07125
13:16 < saxo> [2006.07125] Breaking the Warp Barrier: Hyper-Fast Solitons in Einstein-Maxwell-Plasma Theory
13:16 < lsneff> "This is the first example of hyper-fast solitons resulting from known and familiar sources, reopening the discussion of superluminal mechanisms rooted in conventional physics."
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14:02 < archels> random nanobio machinery movie of the day https://www.youtube.com/watch?v=ihlFqOK5cZM
17:18 < kanzure> patch for a git vulnerability https://github.com/gitster/git/commit/684dd4c2b414bcf648505e74498a608f28de45922
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17:50 < L29Ah> kanzure: 404
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17:59 < fenn> shockingly, search actually works without javascript on scholar.archive.org
18:03 < fenn> i don't think of peptides when i hear "aptamer"
18:05 < fenn> the "peptide aptamer" concept seems more like phage display
18:13 < fenn> whatever it is, the scheme is complicated and i'm just not getting it from the wikipedia explanation. feeling dumb today for obvious reasons
18:16 < fenn> need one of those fancy 3D animations to explain the concept
18:24 < fenn> http://www.cellscape.co.uk/ is doing it right
18:27 < lsneff> As someone interested in graphics, those are very impressive animations
18:31 < lsneff> .t https://www.izhikevich.org/publications/spikes.htm
18:31 < saxo> Simple Model of Spiking Neurons
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18:41 < lsneff> Looks like he simulated one second of 10^11 neurons randomly connected and observed alpha and gamma rhythms
18:58 < kanzure> ooold article
18:59 < kanzure> lsneff: take a look at https://diyhpl.us/~bryan/papers2/ai/ and https://diyhpl.us/~bryan/papers2/neuro/
19:00 < kanzure> this stuff was interesting https://diyhpl.us/~bryan/papers2/neuro/randall-oreilly/
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19:08 < lsneff> Is that neural model in the article I linked still useful, or have they moved on from there?
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20:13 < kanzure> lsneff: i think the blue brain human brain project stuff had more detail? archels will know more.
20:14 < lsneff> 👍
20:14 < lsneff> adam marblestone was talking about a brain scanning FRO a few months ago
20:15 < kanzure> have you considered a geochurch internship?
20:21 < lsneff> easier said than done
20:22 < kanzure> nah the way it works is that you kind of just show up and then you don't leave
20:22 < kanzure> boyden lab also hires software peoples
20:22 < kanzure> and they collaborate a bunch
20:23 < lsneff> interesting...
20:24 < lsneff> i may look into that more
20:25 < L29Ah> http://arep.med.harvard.edu/gmc/email.html :D
20:27 < fenn> i'm pretty sure spammers have figured out how to grep for [at]
20:27 < kanzure> lsneff: boyden lab is somewhere else btw but pretty sure that's where marblestone came from
20:27 < kanzure> i think they pass the good ones around like baseball cards between the labs
20:28 < fenn> draft pick
20:28 < fenn> the 2021 academic tournament season
20:28 < kanzure> i remember davidad was hanging around the hoop for a bit...
20:28 < kanzure> kettner was another one
20:28 < fenn> who's kettner?
20:28 < kanzure> dna synthesis dna data storage person
20:29 < kanzure> https://genetics.med.harvard.edu/lab/church/kgriswold
20:29 < fenn> start a fantasy academia betting website where you make predictions about who gets published in the next year and build your dream lab
20:30 < lsneff> macadaculus
20:31 < lsneff> I'm not really sure I'm what they're looking for, given that I'm not necessarily interested in staying in academia, but I'll think about contacting them
20:33 < lsneff> (I'm also not sure why I want to do, that's probably a bigger issue)
20:33 < lsneff> *what I want to do
20:35 < kanzure> lsneff: try going through boyden lab http://syntheticneurobiology.org/
20:35 < kanzure> iirc he was hiring for software engineers in general a while back
20:36 < kanzure> http://syntheticneurobiology.org/people
20:37 < lsneff> Jeez that's a lot of people
20:38 < kanzure> academia churns through bodies
20:38 < kanzure> just keep feeding the machine
20:42 < lsneff> i guess the only way to fight the dragon is with a equally monsterous machine
20:44 < fenn> mecha-academia
20:45 < fenn> it breathes nuclear fire
20:46 < lsneff> burning with the mass-energy of a million grad students
22:08 < kanzure> where is gradstudentbot?
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22:09 < kanzure> gradstudentbot: welcome back
22:09 < gradstudentbot> I am writing the abstract.
22:09 < kanzure> gradstudentbot: about what?
22:09 < gradstudentbot> Got halfway through figuring out all the cell signalling molecules in psoriasis when the cells died and the data couldn't be replicated, so psoriasis is really hard to cure guys don't get it
22:18 < lsneff> omg
22:20 < lsneff> gradstudentbot: im sorry to hear that
22:20 < gradstudentbot> I don't remember the paper, but someone definitely did that.
23:36 < abetusk> gradstudentbot...
23:36 < gradstudentbot> I haven't seen my PI in like a week.
23:36 < abetusk> gradstudentbot...
23:36 < gradstudentbot> Hey, I got 100% yield! Oh wait, no.
--- Log closed Wed Mar 10 00:00:53 2021