--- Log opened Mon Apr 09 00:00:42 2018
00:17 < mrdata> fltrz, plants use oxygen when they dont get sunlight
00:18 < mrdata> so it isnt high CO2 that suffocates them but low O2
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05:08 < fltrz> fenn, yes I was talking about what to do with CO2 once isolated (by condensation), by allowing them to re-evaporate you can recycle most energy of its condensation, but then where would one store it? not sure what balloon or film one needs with low CO2 diffusion
05:10 < fltrz> mrdata, I knew they needed oxygen, but I didn't know you could set CO2 as high as you want
05:12 < fltrz> l_wl, Firmicutes interesting
06:21 < kanzure> .tw https://twitter.com/kanzure/status/983327764194447360
06:21 < yoleaux> @brucefenton Sending around PDFs to represent private equity is absolutely barbaric but everyone does it, even everyone in the tech industry. Upgrading this "tech" doesn't require trusted third parties-- just tech to replace PDFs. (@kanzure, in reply to tw:983326682219270144)
06:26 < TMA> kanzure: well, it were printed papers with intricate guilloche patterns before the PDFs
06:27 < kanzure> yes they are literally certificates so why not certificate authority model? yes it's annoying to operate a cert root server but companies seem to accept they should have their own accounting ledger...
06:30 < TMA> for the same reason shares were traded in spanish reals on the stock exchange until the 1970's (that is several centuries after spanish reals ceased to exist as a currency) (silver dollars were "pieces of eight" - one spanish silver dollar was eight reales, the shares were traded in 1/8 dollar increments)
06:33 < kanzure> .tw https://twitter.com/andyextance/status/983302504195633153
06:33 < yoleaux> How can we pump up the bases on gene - and even genome - synthesis? http://bit.ly/2H9KHlS I ask @GP_write @emilyleproust @twistbioscience @evonetix @Prof_Tom_Brown @atdbio @jiahao28 and @nuclera for @ChemistryWorld. (@andyextance)
06:39 < TMA> it is the same reason americans will never abandon measuring speed in furlongs per fortnight and alcohol contents in perduocents, why an ounce of gold will be heavier than an ounce of sugar while a pound of gold would be lighter than a pound of sugar -- tradition (which is mostly nothing more than momentum)
06:56 < mrdata> fltrz, i expect there is a maximum CO2; checking
07:00 < mrdata> well, i get plenty of climate change arguments from that, https://www.skepticalscience.com/co2-plant-food.htm
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07:01 < mrdata> https://www.theguardian.com/environment/climate-consensus-97-per-cent/2016/sep/19/new-study-undercuts-favorite-climate-myth-more-co2-is-good-for-plants
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07:01 < fltrz> right any CO2 "limit"/"maximum" etc will invariably be crowded with climate results
07:03 < mrdata> https://science.gu.se/english/News/News_detail/increased-carbon-dioxide-levels-in-air-restrict-plants-ability-to-absorb-nutrients.cid1309352
07:04 < fltrz> thank
07:07 < kanzure> .title https://github.com/sjors/matreon
07:07 < yoleaux> GitHub - Sjors/matreon: Self hosted platform to receive money from your supporters, using Bitcoin Lightning network
07:09 < fltrz> so if eukaryotes can be seen as symbiosis between say nucleus and mitochondria,... does the mitochondrial DNA encode most proteins on the mitochondrial membrane? or is the nucleus in charge of the mitochondrial membrane?
07:10 < kanzure> mitochondrial genome is pretty short, you could go check
07:10 < fltrz> if nucleus and mitochondria are each predominantly in control of their own membrane, does the mitochondria express proteins that end up on the outer cell membrane?
07:11 < kanzure> https://en.wikipedia.org/wiki/Human_mitochondrial_genetics
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07:11 < fltrz> what was the original cell membrane of the nuclear DNA? was the nuclear membrane the original cell membrane, and the symbiotic shared membrane created later?
07:12 < fltrz> or was the current cell membrane always the nuclear DNA's cell membrane, but a new inner membrane added around the time the mitochondria joined?
07:13 < fltrz> what came first, the castle or the city walls?
07:15 < kanzure> phylogenetics has revealed a lot of these details.
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07:25 < fltrz> "Because they provide 30 molecules of ATP per glucose molecule in contrast to the 2 ATP molecules produced by glycolysis, mitochondria are essential to all higher organisms for sustaining life." is glycolysis the only pathway from nuclear DNA that converts glucose into ATP? the efficiency ratio is 15! glycolysis pathway disposes of all the rest as heat? or does it perform some other chemical work?
07:27 < fltrz> perhaps conditions before the great oxygenation event were much colder and the heat was useful?
07:39 < archels> .title https://www.youtube.com/watch?v=49pXOtVSxOU
07:39 < yoleaux> Kale Rogers Talks Spyce Kitchen: The First Automated Restaurant - YouTube
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09:34 < kanzure> huh, there's no good max more video on youtube talking about extropianism?
09:49 < kanzure> .title https://news.ycombinator.com/item?id=16790814
09:49 < yoleaux> FreeCAD 0.17 “Roland” released | Hacker News
09:50 < kanzure> one of the comments says that lulzbot has been financially supporting the development of freecad. great.
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09:51 < kanzure> https://github.com/realthunder/FreeCAD_assembly3
09:51 < kanzure> https://github.com/symbian9/reddit_cad_challenge
09:51 < kanzure> https://github.com/m2n037/awesome-mecheng
09:54 < kanzure> it's sort of disconcerting that there's no good introductory extropianism thing ("hi we're from the future, here's some good reasons to do technology development things, here are some interesting goals, kthxbye").
09:59 < kanzure> .tw https://twitter.com/gwern/status/980856600704487427
09:59 < yoleaux> Why do PGSes matter so little for current embryo selection, counterintuitively? Because with small n of embryos to choose from in IVF, even lousy PGSes have high probability and the differences are small so mistakes matter less. Some simulation estimates of the order statistics: https://pbs.twimg.com/media/DZyzLFJXUAAVCCa.jpg (@gwern)
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10:58 < fenn> from r/cad/ "all the icons, instead of just textual labels. There are far too many to remember, so many of them look practically the same, and you have to hover the mouse over each one for too long for the tooltip to pop up and see what it is. I remember doing a hack once, editing some config file so it couldn't find all the icon artwork, and reverted to text labels instead."
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11:07 < kanzure> next: "so i hacked each icon to turn into an interactive python prompt and i can just type the command that i want inside of the icon instead"
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12:41 < kanzure> http://engineeringbiologycenter.org/2018meeting/
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14:04 < fltrz> over at https://ds9a.nl/amazing-dna/ in the section "Cluttered APIs, dependency hell":
14:04 < fltrz> " As proteins interact in the cell, they rely on each others' characteristics. It has just been shown that proteins that interact with a lot of other proteins cannot evolve, or at least, only do so at a very slow rate. See Nature, 28 June 2001, and M. Kimura, T. Ohta, Science, 26 April 2002. "
14:04 < fltrz> " They propose that this is because of great internal dependencies which inhibit the changing of the 'contract' of the protein. It is also noted that evolution does take place, but very slowly as both parts of the dependency need to evolve in a compatible way at the same time. "
14:05 < fltrz> so does there exist a database to query the covariance of protein variations?
14:07 < fltrz> i.e. protein p1 and p2 each have multiple versions say 10 each, then instead of 10x10=100 combinations you only have on the order of 10 (apart from a constant factor). or if you plot them in a table with columns for p1 and rows for p2 you can put it in diagonal matrix form
14:08 < kanzure> uh i thought genes just get indiscriminately copied and then the copies can be mutated as long as one isn't. copy number variations are a thing.
14:08 < fltrz> i.e. p1v4 tends to only appear in individual with p2v4, but all v1 to v10 appear
14:08 < fltrz> kanzure, this is for directly interacting proteins
14:09 < fltrz> thats why I find it interesting, if the covariances or correlations are available somewhere you can deduce which proteins interact
14:10 < fltrz> so 2 non-interacting proteins each with 10 versions would present as all 100 combinations appearing in the population
14:12 < fltrz> according to that paragraph or the paper it cites: directly interacting (say binding, catalyzing etc) proteins have measurable correlation over the population instead of random combination,because they must couple
14:15 < fltrz> i.e. input: database of many individuals ==using correlation==> output: map or graph of the human proteins where links indicate/suggest a direct interaction
14:15 < kanzure> well there's the reactome and metabolome databases
14:15 < kanzure> so maybe start there.
14:16 < fltrz> those sound like they already contain the interaction graph? was this work already performed?
14:19 < fltrz> if N is the number of sequences (coding for protein, or RNA or anything stemming from DNA but that needs to couple to a complementary part) then we can define N*(N-1)/2 exactly the number of sequence combinations, for what percentage of these have the correlations not yet been measured?
14:21 < fltrz> I can go to these databases as if I were working on a specific problem in biomedicine, except I'm not, I'm wondering if a known technique is being ignored or systematically used (and the progress bar can be defined like I did above as a percentage)
14:23 < fltrz> I read recently some DNA database (full genome) for hundreds of people was released, but it wasn't clear how to download them, or perhaps only released to 'legitimate' users?
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14:25 < fltrz> 500 by 500 seems sufficient (if they are not all drawn from the same locality) to calculate a correlation coefficient
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14:28 < fltrz> damm the databases seem to be regional ones
14:30 < fltrz> how can the scientists that do genetic dating and tracking do their work if they don't have kick-ass databases? or they do, but its all hush-hush?
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14:57 < kanzure> .title https://github.com/stojanovic/scottyjs
14:57 < yoleaux> GitHub - stojanovic/scottyjs: Deploy static websites and single page apps to AWS S3 and CloudFront with a single command
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19:48 < kanzure> blort
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--- Log closed Tue Apr 10 00:00:43 2018