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Bioinformatics, genomics, counterculture, stuff.en-usBiowiki content is in the public domain.IanHolmes [wikigardener@postbox.biowiki.org]IanHolmes [wikigardener@postbox.biowiki.org]BiowikiTWiki.BlogBiowiki.Blog
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Wikipedia:Burgess shale type biota // Reconstructions of half-billion-year-old Cambrian animals from the Burgess Shale in Yoho National Park, BC (via Boing Boing) . // As Gould says: the Old Ones... // They vaguely remind me of Drawings of Balinese Sorcery. // (Images all at wikimedia.org) // Main.IanHolmes 23 Nov 2008 // 2008-11-22T20:07Zyam1.6updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/BurgessTypeBiotahttp://biowiki.org/twiki/bin/rdiff/Blog/BurgessTypeBiotaBioHackerBrunch
http://biowiki.org/view/Blog/BioHackerBrunch
The bio-hacker brunch // A visual meditation along the lines of the FuturistCookbook. // (The FuturistCookbook) // 2008-11-20T19:17Zyam1.29updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/BioHackerBrunchhttp://biowiki.org/twiki/bin/rdiff/Blog/BioHackerBrunchFuturistCookbook
http://biowiki.org/view/Blog/FuturistCookbook
The Futurist Cookbook // “…and the diners were given materials of different textures such as velvet and sandpaper to stroke with their left hand. Sweet was combined with savoury to produce startling effects, and bitter and sour tastes were given their place: sardines with pineapple, mortadella with nougat, cooked salami with coffee and cologne. An aphrodisiac cocktail was devised, consisting of pineapple juice, eggs, cocoa, caviar, red peppers, nutmeg, and cloves…” // Wikipedia:Filippo Tommaso Marinetti was an Italian Futurist. // His cookbook, Wikipedia:Cucina futurista literally Futurist meals is very weird. // It's basically a recipe book, but with random asides about radically avant-garde presentational aspects of the food... texture, setting, ambient music and perfume, costume of waiters, prescribed topics of conversation, and oh: the abolition of decadent pasta. // I intended to write a page on this book, which I remembered as being sort of funny. // Then it occurred to me to check the fascist connections. // After all, the book was written in the 1930's in Italy. Artistic movements from that period are charged with the politics of the time. These connections can easily be overlooked: consider the protagonist of Wikipedia:The Prime of Miss Jean Brodie, or the film recollection scenes of the movie Kiss of the Spider-Woman. // Here's what I read on the Wikipedia page for the book: // Elizabeth David, the cookery writer, comments that Marinetti's ideas about food contained a germ of common sense, but behind his jesting lay the Fascist obsession with nationalism. Marinetti wanted to prepare the Italians for war. "Spaghetti is no food for fighters," he declared. // I like spaghetti. Oh well. // Naively, I did not realize Marinetti was a fascist (a founding member of the Italian fascist party, ulp) when I found the book. It's now a collectors' item. I found it in Pegasus I think, for a song, then valued it in the sadly now-defunct Cody's Books. I bet you could get it at Serendipity. But I digress. // Like I say, I can't claim I consciously detected any fascism when I read the book; though, in my defense, I wasn't looking for it. It's stylistic more than political: proto-surreal, I guess, was how I saw it. // Now, however, reading the Wikipedia page, I note that one of the Futurists' culinary precepts was that mealtime discussion of politics should be banned, which seems a bit of a giveaway. // Why not discuss politics at dinner? You're probably already watching Wikipedia:The Daily Show ... // Another quirk of the Cucinistas is that some food is placed on the table for purely decorative purposes: you must not actually eat it. I thought of this as just being absurd Pythonesque satire at first but am somewhat more horrified by it now. I mean, think about that, for real... so completely fascist. // Anyway, I thought this book might give a new meaning to the phrase Wikipedia:Soup Nazi. // I feel a bit like I have just been caught out at something, by George Orwell. // http://www.tomatom.com/2007/06/the-future-of-food-and-fascism/ // Brief summary of the book // ISBN:0938491318 // Main.IanHolmes 21 Nov 2008 // 2008-11-20T18:48Zyam1.36updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/FuturistCookbookhttp://biowiki.org/twiki/bin/rdiff/Blog/FuturistCookbookImagingGeneMyers
http://biowiki.org/view/Blog/ImagingGeneMyers
Main.GeneMyers on imaging informatics. // http://www.bio-itworld.com/pb/2008/10/23/eugene-myers-imaging-informatics.html // Fun quotable statistic: mouse brain imaging will generate 4.2 trillion voxels/week // Main.IanHolmes 23 Oct 2008 // 2008-10-23T11:30Zyam1.4updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/ImagingGeneMyershttp://biowiki.org/twiki/bin/rdiff/Blog/ImagingGeneMyersExploringOrigins
http://biowiki.org/view/Blog/ExploringOrigins
Via Main.LarsBarquist: // 2008 NSF Science Engineering Visualization Winners: // http://www.nsf.gov/news/special reports/scivis/index.jsp?id win2008 // The honorable mention for interactive media is a site "Exploring Life's Origins" about the RNA World hypothesis, looks pretty neat. // http://www.exploringorigins.org/ // Main.IanHolmes 17 Oct 2008 // 2008-10-17T11:01Zyam1.2updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/ExploringOriginshttp://biowiki.org/twiki/bin/rdiff/Blog/ExploringOriginsPageRank
http://biowiki.org/view/Blog/PageRank
The Wikipedia:PageRank for http://biowiki.org/ is up a point, to 5/10 perhaps indicating a recovery from the spam attacks of yesteryear? // Or just that we're getting more links? // Not that I take this all that seriously we could do a lot of things to improve PageRank if we really cared, like minimizing the number of outgoing links per page (see especially the left bar) but it's nice to be nudging up in the Google rankings... // Now, if only the Dow Jones Industrial Average would go up a few points too... // Main.IanHolmes 15 Oct 2008 // 2008-10-15T06:53Zyam1.3updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/PageRankhttp://biowiki.org/twiki/bin/rdiff/Blog/PageRankSingleSpeciesEcosystem
http://biowiki.org/view/Blog/SingleSpeciesEcosystem
Metagenomics reveals anoxic, single-bacterium ecosystem in a gold mine: // http://newscenter.lbl.gov/press-releases/2008/10/09/bold-traveler’s-journey-toward-the-center-of-the-earth/ // via http://news.bbc.co.uk/2/hi/in depth/7663927.stm // Can't find the Science paper yet but here is an anticipatory methods review article with Main.AdamArkin as co-author: // Main.IanHolmes 10 Oct 2008 // 2008-10-10T10:44Zyam1.3updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/SingleSpeciesEcosystemhttp://biowiki.org/twiki/bin/rdiff/Blog/SingleSpeciesEcosystemGuideToCloudComputing
http://biowiki.org/view/Blog/GuideToCloudComputing
Information Week's Guide to Cloud Computing: // http://www.informationweek.com/news/services/hosted apps/showArticle.jhtml?articleID 208700713 // From June 2008. // Main.IanHolmes 25 Sep 2008 // 2008-09-25T15:31Zyam1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/GuideToCloudComputinghttp://biowiki.org/twiki/bin/rdiff/Blog/GuideToCloudComputingMichaelMateas
http://biowiki.org/view/Blog/MichaelMateas
Michael Mateas: http://www.soe.ucsc.edu/~michaelm/ // 2008-09-03T11:40Zyam1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/MichaelMateashttp://biowiki.org/twiki/bin/rdiff/Blog/MichaelMateasProceduralRhetoric
http://biowiki.org/view/Blog/ProceduralRhetoric
Logic applied to automated game design // Described in this book: // http://www.bogost.com/books/persuasive games.shtml // Recommended by MichaelMateas // Main.IanHolmes 03 Sep 2008 // 2008-09-03T11:40Zyam1.3updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/ProceduralRhetorichttp://biowiki.org/twiki/bin/rdiff/Blog/ProceduralRhetoricJavascriptIPhone
http://biowiki.org/view/Blog/JavascriptIPhone
Writing Javascript for Safari on the iPhone: // http://www.evotech.net/blog/2007/07/web-development-for-the-iphone/ // Nice code snippet for getting the viewport orientation 8-) // Main.IanHolmes 30 Aug 2008 // 2008-08-30T02:21Zyam1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/JavascriptIPhonehttp://biowiki.org/twiki/bin/rdiff/Blog/JavascriptIPhoneAstrobiologyRap
http://biowiki.org/view/Blog/AstrobiologyRap
http://www.youtube.com/v/NL3lhm6oy5I // 2008-08-26T09:52Zyam1.2updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/AstrobiologyRaphttp://biowiki.org/twiki/bin/rdiff/Blog/AstrobiologyRapEvolutionAndMedicine
http://biowiki.org/view/Blog/EvolutionAndMedicine
http://www.evolutionandmedicine.org/ "a resource for scientists and medical professionals working at the interface of evolutionary biology and medicine" // Includes the 2006 Science editorial Why Medicine Needs Evolution (PDF). // via this post on evolgen. // Main.IanHolmes 31 Jul 2008 // 2008-07-30T18:44Zyam1.2updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/EvolutionAndMedicinehttp://biowiki.org/twiki/bin/rdiff/Blog/EvolutionAndMedicineGeneDesignSoftware
http://biowiki.org/view/Blog/GeneDesignSoftware
Clotho // http://2008.igem.org/Team:UC Berkeley Tools // APE: A Plasmid Editor. // http://www.biology.utah.edu/jorgensen/wayned/ape/ // Code Monkey video on the youtubes // Gene Designer. // // http://www.dna20.com/tools.php // Main.IanHolmes 14 Mar 2008 // 2008-03-13T18:01Zyam1.2updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/GeneDesignSoftwarehttp://biowiki.org/twiki/bin/rdiff/Blog/GeneDesignSoftwareXMLandScheme
http://biowiki.org/view/Blog/XMLandScheme
XML as a dialect of Scheme: // http://classes.eclab.byu.edu/330/wiki/index.cgi?XMLandScheme // http://okmij.org/ftp/Scheme/xml.html // Main.IanHolmes 29 Feb 2008 // 2008-02-28T17:43Zyam1.6updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/XMLandSchemehttp://biowiki.org/twiki/bin/rdiff/Blog/XMLandSchemeUrgeMechanics
http://biowiki.org/view/Blog/UrgeMechanics
"Urge Mechanics" is my new sexy name for "Ergonomics". // The old word is so stuffily work-oriented: // ergonomics // "scientific study of the efficiency of people in the workplace," coined 1950 from Gk. ergon "work" (see urge (v.)) (ec)onomics . // The Swedish TCO Congress (English page) were recommended to me as having tougher ergonomic emission standards than anyone else. // My friend who recommended them said: // "Unfortunately they only certified one keyboard and it's a strange one (but maybe worth trying as it is ergonomic, but if you share your computer with someone who expects a regular keyboard you may need 2 keyboards).") // A game workout would be an improvement. // But maybe a better solution is to just get the hell away from a computer. // My former high-school history teacher emailed me to tell me he is headed out to the Xingu reservation: // http://www.amazon-indians.org/page16.html // Main.IanHolmes 27 Feb 2008 // Edited to add a few EM radiation links: // http://bioinitiative.org/ "A Rationale for a Biologically-based Public Exposure Standard for Electromagnetic Fields (ELF and RF)" // http://cellphonesafety.wordpress.com/2006/08/31/microwave-sickness-or-neurasthenia/ irradiating the US Embassy in Moscow // // 2008-02-27T00:17Zyam1.10updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/UrgeMechanicshttp://biowiki.org/twiki/bin/rdiff/Blog/UrgeMechanicsHoneywellKitchenComputer
http://biowiki.org/view/Blog/HoneywellKitchenComputer
The Wikipedia:Honeywell 316 // Marketing line: "If only she could cook as well as Honeywell can compute". // Ewwww. So Mad Men. // Via Kevin Kelly // and this Dr Dobbs article. // Current bioinformatics link: OpenQuestions2008 // So Wikipedia:Mad Men ... // 2008-02-22T09:37Zyam1.7updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/HoneywellKitchenComputerhttp://biowiki.org/twiki/bin/rdiff/Blog/HoneywellKitchenComputerAncestralSequenceReconstruction
http://biowiki.org/view/Blog/AncestralSequenceReconstruction
ISBN:0199299188 // Oxford University Press // Amazon.com // // http://mbe.oxfordjournals.org/cgi/content/full/21/10/1871 // 2008-01-21T00:12Zyam1.5updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/AncestralSequenceReconstructionhttp://biowiki.org/twiki/bin/rdiff/Blog/AncestralSequenceReconstructionOpenQuestions2008
http://biowiki.org/view/Blog/OpenQuestions2008
Open questions (moving into) 2008 // Indel processes // Consider all approximations: // gaps as extra substitution character // closed-form approximations: TKF91, TKF92 // xrate: gap-model; gaps as characters; with context... // discrete-time transducers // Statistical alignment MCMC // The definitive sampler? // Simultaneous alignment gene prediction // Best way to build Main.ReadingFrameConservation into a generative model? // Measurement of indel rates // What's the best way to do this? // How sensitive is it to sequence-localized or branch-specific variations in rate? // See Main.TkfIndelModelEigenfunctions // Reconstruction of ancestral DNA (paleoinformatics) // AncestralSequenceReconstruction // Use outgroups // RNA bioinformatics // Especially noncoding RNA with secondary structure. // RNA gene prediction // Can more careful modeling improve performance? // RNA multiple alignment and structure prediction // Going from two to many RNA sequences... // RNA phylogeny // Challenges of metagenomics with rRNA. // Can we use secondary structure in phylogeny (i) reliably and (ii) fast? // RNA paleoinformatics // RNA biology // Drosophila genetic signals: zipcodes and such // What's the post-transcriptional program and its genomic code? // Drosophila RNome // What RNA genes are in there? // Genome web applications // What do the following mean, moving into 2008? // AJAX genome browser // Genome wiki // AJAX alignment phylogeny tools // // Main.IanHolmes 25 Dec 2007 // 2007-12-25T00:33Zyam1.10updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/OpenQuestions2008http://biowiki.org/twiki/bin/rdiff/Blog/OpenQuestions2008PaleoVirology
http://biowiki.org/view/Blog/PaleoVirology
Paleovirology in the New Yorker. // Mentions Heidmann et al reconstructing the human endogenous retroviral ancestor, "Phoenix". // Thanks to steady advances in computing power and DNA technology, a talented undergraduate with a decent laptop and access to any university biology lab can assemble a virus with ease. // via Bruce Sterling // Main.IanHolmes 19 Dec 2007 // 2007-12-19T09:51Zyam1.6updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Blog/PaleoVirologyhttp://biowiki.org/twiki/bin/rdiff/Blog/PaleoVirology
