--- Log opened Wed Mar 16 00:00:01 2016
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00:02 < esmerelda> Trying to make sense of gene regulatory networks is bewildering
00:02 < esmerelda> Each arrow isn't a simple "increases expression of", there are cofactors, protein-protein binding, and like actual mechanisms that are needed
00:03 < esmerelda> Like the SOX9 protein acts as a transcription factor to promote FGF-9, and if FGF-9 is knocked out SOX9 levels dwindle
00:04 < esmerelda> So the literature says "ah, a positive feedback loop!"
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00:05 < esmerelda> But really, FGF-9 is just responsible for dragging SOX9 back into the nucleus, because it has a Nuclear Export Marker domain on it
00:05 < esmerelda> So if FGF-9 isn't around, all the SOX9 gets pumped out into the cytosol
00:06 < esmerelda> If arrows don't cut it, how do we meaningfully represent and analyse these networks?
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01:12 < esmerelda> Hm, I have an interesting idea. Y'all might find it useful for other purposes.
01:14 < esmerelda> The androgen receptor (AR) is a nuclear receptor which complexes with HDAC-1, which deacetylates a histone causing the region between it and the next histone to be unwound and open for transcription
01:14 < esmerelda> Much of AR's work and it's irreversibility after stopping testosterone is caused by histone modification, I think
01:16 < esmerelda> So what if I modified the AR gene so that instead of having a binding domain for HDAC-1, it had a binding domain for a histone rewinding protein instead?
01:17 < esmerelda> Then that copy of AR would be like the anti-androgen receptor, and it'd cause the androgenic regions of DNA (E.g. body hair with hHa7) to stop being expressed.
01:18 < esmerelda> Boom, I can rewind the cell programming of puberty
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03:17 < kanzure> "Patents and innovation in economic history" http://www.gwern.net/docs/2016-moser.pdf
03:17 < kanzure> spoiler: patents discourage innovation and everyone is awful
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07:51 < JayDugger> Good morning
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08:23 < maaku> ah not politics in here too?
08:25 < maaku> does anyone know of work interpreting neural networks as code?
08:26 < maaku> e.g. lisp interprets nested lists as executable programs
08:26 < maaku> i'm wondering if there's been work on representing nested layers of weights as programs
08:26 < maaku> what that would look like, etc.
08:27 < maaku> a homoiconic neural network
08:32 < JayDugger> maaku, for your first question, test the ignore button.
08:32 < JayDugger> the second is not anywhere near my area of expertise.
08:32 < JayDugger> Sorry.
08:42 < archels> yeah, there was a thing about building Turing machines using a neural network
08:43 < archels> ah, there might have been something about making it go different directions in state space
08:51 < maaku> http://www.dlsi.ua.es/~mlf/docum/forcada01b.pdf
08:51 < maaku> aparantly they quote minsky, which shouldn't be a surprise
08:52 < maaku> archels: link?
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09:38 < kanzure> maaku: iwas thinking of a way to convert code to neural networks and ack the other way. i think that for some functions that this should e possile.
09:38 < kanzure> oairplane wifi is sucky
09:43 < archels> ack?
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10:26 < maaku> kanzure: for finite state machines -- http://dl.acm.org/citation.cfm?id=1362138
10:28 < maaku> kanzure: well i know you can learn general functions, and then extract those functions
10:29 < maaku> CogPrime's approach is to convolutional neural networks for perception, then learn a programmatic form (lisp representation, effectively) using genetic algorithms
10:30 < maaku> They're not using recurrant networks because they are stupid
10:31 < maaku> But the other option is to take the AGI logic of CogPrime and represent that in neural networks
10:31 < maaku> Getting rid of that translation step would get rid of a lot of the messiness of opencog
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11:25 < esmerelda> Kanzure, are there any software suites around for protein-protein docking?
11:25 < esmerelda> Or is it all small-molecule?
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12:28 < Jawmare> 5htp vs theanine?
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16:34 < kanzure> back
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16:41 < Jawmare> FourFire, I just picked up a pack of nicotine gums for $5
16:42 < Jawmare> 25 piece, 2mg ea
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17:28 < kanzure> archels: ack what?
17:31 < maaku> .title http://nautil.us/blog/why-neuroscientists-need-to-study-the-crow
17:31 < yoleaux> Why Neuroscientists Need to Study the Crow - Facts So Romantic - Nautilus
17:36 < kanzure> "Be driven, in a way which is beyond the drive of every other human. This isn't about waiting around until somehow, for some reason, someone else destroys the Earth. This is about you travelling from where you are right now to a point in time when you have brought about the Earth's destruction. You want continuity of purpose between these two events. You want to set events in motion and then live to see their conclusion. The second part ...
17:36 < kanzure> ... is because you need to be sure."
17:36 < kanzure> "So you must need to destroy the Earth. Make that need into the foundation of everything you do, from getting up on any given morning to quitting for any given night. You will need to sustain this drive for a greater period of time than anybody has ever sustained anything. You need to be superhuman, not to say psychotic. You're embarking upon a journey into deep psychological time, across time scales against which the human psyche can ...
17:36 < kanzure> ... certainly have no protective evolutionary adaptations."
17:36 < kanzure> "We do these things not because they are easy, but because they are hard."
17:36  * kanzure fires the missiles
17:38 < kanzure> (of course it was really because "the russians are already doing things")
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18:23 < kanzure> yashgaroth: sup
18:23 < yashgaroth> genscript apparently does ship residential, now to wait patiently for two weeks
18:24 < kanzure> oh that is a good update
18:26 < yashgaroth> just hoping this protein works in e.coli, all I have to go on is reports from academia or industry, who each have their own motivations to exaggerate results
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18:48 < Sishio> What journal was the article published in?
18:57 < yashgaroth> who you asking, me?
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19:02 < yashgaroth> there's at least a dozen articles I'm relying on, the fusion protein has been made in mammalian cells, the subunits have been made in e.coli but not as a fusion; and nobody publishes yield
19:14 < Sishio> rip
19:15 < yashgaroth> yeah rip
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--- Log closed Thu Mar 17 00:00:02 2016