2014-12-22.log

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superkuhpaperbot: http://www.sciencemag.org/content/346/6216/1495.full.pdf06:06
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kanzurebleep07:18
kanzure"Spontaneous generation and colony formation in the Amoeba world"07:24
JayDuggerKanzure, what's Freitas up to these days?07:24
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kanzurenot sure, i think "more of the same"07:26
kanzure.title http://onlinelibrary.wiley.com/doi/10.1002/cplx.10095/abstract07:26
yoleauxSelf-organizing genetic codes and the emergence of digital life - Pargellis - 2003 - Complexity - Wiley Online Library07:26
kanzure"The emergence of self-replicating programs from an initially disordered “prebiotic” phase consisting of randomly generated opcodes (virtual machine instructions) is a challenging problem. The computer world, Amoeba, has many virtual CPUs acting upon sequences of randomly generated codons (opcode templates). An assignment matrix degenerately maps these codons to a genetic basis set of opcodes, analogous to the translation of ...07:26
kanzure... nucleotides to amino acids. Amoeba self-organizes by increasing assignment probabilities for those codon-opcode pairs in successfully generated children. This halves the effective size of the opcode basis set, doubling the rate of emergence over the control case (random assignments)."07:26
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kanzureweird search result https://gowers.wordpress.com/2009/11/07/polymath-and-the-origin-of-life/07:30
kanzurehere is a description of amoeba/pargellis' simulator http://www.cs.man.ac.uk/~toby/writing/PCW/life.htm07:32
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kanzure"Pargellis found that on average, a self-replicating sequence of instructions would spontaneously arise after about 400 generations. Initially, such 'self-reps' were often unnecessarily complex, and contained portions of code which performed no useful task, or were skipped over."07:33
kanzureanp@lucent.com07:37
kanzurehttp://diyhpl.us/~bryan/papers2/ai/The%20evolution%20of%20self-replicating%20computer%20organisms%20-%20A.%20N.%20Pargellis.pdf07:41
kanzurethat is a much better paper than uwe's07:42
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kanzurefenn: try that one07:47
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kanzureeudoxia: try http://diyhpl.us/~bryan/papers2/ai/The%20evolution%20of%20self-replicating%20computer%20organisms%20-%20A.%20N.%20Pargellis.pdf07:49
eudoxiai can open it07:49
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kanzure"Those disembodied lungs are amazing. And incredibly creepy. The business plan -- patching up donor lungs not approved for transplant (which is most of them) and keeping them alive long enough to find a patient they can save... to the tune of perhaps 2,000 lungs and lives per year. That's pretty amazing. Approved in Canada and awaiting FDA approval as well?"08:50
kanzurehttp://www.washingtonpost.com/lifestyle/magazine/martine-rothblatt-she-founded-siriusxm-a-religion-and-a-biotech-for-starters/2014/12/11/5a8a4866-71ab-11e4-ad12-3734c461eab6_story.html08:50
kanzure"On a Virginia farm, she’s also raising genetically altered pigs, in the hope that someday their lungs (and other organs) will be modified for use in human transplant, creating a nearly inexhaustible supply of organ donors."08:50
kanzure"The process is legal in Canada, and Rothblatt’s company is among a few trying to win FDA approval. It has worked on more than 40 lungs since May, practicing and documenting results. Once the process is approved, the company will start putting the lungs in patients on a trial basis."08:51
kanzure"Lung Bioengineering, Inc."08:52
kanzurehttp://www.revivicor.com/index.html08:52
kanzure"Revivicor Inc. is a regenerative medicine company focused on applying leading-edge animal biotechnology platforms to provide a superior quality, high-volume, human-compatible, alternative tissue source for treatment of human degenerative disease. The Virginia-based company was formed in 2003 as a spin-out from the UK company PPL Therapeutics, which produced the first cloned animal: Dolly the Sheep. Revivicor has subsequently built on ...08:53
kanzure... this technology, cloning the first genetically-engineered (GE) pigs, and now produces pig islets, organs, and medical devices aimed at human clinical applications."08:53
kanzure"At $20,000 net sales per transplant, this is a projected $60 billion market. Recently published results demonstrated that pancreatic islet cells from Revivicor pigs, when transplanted into diabetic monkeys, cured diabetes for over 1 year with complete normalization of blood glucose levels (van der Windt et al., 2009). The pigs used in these studies were engineered such that a human gene (“CD46”) was added, and a key pig gene ...08:53
kanzure... (alpha-Gal) was deleted, as a means to overcome transplant rejection issues. It is anticipated that insulin-producing islet cells from Revivicor’s cloned pigs could be in human clinical trials within 3 years time."08:53
kanzurehaha they have an infographic http://www.revivicor.com/images/RevivicorTechPoster-04-2010.jpg08:53
kanzure"James Zhan, left, and specialist Sam Popa work on a lung being kept alive and restored in an incubator at United Therapeutics, which is pioneering new methods for lung transplant."08:55
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archelsso is "Virtually Human" worth the read?09:11
kanzureno idea09:13
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kanzurepoppingtonic: see http://diyhpl.us/~bryan/papers2/ai/The%20evolution%20of%20self-replicating%20computer%20organisms%20-%20A.%20N.%20Pargellis.pdf09:42
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kanzureglobal distribution of chlorophyll http://upload.wikimedia.org/wikipedia/commons/4/44/Seawifs_global_biosphere.jpg10:16
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* fenn bakes a ham10:25
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nmz787_i1I wonder why just above and below the equator there is a drop in chlorophyll10:26
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kanzurehttp://en.wikipedia.org/wiki/List_of_interstellar_and_circumstellar_molecules10:33
kanzure"A particularly large and rich region for detecting interstellar molecules is Sagittarius B2 (Sgr B2). This giant molecular cloud lies near the center of the Milky Way galaxy and is a frequent target for new searches. About half of the molecules listed below were first found near Sgr B2, and nearly every other molecule has since been detected in this feature.[25] "10:37
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archelskanzure: well, A Taxonomy and Metaphysics of Mind-Uploading isn't, at any rate10:58
kanzureheh10:58
kanzurethanks for checking, but no surprise there (martine was the one that wanted "snippets of text from your written content, to be used to reconstruct the entirety of your set of opinions and upload yer mindz")10:59
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archelsthat'll totally work11:04
archelsthis book was from Keith Wiley, by the way, not Rothblatt11:04
kanzureoh, hm11:05
archelsapparently he blogged for Humanity+ before, and this kinda rolled out of that11:05
archelshe actually self-describes it as an extended blogpost--which is exactly how it reads11:05
fenn"so, i feel guilty for not writing in this book more frequently. damn you readers for silently guilt-tripping me!"11:14
kanzure"free wow gold" - j. random commenter11:16
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delinquentmefree??11:35
delinquentmeO_o;11:35
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kanzurehttps://michaelfeathers.silvrback.com/detecting-refactoring-diligence11:58
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fennstop. ham time12:05
delinquentmehoney baked12:06
fennyep12:07
kanzurehttp://upload.wikimedia.org/wikipedia/commons/e/e1/Georgia_Aquarium_-_Ocean_Voyager_Tunnel_Jan_2006.jpg12:19
kanzurei like the kid that's more interested in the floor12:19
nmz787_ihuh, in vegas the floor was also glass12:20
fennthere's some kind of silly irony in rothblatt forsaking judaism for transgenic pigs12:27
fennlet not the meat of the bacon tempt thee12:28
fenn"Terasem is a collective consciousness dedicated to diversity, unity and joyful immortality."12:31
fennwhy is it people always feel the need to append "unity" to every statement of goals involving "diversity"12:31
fennmake up your mind12:32
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fenn"When the Apartheid of Republic of South Africa celebrated 20 years of independence on 31 May 1981, the theme of the celebrations was "unity in diversity" as a cynical attempt to explain away the inequalities in South African life."12:35
kanzureaquarium livefeed http://aqua.org/explore/baltimore/exhibits-experiences/blacktip-reef12:37
fennis that your desktop background12:40
nmz787_ihttp://trends.medicalexpo.com/products/vetigel-stops-arterial-bleeding-in-15-seconds/12:54
nmz787_i"The gel is not yet for sale. If you're a veterinarian interested in a sample of VETIGEL for clinical evaluation, please contact us here."12:55
nmz787_ihrmm12:55
nmz787_iI am tempted to email 'my goats keep getting caught on my adjoining neighbors barbed-wire fence, please VETIGEL, I need your help'12:55
kanzurehttp://en.wikipedia.org/wiki/Ecosphere_(aquarium)12:58
kanzure"The main conceptual interest of these objects lies in the fact that they are materially closed ecological systems which are self-sustaining over a period of years. At room temperature, and with only low inputs of light, the algae produce oxygen which supports the shrimp and bacteria. Bacteria break down the shrimps' wastes. The breakdown products provide nutrients to the algae and bacteria upon which the shrimp feed. The manufacturer ...12:58
kanzure... states that shrimp live in the EcoSphere for an average of 2 to 3 years, and are known to live over 10 years."12:58
kanzure"A magnetic scrubber is enclosed in each EcoSphere. By passing another magnet over the outside of the glass, the owner can manipulate the scrubber to clean the inside of the EcoSphere."12:58
fennnmz787_i: sterile kaolin powder has been used for a long time, optionally with antibacterial silver. you can get it in little expensive sealed packets12:59
fennQuikClot also makes a gauze coated with powder12:59
fennWoundSeal ingredients: Hydrophilic Polymer , Potassium Ferrate13:01
fenni wonder how that works13:01
fenn.title http://first-aid-product.com/industrial/blood-stopper.htm13:02
kanzuregaah "The ecosphere was reviewed by Carl Sagan in a 1986 Parade magazine article entitled "The World That Came in the Mail."[11] The article is reprinted as a chapter in Sagan's last book, Billions and Billions."13:02
yoleauxBlood Stoppers | QuickClot, KytoStat, & WoundSeal (formerly known as QR Powder) Plus Spray bandages and Blood Clotting Spray | Stop Bleeding Instantly | First-Aid-Product.com13:02
kanzureeverything about that was fine until the name of the book13:03
fennbbbillions and bbbillions of ssshrimppp13:03
kanzure"breathless billions"13:03
delinquentmehttp://130.211.172.37/13:05
delinquentmecool13:05
kanzurefirst time using graphite?13:05
delinquentmeyeah13:06
delinquentmeand troubleshooting some bad configs for https://github.com/saltstack-formulas/graphite-formula13:06
kanzure"use more pillars"13:07
* nmz787_i rotated right-most display from portrait to landscape to have that aquarium showing13:12
kanzurehttp://www.montereybayaquarium.org/animals-and-experiences/live-web-cams/open-sea-cam13:14
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fenni'm still trying to figure out how to stream it through mplayer13:21
kanzureyou missed the schoolfish tornado13:22
fennit'll be back13:22
nmz787_ithere it is again13:22
nmz787_iI don't think this is actually the open-sea13:22
nmz787_iI see that shark had a shadow near the bottom13:23
nmz787_ithough their one tank was quite huge as I remember it13:23
fennit's their "open sea" aquarium exhibit which has lots of open sea critters13:23
kanzurethis aquarium looks much larger than that baltimore feed13:24
fennit's huge13:24
nmz787_ieasily 3 stories tall13:24
fennfeeding time: 11 am13:25
fennso that's probably leftovers13:25
fennis there something like ustream that doesn't suck13:31
kanzurelivestream?13:32
fennthe javascript search box isn't looking promising13:34
kanzureinteresting that "ecosphere" is novel or something... i thought many people have made closed ecosystems of all kinds?13:34
kanzurea computer simulation of a closed ecosystem has the interesting property of injecting arbitrary resources13:35
kanzure*interesting ability for13:36
kanzurebut you would need to account for differential benefit of different types of resources.. those string-based replication programs aren't going to build a "shell" because there's no three dimensional space or materials of any kind that provide any selective advantage.13:36
archelswasn't there a 2D grid of cells in one of those papers?13:38
kanzurei don't think they were cells13:38
archelsand critters could leech off their neighbours13:38
kanzurethat was like "neighbor" in the sense of memory mapping13:38
archelsadmittedly I only skimmed it13:38
fennthere are a lot of 2d cellular automata but not so many linear ones13:39
fenni guess people get bored looking at crusty memory maps13:39
kanzuresea turtle keeps swimming by that camera not sure why13:41
nmz787_iTURTLE13:41
kanzurememory maps don't seem like the right sort of environment13:41
kanzureother resources besides computational time and memory must be available and must provide benefit13:42
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kanzurewelcome back narwh4l13:43
narwh4l:)13:43
kanzurenmz787: jupiter's spot is probably just a giant schoolfish tornado13:45
narwh4lWhere is this aquarium I was told about?13:47
kanzurehttp://aqua.org/explore/baltimore/exhibits-experiences/blacktip-reef13:47
kanzurehttp://www.montereybayaquarium.org/animals-and-experiences/live-web-cams/open-sea-cam13:48
narwh4l:D13:48
fennhow can this thing possibly be using 100% cpu at only 240p13:48
narwh4lit's mining dogecoin13:48
kanzurewow13:48
fennok 90%13:49
fennbut still13:49
kanzureenable frameskipping?13:49
fenni can't do that because it's some javascript web bullshit13:49
fennif i were using a reasonable video player i wouldn't be having a problem13:50
kanzurecclive?13:50
narwh4loh hey there turtle13:51
kanzureturtle butt13:51
narwh4lturtle camwhore13:51
kanzuremaybe there was an rna replicator ecosystem prior to cells13:52
kanzureer, food web13:53
poppingtonicthat was huge14:00
fennit's called the "RNA world hypothesis"14:00
kanzurerna world hypothesis does *not* specify an ecosystem14:01
fennare you sure14:02
kanzure"It may, therefore, have played a major step in the evolution of cellular life.[7] The RNA world would have eventually been replaced by the DNA, RNA and protein world of today, likely through an intermediate stage of ribonucleoprotein enzymes such as the ribosome and ribozymes, since proteins large enough to self-fold and have useful activities would only have come about after RNA was available to catalyze peptide ligation or amino acid ...14:04
kanzure... polymerization.[8] DNA is thought to have taken over the role of data storage due to its increased stability, while proteins, through a greater variety of monomers (amino acids), replaced RNA's role in specialized biocatalysis."14:04
poppingtonicrna doesn't require *that* much energy...14:04
kanzurei don't know if any of that counts as an ecosystem14:04
kanzurei agree that rna doesn't require lots of energy, but you don't just go rna self-replicators -> cellular membranes14:04
fennso if RNA #1 eats RNA #2 it doesn't count as a "food web"?14:05
delinquentmehey python comes default installed on macs right?14:07
kanzurecannibalism sort of counts, but i am not sure you can bootstrap cells from only cannibalism14:07
fenncells has nothing to do with this particular question14:07
fenni guess it's some terrible philosophical "identity" problem14:08
poppingtonicwhat would an ecology of rna molecules do? If there's free energy (maybe sunlight or geothermal energy), and a heat bath, and RNA (but no DNA), what's missing from the picture?14:08
poppingtonicdelinquentme: i think it's ruby.14:08
fennscarce resources; RNA molecules that replicate the most win because they're more likely to survive $calamity14:08
kanzurein the case of computer simulations, who knows-- usually the ecosystem collapses and dies off14:08
kanzurewithout the "emergence" of other forms of life14:09
poppingtonicI've seen guns and spaceships designed using GoL elements in Golly.14:11
fennthere are other ways to contain molecules besides lipid membranes14:11
poppingtonicGosper gliders and other elements.14:11
poppingtonicthey can get pretty complex, but the fundamental ops are simple automata.14:12
fennyou could make a net of carbohydrates and stuff your food in there, or hide in a crevice on an inorganic surface14:12
fennor both14:12
fennpoppingtonic: most of those were created (engineered) by humans14:12
fennkinda defeats the purpose14:12
kanzurenone of those methods seem to be usable in a simulation of string-based code-based lifeforms14:12
kanzure"where" would the surface go14:13
poppingtonicfair enough.14:13
fennRNA is a string-based lifeform :P14:13
kanzureyes but there's a spatial dimension as well14:13
kanzureit doesn't have magical memory access to other rna molecules14:13
fennis it possible for a "code" life form to concentrate resources?14:14
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kanzureinstead it has magical physical access to other rna molecules, heh14:14
kanzuremaybe, but there would have to be an idea for how that would look14:14
kanzureprobably something like "different code has different resource binding affinities"14:14
kanzureand then... the binding has to look like something...14:14
fennwhat if you had something like proof of work14:15
kanzure?14:15
fennor did i just send you into a feverish schizophrenic fit where you'll ramble about the simulation argument and the universe being a cryptocurrency miner14:15
kanzureno you're thinking of chaitin14:16
fennuh. so the only scarce resources in a code simulation are: cpu cycles, randomness, memory14:16
kanzureyour simulation can introduce other scarce resources that bundle those together14:17
fennmost of these alife toys feed the system randomness at some low level or it will be terribly boring14:17
kanzureand it's not really "cpu cycles" but rather "simulation cycles" or something14:17
kanzure*simulation ticks14:17
fennright so proof of work is a way of packaging up cpu cycles in a bit string14:18
fennbut in order for it to mean anything, the selection function has to favor it somehow14:18
kanzurethere's certainly a way to favor valid proof of work14:18
fennyeah you just only evaluate code that has a valid proof of work attached to it14:19
fennonce a code string figures out how to make a proof of work string, it counts as self replicating14:20
kanzurehuh?14:20
kanzureso the way that these simulations worked was randomly seeding the memory with random opcodes, then executing code14:21
fennlike a transcription factor; the simulation reads strings of bits and only starts executing if the bit string hashes to 0x00whatever14:21
kanzureand eventually self-replicating programs were found in this mess14:21
kanzurei don't think you need to start with proof-of-work-favoring?14:21
fenni dont see how you would ever develop an ecosystem/food web when everything is equally distributed14:22
kanzurego on?14:23
fennself replicators sure, but they wouldn't *do* anything14:23
kanzureapparently they even infect each other, create copies, have different strategies14:23
poppingtonicdoes rna process information at all?14:24
kanzurei was working on transcriptional logic gates a long time ago, hehe14:24
fennpoppingtonic: it copies strings of RNA...14:25
kanzurearguably, rna stores information14:25
kanzureno, indisputably14:25
fennno, arguably!14:25
* fenn argues14:25
kanzureperhaps there could be a scarcity of bits14:25
kanzureand bytes14:26
kanzureconservation of bits14:26
fennthere's already a limit on the simulation memory size14:26
fennmaybe you mean conservation of entropy14:26
kanzurepossibly, yes14:27
fennwolfram showed that weird stuff happens even in severely entropy constrained systems, i.e. rule 3414:27
kanzureynotds has spent like a thousand hours looking at rule 34 simulations14:28
kanzurehttp://www.thewildca.com/200000r/snake0401_200000r.gif14:29
kanzurehttp://ynotds.com/ under "Cellular Automata Project news"14:29
poppingtonicand that other dude showed that UTMs can be made of extremely simple components.14:29
kragenpoppingtonic: ?14:30
kragenare we talking about automata theory or mechanical engineering here?14:31
poppingtonicBoth.14:31
fennok that's not an animated gif14:33
kanzurethat may just be how golly dumps images14:34
poppingtonicyou should download golly and run a few guns/spaceships. If you haven't already.14:35
kanzureto be honest i do not find cellular automata very interesting at all14:36
narwh4l^14:36
narwh4lThey are neat, like fractals but somehow less useful14:36
fennyou know rule 34 is just an instruction set14:37
kanzurewhat about it?14:37
fennit's not any different from the code alife stuff you're looking at14:37
fennexcept time is shown on the y axis14:39
narwh4lkanzure as a fringe topic that might be relevant but probably is not, you might find it useful to read about quines14:40
narwh4lhttp://en.wikipedia.org/wiki/Quine_%28computing%2914:40
kanzurefenn: then something is fundamentally wrong14:41
kragenpoppingtonic: so who is that other dude that showed that UTMs can be made of extremely simple components?  Was it the same guy who showed that you can build them mechanically out of simple components and who showed UTMs that are simple in automata theory?14:41
kanzureneighbor update rules seem very different to me. i agree that UTMs have been demonstrated using patterns inside different cellular automatas with various rulesets, but why should i care?14:42
kanzureyou know, i think this webcam may be on a loop14:42
fennit's just turtles all the way down14:42
poppingtonickragen: https://en.wikipedia.org/wiki/Wolfram%27s_2-state_3-symbol_Turing_machine14:44
poppingtonicAlex Smith. That's the name.14:44
fenna turing machine is a special case of cellular automata14:45
poppingtonicI don't think it's the same guy who showed14:45
poppingtonic         that you can build them mechanically out of simple components14:45
kanzurei think you mean "a special case of the computation that can be performed by cellular automata"14:50
kragenpoppingtonic: any leads on actually physically constructing one?14:51
kanzure"Around 2000, Matthew Cook published a proof that Rule 110 is Turing complete, i.e., capable of universal computation, which Stephen Wolfram had conjectured in 1985. Cook presented his proof at the Santa Fe Institute conference CA98 before the publishing of Wolfram's book, A New Kind of Science. This resulted in a legal affair based on a non-disclosure agreement with Wolfram Research. Wolfram Research blocked publication of Cook's proof ...14:52
kanzure... for 2 years.[1]"14:52
kanzure"The original emulation of a Turing machine contained an exponential time overhead due to the encoding of the Turing machine's tape using a unary numeral system. Neary and Woods (2006) modified the construction to use only a polynomial overhead.[5]"14:52
poppingtonickragen i thought research in DNA computing did that already?14:53
poppingtonicrather, *demonstrated that already*14:53
kragenno, it didn't work14:55
kragenalso the things that came closest to working weren't close to Turing machines14:55
kragenpresumably someone will get DNA computing working at some point but so far nobody has done so AFAIK14:55
kanzurei was working on that14:56
kanzurehttp://diyhpl.us/~bryan/papers2/ellington/Modelling%20amorphous%20computations%20with%20transcription%20networks%20-%202009.pdf14:56
fenntranscription networks are more like analog circuits14:59
fennit would be nice to use the digital nature of RNA to construct a digital information processing machine that modified sequences15:00
nmz787_ihttps://lh3.googleusercontent.com/-3drtMneLIQ0/U3PPvgWE32I/AAAAAAAAFm8/LLNnHP22Qx0/w401-h535-no/IMG_2976.JPG15:00
kanzure.title http://www.ncbi.nlm.nih.gov/pubmed/1744387615:00
yoleauxRibozyme catalysis of metabolism in the RNA world. - PubMed - NCBI15:00
kanzure"In vitro selection has proven to be a useful means of explore the molecules and catalysts that may have existed in a primordial 'RNA world'. By selecting binding species (aptamers) and catalysts (ribozymes) from random sequence pools, the relationship between biopolymer complexity and function can be better understood, and potential evolutionary transitions between functional molecules can be charted. In this review, we have focused on ...15:00
kanzure... several critical events or transitions in the putative RNA world: RNA self-replication; the synthesis and utilization of nucleotide-based cofactors; acyl-transfer reactions leading to peptide and protein synthesis; and the basic metabolic pathways that are found in modern living systems."15:00
nmz787_i"Best guess a piece of silicon wafer from the small pieces of silicon I saw down the center shaft of the pump. The pump came out of a brooks wafer loading robot that would pick up wafers out of a cassette and place them in a plasma etcher. The pump had a fine shatter screen on top but it there were two holes. I am guessing a wafer broke and fell onto the screen. When the pneumatic butterfly valve over the pump closed it pushed the15:00
nmz787_iwafer through the screen into the blades. It was one of these:http://www.pchemlabs.com/product.asp?pid=3119"15:00
nmz787_i" 54000 rpm to 0 in a fraction of a second. In the manual for the big turbo I am putting on my system it says in the event if a catastrophic failure like this there will be 3800 ft/lbs of force on the pump. A guy I know at intel told me about a large turbo crashing and tearing itself off the tool."15:01
fennnmz787_i: your lunar wainshaft went out of alignment15:01
kanzure"In vitro selection has proven to be a useful means of explore the molecules"15:01
fenntoo much side fumbling15:02
kanzurenobody copyedits this stuff??15:02
poppingtonickanzure: the pdf is broken.15:03
kanzureno it's not?15:03
kanzurewhich pdf?15:03
poppingtonic"Modelling amorphous computations..."15:03
kanzureworks for me15:04
kanzure.title http://www.ncbi.nlm.nih.gov/pubmed/1877579315:04
yoleauxEvolutionary origins and directed evolution of RNA. - PubMed - NCBI15:04
kanzure"In vitro selection experiments show first and foremost that it is possible that functional nucleic acids can arise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove to be robust binding species and catalysts, indicating that it may have been possible to transition from even the earliest self-replicators to a nascent, RNA-catalyzed metabolism."15:04
kanzuresee this is why i like this person15:04
nmz787_ipoppingtonic: works for me too15:04
kanzurethat seems very similar to the computational results15:04
nmz787_ithere was even that MIT assistant prof I posted some new15:05
nmz787_i'theory' of life about a week or two ago15:05
nmz787_ihe did some RNA calcs15:05
poppingtonicI redownloaded it. Works fine.15:06
kanzure"Because of the diversity of aptamers and ribozymes that can be selected, it is possible to construct a 'fossil record' of the evolution of the RNA world, with in vitro selected catalysts filling in as doppelgangers for molecules long gone. In this way a plausible pathway from simple oligonucleotide replicators to genomic polymerases can be imagined, as can a pathway from basal ribozyme activities to the ribosome. Most importantly, ...15:06
kanzure... though, in vitro selection experiments can give a true and quantitative idea of the likelihood that these scenarios could have played out in the RNA world. Simple binding species and catalysts could have evolved into other structures and functions. As replicating sequences grew longer, new, more complex functions or faster catalytic activities could have been accessed. Some activities may have been isolated in sequence space, but ...15:06
kanzure... others could have been approached along large, interconnected neutral networks. As the number, type, and length of ribozymes increased, RNA genomes would have evolved and eventually there would have been no area in a fitness landscape that would have been inaccessible. Self-replication would have inexorably led to life."15:06
nmz787_iJeremy England15:06
nmz787_imaybe this paper http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.481853815:07
kanzure.title15:07
yoleauxStatistical physics of self-replication15:07
poppingtonicI read about that. Did anyone read the Constructor Theory papers? constructortheory.org15:07
kanzure"Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the ...15:07
kanzure... physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids."15:07
poppingtonicwhere's paperbot?15:08
nmz787_ihe had a breakdown15:08
kanzurewhat is john brockman doing here15:08
fennno nmz787_i he's "on a research fellowship"15:09
kanzureresearch sabbatical15:09
poppingtonicthe "Modelling amorphous computations.." paper's supplementary data page is missing. what.15:09
nmz787_ifenn: some artical said he was an asst prog15:09
nmz787_iprof15:09
kanzurepaperbot is on a field expedition15:09
nmz787_iblame the media15:09
fennblame meme media15:09
fennassistant prog sounds more likely15:10
kanzure"Constructor theory seeks to express all fundamental scientific theories in terms of a dichotomy between possible and impossible physical transformations - those that can be caused to happen and those that cannot. This is a departure from the prevailing conception of fundamental physics which is to predict what will happen from initial conditions and laws of motion."15:11
poppingtonic"The hairpin transcriptional gates are uniquely suited to the design of a complementary NAND gate that can serve as an underlying basis of molecular computing that can output matter rather than electronic information."15:11
kanzurei did so many gels :(15:11
poppingtonickanzure: ?15:12
kanzurehow do you think they tested these molecules15:12
kanzurelots and lots of pcr15:12
poppingtonicooh.15:14
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kanzurethis constructor theory stuff is a little long-winded, http://arxiv.org/pdf/1210.7439v2.pdf15:48
kragenfenn: I think RNA processing has a high enough error rate that you need to incorporate error correction coding at a very low level15:50
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poppingtonickragen: has any of the simulations we've been discussing been shown to evolve such codes?15:55
kragenpoppingtonic: I don't know enough about them.  they'd have to introduce random errors into the replication process in order to evolve error correction though15:56
kanzure"For example, the principle of testability is doubly counterfactual: it is that a certain task (the test, resulting in a falsifying outcome) must be possible if the theory is false"15:59
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kanzurepage 27 section 3.1 is okay16:07
kanzure"3.9 Wealth; In constructor theory it is natural to define the wealth of an entity in a nonanthropocentric way as the set of transformations that the entity would be capable of performing without generating new knowledge. Wealth has always consisted fundamentally of knowledge, even though it has been limited by the capacity of relatively fixed installations for harnessing naturally occurring resources. Once universal constructors exist, ...16:14
kanzure... it will consist almost entirely of knowledge."16:14
poppingtonic"No perfect constructors exist in nature. Approximations to them, such as catalysts or robots, have non-zero error rates and also deteriorate with repeated use. But we call a task A possible (which we write as A ✓ ) if the laws of nature impose no limit, short of perfection, on how accurately A could be performed, nor on how well things that are capable of approximately performing it could retain their ability to do so again."16:18
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fennwhy even call it wealth if it's just knowledge16:22
fenncall it knowledge16:22
fenn.wik praxis16:23
yoleaux"Disambiguation: Praxis" — http://en.wikipedia.org/wiki/Praxis16:23
kanzurehaha16:24
kanzure"the set of transformations that the entity would be capable of performing without generating new knowledge" is not the same thing as knowledge, methinks16:24
kanzurei think you can have knowledge that you can't reliably make tasks for, or something16:26
kanzurelocally-useless knowledge16:26
poppingtonicdoes it have anything to do with incompressibility, K-complexity or minimum message length?16:27
fenni'm sort of confused, is this talking about the real world? or some mathematical masturbation fantasy16:27
kanzurehttp://arxiv.org/pdf/1210.7439v2.pdf is talking about possible and impossible physical transformations, and principles as foundational to physics rather than laws of motion16:28
fennhow do you jam messy real world atoms and phonons and fields into an equation with "input state of substrates" on one side16:30
fennthere's a stupidly huge amount of information in every cubic micron of space16:31
kanzurethis paper does not advocate that16:31
kanzureerm16:31
fennthen what the hell are they talking about16:31
kanzurethis is a description not an equation16:31
fennalso, doesn't quantum uncertainty mess all this up16:31
fenn"Quantum indeterminacy is the apparent necessary incompleteness in the description of a physical system,"16:32
fennhow can you say "possible" or "not possible" when you don't even know what's there16:32
kanzuremy pdf search function must be broken16:33
fenni'll believe "probability 1-1e-10000" but not "possible/not possible"16:33
poppingtonicfenn: see the sections re: superinformation. they discuss how CT dissolves/explains the disconnect between classical and quantum information.16:40
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fenn"no perfect constructors can exist in nature" would seem to validate my perception that this has no connection to the real world16:44
poppingtonicthat there can be no error?16:44
poppingtonicsorry16:44
poppingtonicthat there *can* be error?16:45
fennhe goes on to talk about how factories and robots have non-zero error rates, and deteriorate over time16:45
kanzurehe probably just thinks "perfect constructors" are perpetual motion machines16:46
fenna perfect constructor wouldn't be violating any conservation of energy or entropy laws16:47
fenncatalysts aren't perpetual motion machines16:48
fenni dunno what the theory say about maxwell's demon16:50
fenn(for all i know maxwell's demon is possible in reality)16:51
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fennby which i mean a heat pump with arbitrarily high coefficient of performance16:56
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fennwow i did not know this: "Before the discovery of DNA, von Neumann (1948) wondered how organisms can possibly reproduce themselves faithfully and evolve complex adaptations for doing so. He realized that an organism must be a _programmable_ constructor operating in two stages, namely copying its program and executing it to build another instance."16:58
kanzurebefore dna was discovered it was widely hypothesized in biology land17:00
fenni hate the checkmark notation17:06
fennit looks just like an apostrophe17:06
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kanzuretrolloglyphics17:07
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fenni think what this constructor theory really needs in order to be relevant is some realization about the limits of working with noisy systems like Shannon's noisy channel coding theorem17:09
fenn"it is possible to communicate discrete data (digital information) nearly error-free up to a computable maximum rate through the channel." i would add the relevant equation here but for hieroglyphics17:10
fennsimilarly constructors need substrate to work on, which is comparable to discrete data17:11
fennso it would be something like, "it is possible to construct artifacts (physical objects) nearly error-free up to a computable maximum rate in the workspace"17:14
fenncall it the dirty workspace building theorem17:17
nmz787_iI need some code that given a number say, 13, and some constant like 10, would generate the numbers 10 and 317:18
nmz787_ior if it was 23 generate 10 10 and 317:18
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nmz787_ithe only thing I can think of is a while num_left>0: ; num_left-= 10;  if num_left<0: 10+abs(num_left);17:19
nmz787_ibut I really want something more like an assembly instruction, where the subtract operation returns the number removed17:19
nmz787_ibut it would need to be unsigned and not rollover17:20
fenn.wik knapsack problem17:24
nmz787_ioh, i guess a for loop with int division then handling the remainder with a modulo division will work17:24
yoleaux"The knapsack problem or rucksack problem is a problem in combinatorial optimization: Given a set of items, each with a mass and a value, determine the number of each item to include in a collection so that the total weight is less than or equal to a given limit and the total value is as large as possible. It derives its name from the  …" — http://en.wikipedia.org/wiki/Knapsack_problem17:24
fennor just 23%10 = 3 so 23 - 3 = 20 and 20/10 = 217:25
nmz787_i.py t=23; for i in range(0,t/10): t-=10; print 10; ; print t%1017:25
yoleauxSyntaxError: invalid syntax (<string>, line 1)17:25
nmz787_i.py t=23; for i in range(0,t/10): t-=10; print 10; if t%10>0: print t%1017:26
yoleauxSyntaxError: invalid syntax (<string>, line 1)17:26
nmz787_i.py t=23; for i in range(0,t/10): t-=10; print 10; if t%10>0: ;print t%1017:26
yoleauxSyntaxError: invalid syntax (<string>, line 1)17:26
nmz787_iwell i fail at this irc python17:26
fenni had some trouble with it too17:27
fennalso you can't do for loops on one line in python17:27
fennalso int division is the devil17:28
nmz787_ithe devil?17:30
fenni shouldn't give it that much credit. "the devil is in the details"17:30
nmz787_ii heard new python changed division or something to return floats by default, maybe.... something 'new'17:31
fennpython's defaulting to int division has caused more trouble than any other "feature"17:31
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nmz787_ibut isn't that computer's default in general?\17:31
fennno?17:31
nmz787_ino?17:32
nmz787_iC it is the default I think17:32
nmz787_iand assembly too17:32
fennC is not "a computer"17:32
fenni dont really know what happens in the ALU when you try to divide two numbers17:32
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nmz787_ifloating point is more work17:32
nmz787_iunless you have some analog computer maybe17:32
* fenn looks at https://en.wikipedia.org/wiki/Division_algorithm#Integer_division_.28unsigned.29_with_remainder17:34
fennthe problem with python's int division is it silently throws away the remainder17:35
fenn.py 2/317:35
yoleaux017:35
nmz787_ithat seems perfectly legit for an int17:36
fennyeah if you're thinking about in division fine17:36
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fennbut usually this happens buried deep in some program somewhere, and you get a bizarre incorrect result after changing a configuration value17:36
fennsuch rudeness!17:38
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fennhttps://en.wikipedia.org/wiki/File:Order_and_Chaos.tif17:58
fenn"to determine whether to let a molecule through, the demon must acquire information about the state of the molecule and either discard it or store it. Discarding it leads to immediate increase in entropy but the demon cannot store it indefinitely"18:04
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kanzure"The origin of cells was the most important step in the evolution of life on Earth. The birth of the cell marked the passage from pre-biotic chemistry to partitioned units resembling modern cells. The final transition to living entities that fulfill all the definitions of modern cells depended on the ability to evolve effectively by natural selection. This transition has been called the Darwinian transition."19:00
kanzurewikipedia is full of crap19:00
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caternthe origin of cells was the most important step in the evolution of life on Earth from the perspective of things made up of cells19:09
kanzurethe development of cells did not mark some event where natural selection suddenly started -_-19:11
kanzureoh wait19:12
kanzureokay their grammar just sucks19:12
fenni get the feeling that paragraph was edited many times by different people19:16
fennrationale for deletion WP:ThisSucks19:16
kanzurei suppose it is wrong to think that a simulation should have self-replicators developing cells19:17
kanzure"cells" take advantage of lipid biophysics and nobody should have to implement lipid biophysics and the rest of reality19:18
fenncells only make sense if you have brownian motion diffusing concentrations away19:18
fennotherwise piles are fine19:18
kanzurethere are some defense/immune benefits19:19
fennsure, castles19:19
kanzureand environment protection benefits, which i think ounts as defense or immune19:19
superkuhLipid biophysics contributes more to cells than just partitioning.19:19
fennyeah it's an energy storage mechanism like a capacitor19:19
kanzureselective permeability.... bleh.19:19
fennalso it constrains catalysts and substrates to a 2d plane19:21
fennsomething about anaerobic synthesis environments for nitrogen fixation19:22
fennbut that wasn't important until much later19:23
kanzurecould be an entirely non-biological simulator. no need to program in organic chemistry, molecular dynamics, etc.19:24
fennyeah who needs interesting stuff19:25
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fennlet them eat blocks19:25
kanzurei think there's something wrong with those block simulators but i don't quite know what19:25
kanzurethe lack of link between code and blocks is one issue19:26
kanzuredisembodied genes just doesn't make sense19:26
fennwhat block simulators19:26
kanzuretierra turned into some "robot with wheels" simulator :(19:26
fennwhy19:26
kanzurebecause they need bodies and cells!19:27
fennthe dying-inside counter is reaching pretty far into the negative19:27
kanzurehm?19:27
fennearlier you said something like "if any more pieces of me die inside there might be nothing left"19:27
fennafter a particularly heinous IT fail19:28
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fennjust extending that metaphor beyond zero19:28
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fenni think we need more superresolution microscopy photos in the world19:30
fennpeople think cells are just these blobs blobbing around19:30
kanzurethey are antenna forests19:30
fenni mean this is pretty sad really http://en.wikipedia.org/wiki/File:Celltypes.svg19:31
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kanzurehttp://files.arcfn.com/images/cell-vesicle.png19:32
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fenngetting there19:32
fennhttp://mgl.scripps.edu/people/goodsell/illustration/mycoplasma19:32
kanzurei'm not sure simulating that is a priority. that's a lot of extra physics.19:34
fennand talking about eukaryotes (sorry for the low res) http://mgl.scripps.edu/people/goodsell/illustration/pdb/panorama_poster.jpg19:34
kanzurehttps://static1.cosmosmagazine.com/sites/default/files/styles/cosmos_holodeck_image/public/070714_holodeck_2.jpg?itok=Ds1wYMdD19:35
fennit doesnt like the token19:36
kanzurehttp://mgl.scripps.edu/people/goodsell/books/MoL2figures19:37
fennah yes the flagella painting; i had that printed out 1m x 2m on my dorm room wall19:37
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fennhttp://fennetic.net/irc/goodsell/goodsell-2.jpg19:38
kanzurehttp://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure3.9a-reduced.jpg19:39
fennwelp i know what i'll be scraping19:42
fenn"Nanotechnology is available, today, to anyone with a laboratory and imagination. You can create custom nanomachines using commercially available kits and reagents. You can design and build nanoscale assemblers that synthesize interesting molecules. You can construct tiny machines that seek out cancer cells and kill them. You can build molecule-size sensors for detecting light, acidity or trace19:44
fennamounts of poisonous metals. Nanotechnology is a reality today, and nanotechnology is accessible with remarkably modest resources."19:44
kanzureexcept it's highly unstable and totally broken19:45
fenn"Modern cells provide us with an elaborate, efficient set of molecular machines that restructure matter atom-by-atom, exactly to our specifications. And with the well-tested techniques of biotechnology, we can extend the function of these machines for our own goals, modifying existing biomolecular nanomachines or designing entirely new ones."19:45
fennjust think of it as pushing the boundaries of construction performance in a messy workspace19:45
kanzure"atom-by-atom, exactly to our specifications" is stretching it19:45
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fennyou can make any shape you want, as long as it's a string of amino acids19:47
kanzuremost of those strings get folded though19:47
kanzureso that's not really true19:47
fenni meant that to be more snarky19:47
fenn.wik you can get any color you want as long as it's black19:48
yoleauxfenn: Sorry, that command (.wik) crashed.19:48
fennoh well19:48
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fennaw now his webserver hates me19:51
kanzurei viewed all images with at least 2 seconds before each view19:52
kanzurealso, always use a user agent condom19:52
fennmaybe it's just borked; gnusha won't load the page anymore either19:52
fennanyway looks like an interesting book http://mgl.scripps.edu/people/goodsell/books/bionanotech-contents.html19:54
fennBuy eBook - $116.9919:56
fenncoloring books werent so expensive when i was a kid19:57
kanzure"We can start the experiment with a population containing only nude replicators but the environment of the organisms can be arbitrary complex: the environment consists of computable tasks These tasks should be learned by the organisms. The organisms can pick up pieces of data (integer numbers in the current state of the implementation) and after processing them they simply write the result back to the environment. This process can be ...19:57
kanzure... considered as some kind of metabolism. Data transformation is just like eating and digesting."19:57
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kanzurebut....19:58
kanzurewhat's the selective value of "processing some data" to them?19:58
fennhow od you know what's a replicator19:59
kanzurequote is from http://physis.sourceforge.net/old/doc/papers/icai.pdf19:59
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kanzurewell one way of knowing a replicator is if you run BLAST and see the same thing in your population19:59
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kanzureanother way is that i think this author's system has replicators-only19:59
fennapparently20:00
fennwhat if your replicators build other kinds of replicators you hadn't intended20:00
kanzurewhat do you mean "what if" ?20:01
kanzureoh, still asking about classification20:01
kanzuredoes that matter?20:01
fenni mean most of these alife experiments start out with ridiculously boring assumptions and preconceived conclusions20:01
kanzurelike what?20:01
fennlike "here we have a replicator, and here's some data it will digest."20:01
kanzurehehe20:01
fenn"observe as the data is transformed into digital poo"20:02
fennwhere's the room for surprising discoveries and unexpected outcomes20:02
fenndigital systems were created so we could have _unsurprising_ outcomes, so you have to do a bit of work to get back to complexity20:03
kanzure.title http://arxiv.org/abs/physics/030204620:10
yoleaux[physics/0302046] Does the Red Queen reign in the kingdom of digital organisms?20:10
kanzure"In competition experiments between two RNA viruses of equal or almost equal fitness, often both strains gain in fitness before one eventually excludes the other. This observation has been linked to the Red Queen effect, which describes a situation in which organisms have to constantly adapt just to keep their status quo. I carried out experiments with digital organisms (self-replicating computer programs) in order to clarify how the ...20:10
kanzure... competing strains' location in fitness space influences the Red-Queen effect. I found that gains in fitness during competition were prevalent for organisms that were taken from the base of a fitness peak, but absent or rare for organisms that were taken from the top of a peak or from a considerable distance away from the nearest peak. In the latter two cases, either neutral drift and loss of the fittest mutants or the waiting time to ...20:10
kanzure... the first beneficial mutation were more important factors. Moreover, I found that the Red-Queen dynamic in general led to faster exclusion than the other two mechanisms."20:10
kanzureyou could use arbitrary degees of freedom but i wouldn't know what to do with that data or how to tell if it was working20:16
kanzurewhere different resources would be part of that (i guess this is more like a "vector" or "channel")20:16
fennhttp://fennetic.net/irc/David%20S.%20Goodsell%20-Bionanotechnology%20Lessons%20from%20Nature%20%5b2004%5d.pdf20:16
fenndear lazyweb, please read and send me mindstate diffs20:17
kanzureyour wish has been granted, but the diffs can only arrive over years of snarky irc conversations20:18
fennno i said a thousand bucks, not a thousand ducks20:19
fenndoes anyone know what this dolphin exoskeleton is from, and why does it have a huge mechanical cock http://fennetic.net/irc/Neofin-thumb.jpg20:21
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kanzuresomething something david brin20:23
kanzureneofins were from his uplift stuff20:24
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kanzurehttps://medium.com/@jorge_lo/the-future-a-cat-litter-and-drm-6dbda26428f820:37
kanzure"Seriously CatGenie, you added fairly sophisticated DRM to a litter box? I’m a tad hurt you spent my money on building in a restriction instead of figuring out how to avoid constantly cooking poop."20:37
kanzure"I did some Googling, and I found that the “Smart” in SmartCartridge is that it has an RFID chip inside of it to keep track of how much solution it has, and once it runs out, well, you can't refill it. I honestly did not believe this and tore one of the cartridges apart, and there it was, looking back at me, a tiny chip holding up it’s little metal finger."20:39
kanzure"Thankfully, some amazing people are helping the CatGenie community.(Yeah, there’s a CatGenie community). They’ve released products like the custom firmware CatGenius and CartridgeGenius which allows you to use whatever solution you want."20:39
kanzurehah20:39
kanzurewhat a pile of crap20:39
kanzureyeast fermentation power supply https://farm9.staticflickr.com/8455/8008302313_0fc1120a12_b.jpg20:49
fennin future soviet russia, chip tells YOU no refills20:49
fenni can see the discrete cosine blocks20:51
kanzuredata digestion... who comes up with this stuff...20:55
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delinquentmeBTW adblocks quite well for killing the new games feed on facebook21:09
kanzurehttps://www.youtube.com/watch?v=_m97_kL4ox0&t=5m53s21:24
kanzurewut21:24
kanzurei remember the arm reaching one but i don't remember why21:28
fennthe slithy toves did gyre and gimble in the wabe21:29
fennthis looks like hod lipson's stuff21:29
kanzureoh yeah hod still exists21:29
fennyou gotta admit this kind of simulation is way more entertaining than a bunch of colored lines on a memory map21:30
kanzureso why didn't they try to get one that pushes the prize towards them (running with the prize, even), while pushing the enemy away or using a pincher to move the enemy away21:31
fennyou're talking about t=10m20s ?21:31
kanzureyes that program21:32
fenn1994 karl sims21:33
fenni gave a presentation at that very podium, i wonder if there's a recording on the web21:36
kanzurei remember seeing a video of that, so yes21:37
kanzurenope, wrong podium21:40
fennit was 4 years later than that video so they might have changed some stuff21:41
kanzurehttp://vimeo.com/2873527621:42
kanzure?21:42
fennno that was stanford21:43
fennat google we were talking about hacker dojo and i was talking about the hardware lab and why one might want a hardware lab21:44
fennhttp://wiki.hackerdojo.com/w/page/26349587/Dojo@Google21:45
fennyou probably know jeff lindsay (progrium) from his postbin stuff21:51
kanzurestalkerlog has no intersections here21:52
fennit was a link you spammed at me once21:52
kanzurestalkerlog has some leaks occassionally21:53
fenn"I learned that the Internet does not understand the juxtaposition between scientific-graphs and trolling."22:01
fennfrom this graph i deduce that pedophiles are geniuses http://booksthatmakeyoudumb.virgil.gr22:03
kanzurethey have to be geniuses otherwise they get-- well, actually, i have no idea22:05
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fennis this someone we know http://www.phreedom.org/22:23
fennphreedom was from ukraine22:26
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kanzurereminds me of https://www.youtube.com/watch?v=sMnYBHUdk84&t=30s22:29
fennhaha virgil griffith is friends with vitalik buterin22:30
fenn"NNDB is an intelligence aggregator that tracks the activities of people we have determined to be noteworthy, both living and dead."22:31
kanzure"Over 40,000 profiles are available." fucking casuals22:32
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fennit's "notable" people22:33
fennPrime Minister of Belgium22:33
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fennUS Senator from Alabama22:33
fennGlobal Positioning System22:33
fennAlien designer22:34
fennyou know, the important stuff22:34
kanzure"known alien"22:34
fennH. R. Giger was the most notable of those22:35
fennimho22:36
fennKing Zog - Royalty - King of Albania22:38
kanzure.title http://scholar.google.com/scholar?cites=14781935138049637300&as_sdt=5,44&sciodt=0,44&hl=en22:44
yoleauxSorry...22:44
fennjust "Sorry..."22:44
kanzurea lifeform without rna/dna binding to external materials would be pretty boring or going nowhere fast22:51
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