--- Log opened Fri Jan 27 00:00:26 2023
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08:18 < kanzure> what machine learning phd candidates are learning these days https://kidger.site/thoughts/just-know-stuff/
09:45 < kanzure> "A universal deep-learning model for zinc finger design enables transcription factor reprogramming" https://www.nature.com/articles/s41587-022-01624-4 
09:45 < kanzure> i thought zinc finger domain design was fairly routine?
09:46 < kanzure> oh, alright: "This is not for lack of effort, they continued, because multiple approaches have been used to generate ZF libraries and ZF modules to provide designer ZF arrays. Even so, the team stated, “These approaches either require multiple rounds of laborious selection that produce ZFs with inconsistent activity or the application of preselected modules that often fail when expressed out ...
09:46 < kanzure> ...of their selected context.”"
09:47 < kanzure> "The model is based on data generated by the screen of billions of possible ZF-DNA interactions in the researchers’ labs. The Noyes lab has studied zinc fingers for years, and compiled data on 49 billion interactions among zinc finger proteins and DNA by creating high-throughput screens of several zinc finger libraries."
09:49 < kanzure> reprogrammable transcription factors sounds useful.. eg more than dCas9 TF activity (this one had 27x repressive activity https://www.embopress.org/doi/full/10.15252/msb.202110512 )
10:03 < lsneff> I hadn't heard of zinc fingers before
10:03 < kanzure> what about TALENs
10:04 < kanzure> see http://diyhpl.us/wiki/gene-editing/
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11:36 < kanzure> current methods in directed evolution https://pubs.rsc.org/en/Content/ArticleLanding/2023/CB/D2CB00231K (2023)
11:43 < hprmbridge> nmz787> https://www.youtube.com/watch?v=7-LamoxBvW0
11:44 < hprmbridge> nmz787> speaking of directed evolution...
11:44 < hprmbridge> nmz787> this seems like a chicken and egg situation
11:44 < kanzure> yeah i saw that, but didn't think it was that interesting? why wouldn't they be testing mutations?
11:44 < hprmbridge> nmz787> you want variants and their phenotypes understood so you can react quickly if they appear in the wild
11:45 < hprmbridge> nmz787> but you also want/need to avoid conspiracy and potential accidental release
11:45 < kanzure> also i think the technique's term ("directed evolution") is not widely known by the general public, so it's probably a little bewildering why that would be a common technique
11:45 < kanzure> i think it would be more interesting if pfizer was not doing its job at all
11:46 < hprmbridge> nmz787> it seems like the only solution everyone (except potential bad actors) would be happy with is rapid GMO (however you get there) and rapid phenotype discovery
11:46 < hprmbridge> nmz787> (or ignoring phenotype, simply rapid sequencing of active/novel variants, and rapid vaccine production)
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13:58 < kanzure> "extract bits from ROM photographs" https://github.com/travisgoodspeed/maskromtool/ 
13:59 < hprmbridge> MatthewGoodman> Also, @kanzure I know some peeps that do this occupationally if that is of interest
13:59 < kanzure> john mcmaster is the one i know
14:00 < kanzure> talked with bunnie recently.. he has been working on an infrared light source to image and verify chip circuits at home.
14:00 < L29Ah> why infrared?
14:01 < hprmbridge> lachlan> you know bunnie?
14:01 < kanzure> https://www.bunniestudios.com/blog/?p=6656
14:01 < kanzure> "Silicon is transparent to IR, and so, photographs taken in infra-red can be used to verify, at a coarse level, the construction of a chip!"
14:02 < lsneff> some semiconductors are transparent in visible, depends on the bandgap
15:27 < L29Ah> cute, but i don't quite understand what it's useful for
15:28 < L29Ah> could be used to check if the chip was tampered with in a crude fashion, and that's it?
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16:29 < kanzure> yes
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17:14 < hprmbridge> MatthewGoodman> John is who I was thinking of too. Bunnie is super nice, bit overcommitted to about a dozen projects:p
17:16 < L29Ah> yes very nice, i hope he gets back to open hardware-ish laptop someday :3
17:17 < hprmbridge> MatthewGoodman> Heh. It's a good notion, but the market doesn't exist to make it terribly economical IMHO
17:17 < hprmbridge> MatthewGoodman> Also, if you want a slightly shitty laptop you can do worse with rpi
17:17 < L29Ah> i think the market for the open hardware-ish handheld gizmo is even smaller
17:17 < L29Ah> broadcom = shit
17:25 < hprmbridge> kanzure> @MatthewGoodman have you used his precursor device ?
17:25 < hprmbridge> MatthewGoodman> Naw, I'm not really into privacy personally
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--- Log closed Sat Jan 28 00:00:27 2023