Tag Archives: evolution

Items of some interest:

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These are my recent Pin​board​.in links:

  • A Way To Think About Online Courses (By Apple, For Exam­ple) | Eas­ily Distracted

    “One thing that struck me dur­ing the meet­ing, though, was that if you cre­ated a really rich body of mate­ri­als that looked some­what like an “online course”, what you really might be doing was craft­ing a com­pletely novel form of pub­li­ca­tion. Imag­ine a work of his­tor­i­cal schol­ar­ship that included video of the author giv­ing an explana­tory lec­ture at the begin­ning of a sec­tion of the read­ing; that had direct links to a huge body of archival pic­tures, audio record­ings, maps, and other sup­port­ing mate­ri­als; that exten­sively linked to rel­e­vant (or com­pet­ing) analy­ses avail­able in dig­i­tal col­lec­tions like JSTOR; and where the author would appear live once every week to take ques­tions from stu­dents read­ing the book in a class.”

    media academic-​​culture ped­a­gogy pub­lish­ing a-​​new-​​tent-​​and-​​a-​​new-​​camel

  • Evo­lu­tion of increased com­plex­ity in a mol­e­c­u­lar machine : Nature : Nature Pub­lish­ing Group

    “Many cel­lu­lar processes are car­ried out by mol­e­c­u­lar ‘machines’—assemblies of mul­ti­ple dif­fer­en­ti­ated pro­teins that phys­i­cally inter­act to exe­cute bio­log­i­cal functions1, 2, 3, 4, 5, 6, 7, 8. Despite much spec­u­la­tion, strong evi­dence of the mech­a­nisms by which these assem­blies evolved is lack­ing. Here we use ances­tral gene resurrection9, 10, 11 and manip­u­la­tive genetic exper­i­ments to deter­mine how the com­plex­ity of an essen­tial mol­e­c­u­lar machine—the hexa­m­eric trans­mem­brane ring of the eukary­otic V-​​ATPase pro­ton pump—increased hun­dreds of mil­lions of years ago. We show that the ring of Fungi, which is com­posed of three par­al­o­gous pro­teins, evolved from a more ancient two-​​paralogue com­plex because of a gene dupli­ca­tion that was fol­lowed by loss in each daugh­ter copy of spe­cific inter­faces by which it inter­acts with other ring pro­teins. These losses were com­ple­men­tary, so both copies became oblig­ate com­po­nents with restricted spa­tial roles in the com­plex. Rein­tro­duc­ing a sin­gle his­tor­i­cal muta­tion from each par­alogue lin­eage into the res­ur­rected ances­tral pro­teins is suf­fi­cient to reca­pit­u­late their asym­met­ric degen­er­a­tion and trig­ger the require­ment for the more elab­o­rate three-​​component ring. Our exper­i­ments show that increased com­plex­ity in an essen­tial mol­e­c­u­lar machine evolved because of sim­ple, high-​​probability evo­lu­tion­ary processes, with­out the appar­ent evo­lu­tion of novel func­tions. They point to a plau­si­ble mech­a­nism for the evo­lu­tion of com­plex­ity in other multi-​​paralogue pro­tein complexes.”

    via:cshalizi evo­lu­tion structural-​​biology par­si­mony dangers-​​of-​​premature-​​optimization lesson-​​for-​​genetic-​​programming

  • Bien­v­enue sur le site de CaRMetal


    geom­e­try sim­u­la­tor nudge-​​targets

Items of some interest…

Posted on by

These are my recent Pin​board​.in links:

  • Hebrew Typog­ra­phy

    beau­ti­ful lettering

    typog­ra­phy hebrew graphic-​​design cal­lig­ra­phy let­ter­ing

  • [1110.5376] A Quan­ti­ta­tive Test of Pop­u­la­tion Genet­ics Using Spatio-​​Genetic Pat­terns in Bac­te­r­ial Colonies

    “It is widely accepted that pop­u­la­tion genet­ics the­ory is the cor­ner­stone of evo­lu­tion­ary analy­ses. Empir­i­cal tests of the the­ory, how­ever, are chal­leng­ing because of the com­plex rela­tion­ships between space, dis­per­sal, and evo­lu­tion. Crit­i­cally, we lack quan­ti­ta­tive val­i­da­tion of the spa­tial mod­els of pop­u­la­tion genet­ics. Here we com­bine ana­lyt­ics, on and off-​​lattice sim­u­la­tions, and exper­i­ments with bac­te­ria to per­form quan­ti­ta­tive tests of the the­ory. We study two bac­te­r­ial species, the gut microbe Escherichia coli and the oppor­tunis­tic pathogen Pseudomonas aerug­i­nosa, and show that spatio-​​genetic pat­terns in colony biofilms of both species are accu­rately described by an exten­sion of the one-​​dimensional stepping-​​stone model. We use one empir­i­cal mea­sure, genetic diver­sity at the colony periph­ery, to para­me­ter­ize our mod­els and show that we can then accu­rately pre­dict another key vari­able: the degree of short-​​range cell migra­tion along an edge. More­over, the model allows us to esti­mate other key para­me­ters includ­ing effec­tive pop­u­la­tion size (den­sity) at the expan­sion fron­tier. While our exper­i­men­tal sys­tem is a sim­pli­fi­ca­tion of nat­ural micro­bial com­mu­nity, we argue it is a proof of prin­ci­ple that the spa­tial mod­els of pop­u­la­tion genet­ics can quan­ti­ta­tively cap­ture organ­is­mal evolution.”

    bacterial-​​genetics evo­lu­tion micro­bi­ol­ogy exper­i­ment cute

  • NDFD Data­base Contents

    “You can access NDFD ele­ments via file trans­fer pro­to­col (ftp), http, eXten­si­ble Markup Lan­guage (XML), or web browser. Links to the data, sup­port­ing infor­ma­tion and soft­ware are listed below:…”

    weather data raw-​​data-​​now government2.0 nudge-​​targets ref­er­ence fore­casts

  • The Per­for­ma­tiv­ity of Net­works — Kieran Healy

    “The “per­for­ma­tiv­ity the­sis” is the claim that parts of con­tem­po­rary eco­nom­ics and finance, when car­ried out into the world by pro­fes­sion­als and pop­u­lar­iz­ers, refor­mat and reor­ga­nize the phe­nom­ena they pur­port to describe, in ways that bring the world into line with the­ory. Prac­ti­cal tech­nolo­gies, cal­cu­la­tive devices and portable algo­rithms give actors tools to imple­ment par­tic­u­lar mod­els of action. I argue that social net­work analy­sis is per­for­ma­tive in the same sense as the cases stud­ied in this lit­er­a­ture. Social net­work analy­sis and finance the­ory are sim­i­lar in key aspects of their devel­op­ment and effects. For the case of eco­nom­ics, evi­dence for weaker ver­sions of the per­for­ma­tiv­ity the­sis in quite good, and the strong for­mu­la­tion is cir­cum­stan­tially sup­ported. Net­work the­ory eas­ily meets the evi­den­tial thresh­old for the weaker ver­sions; I offer empir­i­cal exam­ples that sup­port the strong (or “Bar­ne­sian”) for­mu­la­tion. Whether these par­al­lels are a mark in favor of the the­sis or a strike against it is an open ques­tion. I argue that the social net­work tech­nolo­gies and mod­els now being “per­formed” build out sys­tems of gen­er­al­ized reci­procity, con­nec­tiv­ity, and commons-​​based pro­duc­tion. This is in con­trast both to an ear­lier net­work imagery that empha­sized self-​​interest and entre­pre­neur­ial exploita­tion of struc­tural oppor­tu­ni­ties, and to the model of action typ­i­cally con­sid­ered to be per­formed by eco­nomic technologies.”

    network-​​theory network-​​culture eco­nom­ics cultural-​​dynamics theory-​​and-​​practice-​​sitting-​​in-​​a-​​tree