--- Log opened Tue Feb 26 00:00:11 2013
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01:37 <@kanzure> paperbot: http://jn.nutrition.org/content/134/10/2517.full
01:38 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20Effect%20of%20Dietary%20Fat%20on%20LDL%20Size%20Is%20Influenced%20by%20Apolipoprotein%20E%20Genotype%20in%20Healthy%20Subjects.pdf
01:55 <@kanzure> man, the lack of quality in nutrition discussions is really sad http://news.ycombinator.com/item?id=5279307
01:57 <@kanzure> i'm not sure how to make better nutrition discussion happen.
02:14 < jrayhawk> actually that seems higher quality than most
02:17 <@kanzure> it still feels painful to read
02:17 <@kanzure> this is not what science feels like. i know a science when i read it.
02:22 <@kanzure> http://scholar.google.com/scholar?q=intitle%3Asimulation+insulin+resistance+nutrition
02:22 <@kanzure> only 52 results? wtf?
02:22 < jrayhawk> why are you expecting science in an internet forum
02:26 <@kanzure> i'm just concerned that nobody seems to be well-read in this subject.
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02:30 <@kanzure> i'm also a little concerned about the lack of modeling/simulation that ties in knowledge about molecular metabolism/pathways, vitamins, thermoregulation, or the various different systems in homeostasis.
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02:34 <@kanzure> paperbot: http://www.springerlink.com/content/685ve8le7fmvy0b1/
02:34 <@kanzure> "This paper proposes the utilisation of fuzzy logic so as to design a system which models the biological regulator of blood glucose. That system consists of several fuzzy relations, each one of them modeling a component of the biological glycemia regulator, that is, pancreatic insulin production, net hepatic glucose balance, insulin dependent and independent glucose uptake, and kidney function."
02:34 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/929b8c28f7f6144de6d1822b00161e95.txt
02:35 <@kanzure> http://www.journalofdst.org/Journal/pdf/July2008/VOL-2-4-ORG7-CAMERON.pdf "We propose a
02:35 <@kanzure> predictive hypoglycemia detection algorithm that uses continuous glucose monitor (CGM) data with explicit
02:36 <@kanzure> certainty measures to enable early corrective action. The algorithm uses multiple statistical linear predictions with regression windows between 5 and 75 minutes
02:36 <@kanzure> and prediction horizons of 0 to 20 minutes."
02:36 <@kanzure> so that's neat and all, but i wonder about non-hypoglycemia situations.
02:39 <@kanzure> here's one that models cholesterol metabolism http://www.ie.boun.edu.tr/labs/sesdyn/publications/theses/MS_demirezen.pdf
02:46 <@kanzure> i see a lot of simulation articles that seem to talk about "energy balance".
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03:12 <@kanzure> paperbot: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000554
03:12 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Nutritional%20Systems%20Biology%20Modeling%3A%20From%20Molecular%20Mechanisms%20to%20Physiology.pdf
03:16 <@kanzure> paperbot: http://www.springerlink.com/content/9n286t786n25236l/
03:16 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/4cf577b8dc864739140abaae58de92e8.txt
03:17 <@kanzure> paperbot: http://ieeexplore.ieee.org/xpl/abs_all.jsp?arnumber%=5415974
03:17 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/1a7d281d4f42e0977653a14c160faf26.txt
03:17 <@kanzure> paperbot: http://ieeexplore.ieee.org/xpl/abs_all.jsp?arnumber=5415974
03:17 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/e6bc0806e6d56ec1a99b2517160b971a.txt
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03:19 <@kanzure> paperbot: http://www.annualreviews.org/doi/full/10.1146/annurev-nutr-071811-150705
03:19 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Modeling%20Metabolic%20Adaptations%20and%20Energy%20Regulation%20in%20Humans%2A.pdf
03:30 <@kanzure> the explanation around equation 5 in that one is a little curious (it includes energy from dietary fat intake, energy from fat oxidation, rates of gluconeogenesis, de novo lipogenesis, and ketogenesis) but goes on to say ".. To date, this is the only mathematical model of human metabolism to consider all three dietary macronutrients and accurately simulate the metabolic and body composition changes in response to diet and physical activity ...
03:30 <@kanzure> ... changes in a wide variety of subject groups."
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03:34 <@kanzure> "For example, the breakdown and resynthesis of body fat requires eight molecules of adenosine triphosphate (ATP) per molecule of triglyceride (22), and the flux through this pathway is strongly influenced by dietary carbohydrate via insulin’s inhibition of lipolysis. Similarly, protein synthesis requires four ATP per peptide bond plus one ATP for amino acid transport (6). Such energy-requiring metabolic fluxes have been incorporated into ...
03:34 <@kanzure> ... computational models of macronutrient balance (33, 38) and may explain the observed energy cost of tissue deposition that is especially important during growth and weight gain (36)"
03:34 <@kanzure> neat, someone bothered to make a model that includes that.
03:46 <@kanzure> "Furthermore, even the most detailed computational models of macronutrient metabolism implicitly represent the effect of hormones such as insulin, but an explicit representation of organ systems along with concentrations of hormones and metabolites would be desirable—especially on shorter time scales so that the response to individual meals could be simulated (17, 73)."
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08:10 < eudoxia> kanzure, what happened to that lego skdb package?
08:11 < eudoxia> it was mentioned in the Updates from Austin presentation
08:11 < eudoxia> but it's not in skdb/packages/, the address in fenn's titlebar
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08:32 < eudoxia> derp, connection problems
08:32 < eudoxia> did it become outdated as the package spec evolve?
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09:12 <@fenn> hrm. one would expect ikiwiki to let you to clone a wiki by default
09:12 <@fenn> somehow it moved to http://diyhpl.us/lego/ and got an ikiwiki layer pasted on top of it
09:13 <@fenn> i expect this was done without much thinking through
09:13 < eudoxia> i'm seeing it http://diyhpl.us/lego/lego.py
09:13 < eudoxia> http://diyhpl.us/lego/dimensions.yaml
09:14 <@fenn> yeah but you can only get the files that are listed in "recent changes" right?
09:14 < eudoxia> yes
09:15 <@fenn> https://secure.diyhpl.us/cgit/lego/tree/
09:16 <@fenn> i'm not sure that's actually the same repo, oh well
09:16 < eudoxia> why remove it from ksd
09:16 < eudoxia> skdb*
09:17 <@fenn> i don't know. apparently someone doesn't like symlinks
09:17 < eudoxia> these are the blocks you used for those screenshots right?
09:18 <@fenn> yeah
09:19 < eudoxia> are there any other sample packages that got removed from the main skdb repo?
09:20 <@fenn> well there's no gnusha.org/skdb/packages/ so apparently all of them
09:20 <@fenn> i'm trying to find out where the content for gnusha.org is located on the filesystem
09:21 < eudoxia> i mean, did you write anything other than that lego package? like packages to represent machines from the GCS?
09:21 < eudoxia> GVCS*
09:22 <@fenn> http://diyhpl.us/cgit should have them; i think the only reasonably filled out ones are "threads" "screw" and maybe "dremelfuge"
09:23 <@fenn> the idea was to convert a lot more but we got hung up on data format issues
09:23 < eudoxia> i heard
09:24 < eudoxia> since mating legos and screws only requires pressing i guess you didn't run into that problem you mentioned of representing processes
09:24 <@fenn> i mean sure you can just dump a bunch of files on a web server and call it a day, but what's the point of that
09:24 <@fenn> press-fit is a construction process
09:25 < ThomasEgi> is case of actual lego. you have thight tollerances to make that work
09:26 <@fenn> i didnt know how to represent tolerances in STEP
09:27 <@fenn> it wouldn't have been a general solution anyway
09:27 < eudoxia> it is, but "process: press-fit" is simpler than "process: weld: {insensity: x, area: y, duration: z, trajectory: [...]}"
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09:31 <@fenn> now i forget how to actually run the random growth demo
09:32 <@fenn> oh it's in the main repo
09:33 <@fenn> paths.py
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09:44 < delinquentme> paperbot, http://jnci.oxfordjournals.org/content/104/5/347.full
09:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/5d3f11f54d6c85a2c479fe9e8bacb281.txt
09:45 < delinquentme> paperbot, http://jnci.oxfordjournals.org/content/104/5/347
09:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/45580c4306964a8c255a849acfe3cfe1.txt
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09:50 < delinquentme> kanzure, paperbot is failing =/
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10:49 <@kanzure> delinquentme: give me your password and i'll add it to paperbot.
10:52 < klafka_> http://www.reddit.com/r/IAmA/comments/199f0n/im_andras_forgacs_ceo_of_modern_meadow_a_company/
10:52 < klafka_> interesting because - meat printing
10:53 < ThomasEgi> bacoooooon!
10:54 <@kanzure> burn the redditor
10:56 < ThomasEgi> bacon dragons!
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11:58 < EnLilaSko> http://rpd.oxfordjournals.org/content/150/3/278.abstract - Very important for guys
11:58 <@kanzure> paperbot: http://rpd.oxfordjournals.org/content/150/3/278.abstract
11:59 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/acc471c9c4e01cb8350ef81ccb306d32.txt
11:59 <@kanzure> someone should fix paperbot.
12:01 <@kanzure> eudoxia: well, it seems drexler has been up to a bunch of nothing
12:01 <@kanzure> http://www.forbes.com/sites/brucedorminey/2013/02/26/nanotechnologys-civilization-changing-revolutionary-next-phase/
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13:46 < jrayhawk> fenn: I am awake for gnusha.org questions if any remain.
13:47 <@kanzure> iirc lego is served from /srv/ikiwiki/legosomething/
13:47 <@kanzure> also, i am disappointed about the banhammer in ##ketotic - wtf
13:57 <@fenn> where gnusha.org/skdb/ from?
13:58 <@kanzure> /srv/www/diyhpl.us/skdb/
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14:27 <@kanzure> 13:59 -!- mode/##ketotic [+b *!*@131.252.130.*] by amiller
14:27 <@kanzure> wow
14:30 <@kanzure> 14:29 <amiller> i'm not sure a ban was necessary in any case so i apologize
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15:31 < jrayhawk> Neat.
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15:34 <@kanzure> jrayhawk: someone else is trying to make the claim that you were trolling because you made a hypothesis and prediction about exarkun's possible response. i'm really thinking that's a stretch of the definition of trolling. but i'm not sure.
15:35 <@kanzure> while that seems like some necessary conditions for trolling to occur, i don't think that's all of them.
15:37 < jrayhawk> Trolling is the manipulation of a conversation towards ends ostensibly undesirable to its other participants. It's entirely plausible that the other regular participants found the interaction I disrupted desirable.
15:37 <@kanzure> theoretically the desirable conclusion was "use the other scrapers, duh"
15:43 < jrayhawk> For sane people, maybe.
15:43 <@kanzure> nobody sane would want to use vimeo, problem solved
15:45 <@kanzure> anyway, i'd still like to figure out some practical simulations of meal feeding
15:46 <@kanzure> i think this could possibly improve discussions (and results) about nutrition
15:52 < klafka_> why
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15:52 <@kanzure> because certain theories (like "energy balance") have been shown to be wrong
15:52 <@kanzure> and if you want to test a prediction about a certain meal, what better way than to use actual data to check yourself?
15:52 < jrayhawk> well, "misleading"
15:52 <@kanzure> paperbot: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000511
15:52 < jrayhawk> "wrong" is overstating things.
15:53 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Estimating%20the%20Continuous-Time%20Dynamics%20of%20Energy%20and%20Fat%20Metabolism%20in%20Mice.pdf
15:55 <@kanzure> why do papers call it "macronutrients" when the topic of digestion or metabolism comes up? why not just call it a nutrient?
15:55 < jrayhawk> They're being specific; macronutrient refers to the fat/carb/protein constituents.
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15:56 <@kanzure> then, what does nutrient refer to that macronutrient does not include?
15:56 < jrayhawk> micronutrients.
15:56 <@kanzure> are amino acids considered a micronutrient?
15:57 < jrayhawk> No, those are proteins.
15:57 <@kanzure> calcium?
15:57 < jrayhawk> That's a mineral. Micronutrient, yes.
15:57 <@kanzure> yes i know it's a mineral. i didn't know if it was classified as a "micro" nutrient.
15:59 < jrayhawk> You normally use google/wikipedia so I'm left to assume you've gone bananas in serializing this learning process and routing it through me.
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16:01 <@kanzure> it's partly because i have trouble predicting which things wikipedia will have or not have. it seems in this case that wikipedia does have an article on "micronutrients".
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16:01 <@kanzure> often wikipedia has nothing about a particular topic deep in the confines of science, which doesn't surprise me anymore.
16:01 < jrayhawk> I blame deletionism.
16:02 <@kanzure> oh man there's even a list http://en.wikipedia.org/wiki/List_of_micronutrients
16:06 < jrayhawk> macromineral micronutrients. Intuitive!
16:11 <@kanzure> that last paper is only considering the gluconeogenic rate, de novo lipogenic rate, fat oxidation rate, carboydrate oxidation rate, and the protein oxidation rate based on body protein and glycogen. aren't there supposed to be other factors, like blood insulin levels influencing glucose uptake?
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16:17 < nmz787> kanzure: seen this? have an opinion? http://www.generative-modeling.org/
16:18 <@kanzure> "Perhaps the GML is a valid successor of VRML" uh oh
16:19 <@kanzure> their development stuff is saying 'access denied' http://www.generative-modeling.org/GenerativeModeling/DEVELOPER/software
16:21 <@kanzure> http://www.generative-modeling.org/GenerativeModeling/Documents/gml_tutorial.pdf
16:21 <@kanzure> they seem to have a custom language.. i'm not sure why that is necessary. why not just use the library calls directly?
16:23 <@kanzure> hrm. so this paper seems to do simulations about "the catabolic potential of an arbitrary nutrient" for microbial cultures (for carbon sources).
16:23 <@kanzure> paperbot: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002762
16:23 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Phenomenological%20Model%20for%20Predicting%20the%20Catabolic%20Potential%20of%20an%20Arbitrary%20Nutrient.pdf
16:24 < nmz787> what about that paper?
16:25 < nmz787> oh, simulations
16:26 < nmz787> kanzure: http://www.3d-coform.eu/index.php/tools/gml
16:26 <@kanzure> i used to have this list of like 10-15 different homeostatic processes in the human body that are influenced directly by food intake. don't know where i put that list. and for some reason none of these papers mention more than one or two at a time. i'm very confused.
16:26 <@kanzure> nmz787: have you seen shape grammars before?
16:27 <@kanzure> or generative grammars.
16:27 < nmz787> hmm, no
16:27 < nmz787> it seems that site has something to do wth meshlab
16:28 <@kanzure> meshlab came out of some research group somewhere, so it wouldn't surprise me that its authors work on other things.
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16:28 <@kanzure> oh, hm, it was a student's project.
16:28 < eudoxia> kanzure: oh i was almost looking forward to reading that book
16:29 <@kanzure> .. why?
16:29 < eudoxia> it's been over 20 years since Nanosystems
16:29 <@kanzure> things i would be interested in from drexler: software, hardware plans, updates about probe tips, things like that.
16:29 < eudoxia> i wasn't alive for some of that time
16:29 <@kanzure> ok that's a reasonable answer.
16:30 < eudoxia> i would certainly like to see drexler in the commit logs
16:30 < eudoxia> that would be kinda futuristic
16:31 <@kanzure> the best i can give you is "Damian Allis <damian@somewhereville.com>" in the nanoengineer.git commit log
16:31 < eudoxia> "completed skdb integration and fixed some bugs on the mechanosynthesis gcode generator | Eric Drexler <edrexler@metamodern.com>"
16:31 <@kanzure> gcode haha
16:32 < eudoxia> ;_;
16:32 < eudoxia> i don't know anything else lol
16:32 < eudoxia> it should be 'nanocode'
16:32 <@kanzure> well i don't really see gcode as useful for layinger things in flat arrays
16:32 <@kanzure> *layering
16:33 < eudoxia> "completed stl->pdb translator | Eric Drexler <edrexler@metamodern.com>"
16:33 < eudoxia> that better?
16:33 <@kanzure> there's already a pdb2stl tool
16:33 <@kanzure> based on pdb2pov
16:33 < eudoxia> O:
16:34 < eudoxia> the future is here
16:40 < nmz787> there's a pdb2stl?
16:42 < nmz787> google only shows a log of this room for pdb2stl
16:43 <@kanzure> heh
16:43 <@kanzure> oh. hrm.
16:44 <@kanzure> there's a podb2pov http://chem.skku.ac.kr/~wkpark/tutor/chem/pdb2pov/
16:44 <@kanzure> then you can use pov2stl
16:45 <@kanzure> oh interesting. that doesn't exist either?
16:45 <@kanzure> i have a file called stl2pov.py, pov2png.py, iges2stl.py, iges2png.py
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16:46 <@kanzure> i have pdb2mdb
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16:47 <@kanzure> and noah bedford (via davidad) said that neil gershenfeld has a stl2png script somewhere.
16:49 <@kanzure> http://www.biohackers.la/BuildAGenome.pdf
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16:54 <@kanzure> paperbot: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000960
16:55 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Metabolic%20Factors%20Limiting%20Performance%20in%20Marathon%20Runners.pdf
17:00 < eudoxia> http://www.forbes.com/sites/joannmuller/2013/02/26/elon-musk-bad-review-in-new-york-times-cost-tesla-100-million/
17:00 < eudoxia> hnhhfghggg
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18:47 < nmz787> http://www.wired.com/design/2013/02/freescales-tiny-arm-chip/
18:48 < nmz787> "We are working with our customers and partners on providing technology for their products that can be swallowed but we cant really comment on unannounced products, says Steve Tateosian, global product marketing manager.
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21:58 <@kanzure> pfft "Sign That Chinese Hackers Have Become Professional: They Take Weekends Off"
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23:03 < nmz787> can wpa2 wifi be jammed?
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--- Log closed Wed Feb 27 00:00:12 2013